Subjects -> ENVIRONMENTAL STUDIES (Total: 945 journals)
    - ENVIRONMENTAL STUDIES (842 journals)
    - POLLUTION (31 journals)
    - TOXICOLOGY AND ENVIRONMENTAL SAFETY (54 journals)
    - WASTE MANAGEMENT (18 journals)

ENVIRONMENTAL STUDIES (842 journals)                  1 2 3 4 5 | Last

Showing 1 - 200 of 378 Journals sorted alphabetically
ACS Chemical Health & Safety     Hybrid Journal   (Followers: 5)
ACS ES&T Engineering     Hybrid Journal   (Followers: 9)
Acta Brasiliensis     Open Access   (Followers: 3)
Acta Ecologica Sinica     Open Access   (Followers: 11)
Acta Environmentalica Universitatis Comenianae     Open Access   (Followers: 1)
Acta Oecologica     Hybrid Journal   (Followers: 12)
Acta Regionalia et Environmentalica     Open Access   (Followers: 1)
Advanced Electronic Materials     Hybrid Journal   (Followers: 7)
Advanced Energy and Sustainability Research     Open Access   (Followers: 7)
Advanced Sustainable Systems     Hybrid Journal   (Followers: 9)
Advances in Ecological Research     Full-text available via subscription   (Followers: 45)
Advances in Environmental Chemistry     Open Access   (Followers: 12)
Advances in Environmental Sciences - International Journal of the Bioflux Society     Open Access   (Followers: 21)
Advances in Environmental Technology     Open Access   (Followers: 1)
Advances in Life Science and Technology     Open Access   (Followers: 23)
Advances in Tropical Biodiversity and Environmental Sciences     Open Access   (Followers: 5)
Aeolian Research     Hybrid Journal   (Followers: 6)
African Journal of Environmental Science and Technology     Open Access   (Followers: 5)
Agricultura Tecnica     Open Access   (Followers: 5)
Agricultural & Environmental Letters     Open Access   (Followers: 3)
Agro-Science     Full-text available via subscription   (Followers: 3)
Agroecological journal     Open Access  
Agronomy for Sustainable Development     Open Access   (Followers: 22)
Agrosystems, Geosciences & Environment     Open Access   (Followers: 7)
Amazon's Research and Environmental Law     Open Access   (Followers: 5)
Ambiência     Open Access  
Ambiens. Revista Iberoamericana Universitaria en Ambiente, Sociedad y Sustentabilidad     Open Access   (Followers: 1)
Ambiente & Agua : An Interdisciplinary Journal of Applied Science     Open Access   (Followers: 1)
American Journal of Energy and Environment     Open Access   (Followers: 5)
American Journal of Environmental Engineering     Open Access   (Followers: 16)
American Journal of Environmental Protection     Open Access   (Followers: 9)
American Journal of Environmental Sciences     Open Access   (Followers: 11)
American Naturalist     Full-text available via subscription   (Followers: 85)
Annals of Civil and Environmental Engineering     Open Access   (Followers: 3)
Annals of Environmental Science and Toxicology     Open Access   (Followers: 5)
Annals of GIS     Open Access   (Followers: 31)
Annual Review of Ecology, Evolution, and Systematics     Full-text available via subscription   (Followers: 89)
Annual Review of Environment and Resources     Full-text available via subscription   (Followers: 16)
Annual Review of Pharmacology and Toxicology     Full-text available via subscription   (Followers: 37)
Annual Review of Resource Economics     Full-text available via subscription   (Followers: 10)
Applied and Environmental Soil Science     Open Access   (Followers: 20)
Applied Ecology and Environmental Sciences     Open Access   (Followers: 30)
Applied Environmental Education & Communication     Hybrid Journal   (Followers: 19)
Applied Journal of Environmental Engineering Science     Open Access   (Followers: 2)
Aquatic Ecology     Hybrid Journal   (Followers: 40)
Aquatic Toxicology     Hybrid Journal   (Followers: 26)
Arcada : Revista de conservación del patrimonio cultural     Open Access   (Followers: 2)
Architecture, Civil Engineering, Environment     Open Access   (Followers: 4)
Archives des Maladies Professionnelles et de l'Environnement     Full-text available via subscription  
Archives of Environmental and Occupational Health     Hybrid Journal   (Followers: 12)
Archives of Environmental Contamination and Toxicology     Hybrid Journal   (Followers: 15)
Archives of Environmental Protection     Open Access   (Followers: 6)
Archives of Toxicology     Hybrid Journal   (Followers: 21)
Arctic Environmental Research     Open Access   (Followers: 1)
Asian Journal of Environment & Ecology     Open Access   (Followers: 1)
Asian Journal of Rural Development     Open Access   (Followers: 9)
Asian Review of Environmental and Earth Sciences     Open Access   (Followers: 3)
ATBU Journal of Environmental Technology     Open Access   (Followers: 5)
Atmospheric and Climate Sciences     Open Access   (Followers: 35)
Atmospheric Environment     Hybrid Journal   (Followers: 75)
Atmospheric Environment : X     Open Access   (Followers: 3)
Augm Domus : Revista electrónica del Comité de Medio Ambiente de AUGM     Open Access  
Austral Ecology     Hybrid Journal   (Followers: 18)
Australasian Journal of Environmental Management     Hybrid Journal   (Followers: 13)
Australasian Journal of Human Security     Full-text available via subscription   (Followers: 1)
Australian Journal of Environmental Education     Full-text available via subscription   (Followers: 11)
Basic & Clinical Pharmacology & Toxicology     Hybrid Journal   (Followers: 14)
Basic and Applied Ecology     Hybrid Journal   (Followers: 26)
Behavioral Ecology     Hybrid Journal   (Followers: 60)
Behavioral Ecology and Sociobiology     Hybrid Journal   (Followers: 38)
Biocenosis     Open Access  
Biochar     Hybrid Journal   (Followers: 3)
Biodegradation     Hybrid Journal   (Followers: 2)
Biodiversity     Hybrid Journal   (Followers: 31)
Biofouling: The Journal of Bioadhesion and Biofilm Research     Hybrid Journal   (Followers: 7)
Bioremediation Journal     Hybrid Journal   (Followers: 5)
BioRisk     Open Access   (Followers: 3)
BMC Ecology     Open Access   (Followers: 24)
Boletín Instituto de Derecho Ambiental y de los Recursos Naturales     Open Access  
Boletín Semillas Ambientales     Open Access  
Boston College Environmental Affairs Law Review     Open Access   (Followers: 7)
Bothalia : African Biodiversity & Conservation     Open Access   (Followers: 1)
Built Environment     Full-text available via subscription   (Followers: 5)
Bulletin of Environmental Contamination and Toxicology     Hybrid Journal   (Followers: 15)
Bulletin of the American Meteorological Society     Open Access   (Followers: 65)
Bumi Lestari Journal of Environment     Open Access  
Canadian Journal of Earth Sciences     Hybrid Journal   (Followers: 23)
Canadian Journal of Remote Sensing     Full-text available via subscription   (Followers: 51)
Canadian Journal of Soil Science     Full-text available via subscription   (Followers: 14)
Canadian Water Resources Journal     Hybrid Journal   (Followers: 20)
Capitalism Nature Socialism     Hybrid Journal   (Followers: 28)
Carbon Capture Science & Technology     Open Access  
Carbon Resources Conversion     Open Access   (Followers: 3)
Case Studies in Chemical and Environmental Engineering     Open Access   (Followers: 1)
Casopis Slezskeho Zemskeho Muzea - serie A - vedy prirodni     Open Access  
Cell Biology and Toxicology     Hybrid Journal   (Followers: 12)
Chain Reaction     Full-text available via subscription  
Challenges in Sustainability     Open Access   (Followers: 12)
Chemical Research in Toxicology     Hybrid Journal   (Followers: 26)
Chemico-Biological Interactions     Hybrid Journal   (Followers: 3)
Chemosphere     Hybrid Journal   (Followers: 17)
Child and Adolescent Mental Health     Hybrid Journal   (Followers: 71)
China Population, Resources and Environment     Full-text available via subscription   (Followers: 4)
Ciencia, Ambiente y Clima     Open Access   (Followers: 3)
City and Environment Interactions     Open Access   (Followers: 4)
Civil and Environmental Engineering     Open Access   (Followers: 8)
Civil and Environmental Engineering Reports     Open Access   (Followers: 9)
Civil and Environmental Research     Open Access   (Followers: 22)
CLEAN - Soil, Air, Water     Hybrid Journal   (Followers: 21)
Clean Technologies     Open Access   (Followers: 1)
Clean Technologies and Environmental Policy     Hybrid Journal   (Followers: 5)
Cleaner Environmental Systems     Open Access  
Cleaner Production Letters     Hybrid Journal  
Cleanroom Technology     Full-text available via subscription   (Followers: 1)
Climate and Energy     Full-text available via subscription   (Followers: 7)
Climate Change Ecology     Open Access   (Followers: 2)
Climate Change Economics     Hybrid Journal   (Followers: 36)
Climate Policy     Hybrid Journal   (Followers: 52)
Climate Resilience and Sustainability     Open Access   (Followers: 21)
Coastal Engineering Journal     Hybrid Journal   (Followers: 9)
Cogent Environmental Science     Open Access  
Columbia Journal of Environmental Law     Open Access   (Followers: 15)
Computational Ecology and Software     Open Access   (Followers: 11)
Computational Water, Energy, and Environmental Engineering     Open Access   (Followers: 5)
Conservation and Society     Open Access   (Followers: 14)
Conservation Letters     Open Access   (Followers: 52)
Conservation Science     Open Access   (Followers: 30)
Consilience : The Journal of Sustainable Development     Open Access   (Followers: 3)
Contemporary Problems of Ecology     Hybrid Journal   (Followers: 4)
Critical Reviews in Environmental Science and Technology     Hybrid Journal   (Followers: 15)
Critical Reviews in Toxicology     Hybrid Journal   (Followers: 27)
Cuadernos de Investigación Geográfica / Geographical Research Letters     Open Access  
Culture, Agriculture, Food and Environment     Hybrid Journal   (Followers: 26)
Culture, Agriculture, Food and Environment     Hybrid Journal   (Followers: 11)
Current Environmental Engineering     Hybrid Journal  
Current Environmental Health Reports     Hybrid Journal   (Followers: 2)
Current Forestry Reports     Hybrid Journal   (Followers: 1)
Current Landscape Ecology Reports     Hybrid Journal   (Followers: 2)
Current Opinion in Environmental Science & Health     Hybrid Journal   (Followers: 1)
Current Opinion in Environmental Sustainability     Hybrid Journal   (Followers: 17)
Current Research in Ecological and Social Psychology     Open Access   (Followers: 1)
Current Research in Environmental Sustainability     Open Access   (Followers: 2)
Current Research in Green and Sustainable Chemistry     Open Access   (Followers: 1)
Current Research in Microbiology     Open Access   (Followers: 27)
Current Sustainable/Renewable Energy Reports     Hybrid Journal   (Followers: 9)
Current World Environment     Open Access   (Followers: 7)
Developments in Environmental Modelling     Full-text available via subscription   (Followers: 8)
Die Bodenkultur : Journal of Land Management, Food and Environment     Open Access   (Followers: 2)
Disaster Prevention and Management     Hybrid Journal   (Followers: 32)
Discover Sustainability     Open Access   (Followers: 2)
disP - The Planning Review     Hybrid Journal   (Followers: 1)
Drug and Chemical Toxicology     Hybrid Journal   (Followers: 17)
Duke Environmental Law & Policy Forum     Open Access   (Followers: 7)
Dynamiques Environnementales     Open Access   (Followers: 1)
E3S Web of Conferences     Open Access   (Followers: 2)
Earth and Environmental Science Transactions of the Royal Society of Edinburgh     Hybrid Journal   (Followers: 6)
Earth Interactions     Open Access   (Followers: 13)
Earth Science Informatics     Hybrid Journal   (Followers: 5)
Earth System Governance     Open Access  
Earth System Science Data (ESSD)     Open Access   (Followers: 8)
Earth Systems and Environment     Hybrid Journal   (Followers: 3)
Earthquake Science     Hybrid Journal   (Followers: 15)
EchoGéo     Open Access  
Eco-Thinking     Open Access   (Followers: 5)
Ecocycles     Open Access   (Followers: 6)
Ecohydrology     Hybrid Journal   (Followers: 11)
Ecohydrology & Hydrobiology     Full-text available via subscription   (Followers: 4)
Ecologia Aplicada     Open Access  
Ecología en Bolivia     Open Access  
Ecological Applications     Full-text available via subscription   (Followers: 220)
Ecological Chemistry and Engineering S     Open Access   (Followers: 4)
Ecological Complexity     Hybrid Journal   (Followers: 7)
Ecological Engineering     Hybrid Journal   (Followers: 4)
Ecological Indicators     Hybrid Journal   (Followers: 22)
Ecological Informatics     Hybrid Journal   (Followers: 4)
Ecological Management & Restoration     Hybrid Journal   (Followers: 15)
Ecological Modelling     Hybrid Journal   (Followers: 96)
Ecological Monographs     Full-text available via subscription   (Followers: 39)
Ecological Processes     Open Access   (Followers: 2)
Ecological Questions     Open Access   (Followers: 4)
Ecological Research     Hybrid Journal   (Followers: 12)
Ecological Restoration     Full-text available via subscription   (Followers: 23)
Ecologist, The     Full-text available via subscription   (Followers: 23)
Ecology     Full-text available via subscription   (Followers: 490)
Ecology and Evolution     Open Access   (Followers: 106)
Ecology Letters     Hybrid Journal   (Followers: 346)
EcoMat : Functional Materials for Green Energy and Environment     Open Access   (Followers: 2)
Economics and Policy of Energy and the Environment     Full-text available via subscription   (Followers: 14)
Économie rurale     Open Access   (Followers: 3)
Ecoprint : An International Journal of Ecology     Open Access   (Followers: 6)
Ecopsychology     Hybrid Journal   (Followers: 8)
Ecosphere     Open Access   (Followers: 9)
Ecosystem Services     Hybrid Journal   (Followers: 10)
Ecosystems     Hybrid Journal   (Followers: 33)
Ecosystems and People     Open Access   (Followers: 3)
Ecotoxicology     Hybrid Journal   (Followers: 11)
Ecotoxicology and Environmental Safety     Hybrid Journal   (Followers: 12)
Ecotrophic : Journal of Environmental Science     Open Access  
Ecozon@ : European Journal of Literature, Culture and Environment     Open Access   (Followers: 5)
Éducation relative à l'environnement     Open Access  

        1 2 3 4 5 | Last

Similar Journals
Journal Cover
Ecotoxicology
Journal Prestige (SJR): 0.797
Citation Impact (citeScore): 2
Number of Followers: 11  
 
  Hybrid Journal Hybrid journal (It can contain Open Access articles)
ISSN (Print) 1573-3017 - ISSN (Online) 0963-9292
Published by Springer-Verlag Homepage  [2659 journals]
  • metaGEM: reconstruction of genome scale metabolic models directly from
           metagenomes

    • Free pre-print version: Loading...

      Authors: Zorrilla F; Buric F, Patil K, et al.
      Abstract: AbstractMetagenomic analyses of microbial communities have revealed a large degree of interspecies and intraspecies genetic diversity through the reconstruction of metagenome assembled genomes (MAGs). Yet, metabolic modeling efforts mainly rely on reference genomes as the starting point for reconstruction and simulation of genome scale metabolic models (GEMs), neglecting the immense intra- and inter-species diversity present in microbial communities. Here, we present metaGEM (https://github.com/franciscozorrilla/metaGEM), an end-to-end pipeline enabling metabolic modeling of multi-species communities directly from metagenomes. The pipeline automates all steps from the extraction of context-specific prokaryotic GEMs from MAGs to community level flux balance analysis (FBA) simulations. To demonstrate the capabilities of metaGEM, we analyzed 483 samples spanning lab culture, human gut, plant-associated, soil, and ocean metagenomes, reconstructing over 14,000 GEMs. We show that GEMs reconstructed from metagenomes have fully represented metabolism comparable to isolated genomes. We demonstrate that metagenomic GEMs capture intraspecies metabolic diversity and identify potential differences in the progression of type 2 diabetes at the level of gut bacterial metabolic exchanges. Overall, metaGEM enables FBA-ready metabolic model reconstruction directly from metagenomes, provides a resource of metabolic models, and showcases community-level modeling of microbiomes associated with disease conditions allowing generation of mechanistic hypotheses.
      PubDate: Wed, 06 Oct 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab815
      Issue No: Vol. 49, No. 21 (2021)
       
  • Combinatorial assembly platform enabling engineering of genetically stable
           metabolic pathways in cyanobacteria

    • Free pre-print version: Loading...

      Authors: Taylor G; Hitchcock A, Heap J.
      Abstract: AbstractCyanobacteria are simple, efficient, genetically-tractable photosynthetic microorganisms which in principle represent ideal biocatalysts for CO2 capture and conversion. However, in practice, genetic instability and low productivity are key, linked problems in engineered cyanobacteria. We took a massively parallel approach, generating and characterising libraries of synthetic promoters and RBSs for the cyanobacterium Synechocystis sp. PCC 6803, and assembling a sparse combinatorial library of millions of metabolic pathway-encoding construct variants. Genetic instability was observed for some variants, which is expected when variants cause metabolic burden. Surprisingly however, in a single combinatorial round without iterative optimisation, 80% of variants chosen at random and cultured photoautotrophically over many generations accumulated the target terpenoid lycopene from atmospheric CO2, apparently overcoming genetic instability. This large-scale parallel metabolic engineering of cyanobacteria provides a new platform for development of genetically stable cyanobacterial biocatalysts for sustainable light-driven production of valuable products directly from CO2, avoiding fossil carbon or competition with food production.
      PubDate: Thu, 23 Sep 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab791
      Issue No: Vol. 49, No. 21 (2021)
       
  • High resolution copy number inference in cancer using short-molecule
           nanopore sequencing

    • Free pre-print version: Loading...

      Authors: Baslan T; Kovaka S, Sedlazeck F, et al.
      Abstract: AbstractGenome copy number is an important source of genetic variation in health and disease. In cancer, Copy Number Alterations (CNAs) can be inferred from short-read sequencing data, enabling genomics-based precision oncology. Emerging Nanopore sequencing technologies offer the potential for broader clinical utility, for example in smaller hospitals, due to lower instrument cost, higher portability, and ease of use. Nonetheless, Nanopore sequencing devices are limited in the number of retrievable sequencing reads/molecules compared to short-read sequencing platforms, limiting CNA inference accuracy. To address this limitation, we targeted the sequencing of short-length DNA molecules loaded at optimized concentration in an effort to increase sequence read/molecule yield from a single nanopore run. We show that short-molecule nanopore sequencing reproducibly returns high read counts and allows high quality CNA inference. We demonstrate the clinical relevance of this approach by accurately inferring CNAs in acute myeloid leukemia samples. The data shows that, compared to traditional approaches such as chromosome analysis/cytogenetics, short molecule nanopore sequencing returns more sensitive, accurate copy number information in a cost effective and expeditious manner, including for multiplex samples. Our results provide a framework for short-molecule nanopore sequencing with applications in research and medicine, which includes but is not limited to, CNAs.
      PubDate: Wed, 22 Sep 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab812
      Issue No: Vol. 49, No. 21 (2021)
       
  • FACT-seq: profiling histone modifications in formalin-fixed
           paraffin-embedded samples with low cell numbers

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      Authors: Zhao L; Xing P, Polavarapu V, et al.
      Abstract: AbstractThe majority of biopsies in both basic research and translational cancer studies are preserved in the format of archived formalin-fixed paraffin-embedded (FFPE) samples. Profiling histone modifications in archived FFPE tissues is critically important to understand gene regulation in human disease. The required input for current genome-wide histone modification profiling studies from FFPE samples is either 10–20 tissue sections or whole tissue blocks, which prevents better resolved analyses. But it is desirable to consume a minimal amount of FFPE tissue sections in the analysis as clinical tissues of interest are limited. Here, we present FFPE tissue with antibody-guided chromatin tagmentation with sequencing (FACT-seq), the first highly sensitive method to efficiently profile histone modifications in FFPE tissues by combining a novel fusion protein of hyperactive Tn5 transposase and protein A (T7−pA−Tn5) transposition and T7 in vitro transcription. FACT-seq generates high-quality chromatin profiles from different histone modifications with low number of FFPE nuclei. We proved a very small piece of FFPE tissue section containing ∼4000 nuclei is sufficient to decode H3K27ac modifications with FACT-seq. H3K27ac FACT-seq revealed disease-specific super enhancers in the archived FFPE human colorectal and human glioblastoma cancer tissue. In summary, FACT-seq allows decoding the histone modifications in archival FFPE tissues with high sensitivity and help researchers to better understand epigenetic regulation in cancer and human disease.
      PubDate: Fri, 17 Sep 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab813
      Issue No: Vol. 49, No. 21 (2021)
       
  • A rapid method to visualize human mitochondrial DNA replication through
           rotary shadowing and transmission electron microscopy

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      Authors: Kosar M; Piccini D, Foiani M, et al.
      Abstract: AbstractWe report a rapid experimental procedure based on high-density in vivo psoralen inter-strand DNA cross-linking coupled to spreading of naked purified DNA, positive staining, low-angle rotary shadowing, and transmission electron microscopy (TEM) that allows quick visualization of the dynamic of heavy strand (HS) and light strand (LS) human mitochondrial DNA replication. Replication maps built on linearized mitochondrial genomes and optimized rotary shadowing conditions enable clear visualization of the progression of the mitochondrial DNA synthesis and visualization of replication intermediates carrying long single-strand DNA stretches. One variant of this technique, called denaturing spreading, allowed the inspection of the fine chromatin structure of the mitochondrial genome and was applied to visualize the in vivo three-strand DNA structure of the human mitochondrial D-loop intermediate with unprecedented clarity.
      PubDate: Thu, 09 Sep 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab770
      Issue No: Vol. 49, No. 21 (2021)
       
  • scDeepSort: a pre-trained cell-type annotation method for single-cell
           transcriptomics using deep learning with a weighted graph neural network

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      Authors: Shao X; Yang H, Zhuang X, et al.
      Abstract: AbstractAdvances in single-cell RNA sequencing (scRNA-seq) have furthered the simultaneous classification of thousands of cells in a single assay based on transcriptome profiling. In most analysis protocols, single-cell type annotation relies on marker genes or RNA-seq profiles, resulting in poor extrapolation. Still, the accurate cell-type annotation for single-cell transcriptomic data remains a great challenge. Here, we introduce scDeepSort (https://github.com/ZJUFanLab/scDeepSort), a pre-trained cell-type annotation tool for single-cell transcriptomics that uses a deep learning model with a weighted graph neural network (GNN). Using human and mouse scRNA-seq data resources, we demonstrate the high performance and robustness of scDeepSort in labeling 764 741 cells involving 56 human and 32 mouse tissues. Significantly, scDeepSort outperformed other known methods in annotating 76 external test datasets, reaching an 83.79% accuracy across 265 489 cells in humans and mice. Moreover, we demonstrate the universality of scDeepSort using more challenging datasets and using references from different scRNA-seq technology. Above all, scDeepSort is the first attempt to annotate cell types of scRNA-seq data with a pre-trained GNN model, which can realize the accurate cell-type annotation without additional references, i.e. markers or RNA-seq profiles.
      PubDate: Thu, 09 Sep 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab775
      Issue No: Vol. 49, No. 21 (2021)
       
  • Engineering large-scale chromosomal deletions by CRISPR-Cas9

    • Free pre-print version: Loading...

      Authors: Eleveld T; Bakali C, Eijk P, et al.
      Pages: 12007 - 12016
      Abstract: AbstractLarge-scale chromosomal deletions are a prevalent and defining feature of cancer. A high degree of tumor-type and subtype specific recurrencies suggest a selective oncogenic advantage. However, due to their large size it has been difficult to pinpoint the oncogenic drivers that confer this advantage. Suitable functional genomics approaches to study the oncogenic driving capacity of large-scale deletions are limited. Here, we present an effective technique to engineer large-scale deletions by CRISPR-Cas9 and create isogenic cell line models. We simultaneously induce double-strand breaks (DSBs) at two ends of a chromosomal arm and select the cells that have lost the intermittent region. Using this technique, we induced large-scale deletions on chromosome 11q (65 Mb) and chromosome 6q (53 Mb) in neuroblastoma cell lines. A high frequency of successful deletions (up to 30% of selected clones) and increased colony forming capacity in the 11q deleted lines suggest an oncogenic advantage of these deletions. Such isogenic models enable further research on the role of large-scale deletions in tumor development and growth, and their possible therapeutic potential.
      PubDate: Wed, 07 Jul 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab557
      Issue No: Vol. 49, No. 21 (2021)
       
  • The nuclear and cytoplasmic activities of RNA polymerase III, and an
           evolving transcriptome for surveillance

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      Authors: Kessler A; Maraia R.
      Pages: 12017 - 12034
      Abstract: AbstractA 1969 report that described biochemical and activity properties of the three eukaryotic RNA polymerases revealed Pol III as highly distinguishable, even before its transcripts were identified. Now known to be the most complex, Pol III contains several stably-associated subunits referred to as built-in transcription factors (BITFs) that enable highly efficient RNA synthesis by a unique termination-associated recycling process. In vertebrates, subunit RPC7(α/β) can be of two forms, encoded by POLR3G or POLR3GL, with differential activity. Here we review promoter-dependent transcription by Pol III as an evolutionary perspective of eukaryotic tRNA expression. Pol III also provides nonconventional functions reportedly by promoter-independent transcription, one of which is RNA synthesis from DNA 3′-ends during repair. Another is synthesis of 5′ppp-RNA signaling molecules from cytoplasmic viral DNA in a pathway of interferon activation that is dysfunctional in immunocompromised patients with mutations in Pol III subunits. These unconventional functions are also reviewed, including evidence that link them to the BITF subunits. We also review data on a fraction of the human Pol III transcriptome that evolved to include vault RNAs and snaRs with activities related to differentiation, and in innate immune and tumor surveillance. The Pol III of higher eukaryotes does considerably more than housekeeping.
      PubDate: Fri, 26 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1145
      Issue No: Vol. 49, No. 21 (2021)
       
  • Cisplatin fastens chromatin irreversibly even at a high chloride
           concentration

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      Authors: Moon H; Park J, Lee I, et al.
      Pages: 12035 - 12047
      Abstract: AbstractCisplatin is one of the most potent anti-cancer drugs developed so far. Recent studies highlighted several intriguing roles of histones in cisplatin's anti-cancer effect. Thus, the effect of nucleosome formation should be considered to give a better account of the anti-cancer effect of cisplatin. Here we investigated this important issue via single-molecule measurements. Surprisingly, the reduced activity of cisplatin under [NaCl] = 180 mM, corresponding to the total concentration of cellular ionic species, is still sufficient to impair the integrity of a nucleosome by retaining its condensed structure firmly, even against severe mechanical and chemical disturbances. Our finding suggests that such cisplatin-induced fastening of chromatin can inhibit nucleosome remodelling required for normal biological functions. The in vitro chromatin transcription assay indeed revealed that the transcription activity was effectively suppressed in the presence of cisplatin. Our direct physical measurements on cisplatin-nucleosome adducts suggest that the formation of such adducts be the key to the anti-cancer effect by cisplatin.
      PubDate: Tue, 23 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab922
      Issue No: Vol. 49, No. 21 (2021)
       
  • Enzymatic deamination of the epigenetic nucleoside N6-methyladenosine
           regulates gene expression

    • Free pre-print version: Loading...

      Authors: Jiang Z; Wang C, Wu Z, et al.
      Pages: 12048 - 12068
      Abstract: AbstractN6-methyladenosine (m6A) modification is the most extensively studied epigenetic modification due to its crucial role in regulating an array of biological processes. Herein, Bsu06560, formerly annotated as an adenine deaminase derived from Bacillus subtilis 168, was recognized as the first enzyme capable of metabolizing the epigenetic nucleoside N6-methyladenosine. A model of Bsu06560 was constructed, and several critical residues were putatively identified via mutational screening. Two mutants, F91L and Q150W, provided a superiorly enhanced conversion ratio of adenosine and N6-methyladenosine. The CRISPR-Cas9 system generated Bsu06560-knockout, F91L, and Q150W mutations from the B. subtilis 168 genome. Transcriptional profiling revealed a higher global gene expression level in BS-F91L and BS-Q150W strains with enhanced N6-methyladenosine deaminase activity. The differentially expressed genes were categorized using GO, COG, KEGG and verified through RT-qPCR. This study assessed the crucial roles of Bsu06560 in regulating adenosine and N6-methyladenosine metabolism, which influence a myriad of biological processes. This is the first systematic research to identify and functionally annotate an enzyme capable of metabolizing N6-methyladenosine and highlight its significant roles in regulation of bacterial metabolism. Besides, this study provides a novel method for controlling gene expression through the mutations of critical residues.
      PubDate: Wed, 24 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1124
      Issue No: Vol. 49, No. 21 (2021)
       
  • Structurally constrained phosphonate internucleotide linkage impacts
           oligonucleotide-enzyme interaction, and modulates siRNA activity and
           allele specificity

    • Free pre-print version: Loading...

      Authors: Yamada K; Hildebrand S, Davis S, et al.
      Pages: 12069 - 12088
      Abstract: AbstractOligonucleotides is an emerging class of chemically-distinct therapeutic modalities, where extensive chemical modifications are fundamental for their clinical applications. Inter-nucleotide backbones are critical to the behaviour of therapeutic oligonucleotides, but clinically explored backbone analogues are, effectively, limited to phosphorothioates. Here, we describe the synthesis and bio-functional characterization of an internucleotide (E)-vinylphosphonate (iE-VP) backbone, where bridging oxygen is substituted with carbon in a locked stereo-conformation. After optimizing synthetic pathways for iE-VP-linked dimer phosphoramidites in different sugar contexts, we systematically evaluated the impact of the iE-VP backbone on oligonucleotide interactions with a variety of cellular proteins. Furthermore, we systematically evaluated the impact of iE-VP on RNA-Induced Silencing Complex (RISC) activity, where backbone stereo-constraining has profound position-specific effects. Using Huntingtin (HTT) gene causative of Huntington's disease as an example, iE-VP at position 6 significantly enhanced the single mismatch discrimination ability of the RISC without negative impact on silencing of targeting wild type htt gene. These findings suggest that the iE-VP backbone can be used to modulate the activity and specificity of RISC. Our study provides (i) a new chemical tool to alter oligonucleotide-enzyme interactions and metabolic stability, (ii) insight into RISC dynamics and (iii) a new strategy for highly selective SNP-discriminating siRNAs.
      PubDate: Thu, 25 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1126
      Issue No: Vol. 49, No. 21 (2021)
       
  • 7′,5′-alpha-bicyclo-DNA: new chemistry for oligonucleotide exon
           splicing modulation therapy

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      Authors: Evéquoz D; Verhaart I, van de Vijver D, et al.
      Pages: 12089 - 12105
      Abstract: AbstractAntisense oligonucleotides are small pieces of modified DNA or RNA, which offer therapeutic potential for many diseases. We report on the synthesis of 7′,5′-α-bc-DNA phosphoramidite building blocks, bearing the A, G, T and MeC nucleobases. Solid-phase synthesis was performed to construct five oligodeoxyribonucleotides containing modified thymidine residues, as well as five fully modified oligonucleotides. Incorporations of the modification inside natural duplexes resulted in strong destabilizing effects. However, fully modified strands formed very stable duplexes with parallel RNA complements. In its own series, 7′,5′-α-bc-DNA formed duplexes with a surprising high thermal stability. CD spectroscopy and extensive molecular modeling indicated the adoption by the homo-duplex of a ladder-like structure, while hetero-duplexes with DNA or RNA still form helical structure. The biological properties of this new modification were investigated in animal models for Duchenne muscular dystrophy and spinal muscular atrophy, where exon splicing modulation can restore production of functional proteins. It was found that the 7′,5′-α-bc-DNA scaffold confers a high biostability and a good exon splicing modulation activity in vitro and in vivo.
      PubDate: Fri, 26 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1097
      Issue No: Vol. 49, No. 21 (2021)
       
  • ImmReg: the regulon atlas of immune-related pathways across cancer types

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      Authors: Jiang T; Zhou W, Chang Z, et al.
      Pages: 12106 - 12118
      Abstract: AbstractImmune system gene regulation perturbation has been found to be a major cause of the development of various types of cancer. Numbers of mechanisms contribute to gene expression regulation, thus, systematically identification of potential regulons of immune-related pathways is critical to cancer immunotherapy. Here, we comprehensively chart the landscape of transcription factors, microRNAs, RNA binding proteins and long noncoding RNAs regulation in 17 immune-related pathways across 33 cancers. The potential immunology regulons are likely to exhibit higher expressions in immune cells, show expression perturbations in cancer, and are significantly correlated with immune cell infiltrations. We also identify a panel of clinically relevant immunology regulons across cancers. Moreover, the regulon atlas of immune-related pathways helps prioritizing cancer-related genes (i.e. ETV7, miR-146a-5p, ZFP36 and HCP5). We further identified two molecular subtypes of glioma (cold and hot tumour phenotypes), which were characterized by differences in immune cell infiltrations, expression of checkpoints, and prognosis. Finally, we developed a user-friendly resource, ImmReg (http://bio-bigdata.hrbmu.edu.cn/ImmReg/), with multiple modules to visualize, browse, and download immunology regulation. Our study provides a comprehensive landscape of immunology regulons, which will shed light on future development of RNA-based cancer immunotherapies.
      PubDate: Wed, 10 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1041
      Issue No: Vol. 49, No. 21 (2021)
       
  • The human telomeric proteome during telomere replication

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      Authors: Lin C; Näger A, Lunardi T, et al.
      Pages: 12119 - 12135
      Abstract: AbstractTelomere shortening can cause detrimental diseases and contribute to aging. It occurs due to the end replication problem in cells lacking telomerase. Furthermore, recent studies revealed that telomere shortening can be attributed to difficulties of the semi-conservative DNA replication machinery to replicate the bulk of telomeric DNA repeats. To investigate telomere replication in a comprehensive manner, we develop QTIP-iPOND - Quantitative Telomeric chromatin Isolation Protocol followed by isolation of Proteins On Nascent DNA - which enables purification of proteins that associate with telomeres specifically during replication. In addition to the core replisome, we identify a large number of proteins that specifically associate with telomere replication forks. Depletion of several of these proteins induces telomere fragility validating their importance for telomere replication. We also find that at telomere replication forks the single strand telomere binding protein POT1 is depleted, whereas histone H1 is enriched. Our work reveals the dynamic changes of the telomeric proteome during replication, providing a valuable resource of telomere replication proteins. To our knowledge, this is the first study that examines the replisome at a specific region of the genome.
      PubDate: Mon, 08 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1015
      Issue No: Vol. 49, No. 21 (2021)
       
  • Epigenetic regulation of nuclear lamina-associated heterochromatin by HAT1
           and the acetylation of newly synthesized histones

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      Authors: Popova L; Nagarajan P, Lovejoy C, et al.
      Pages: 12136 - 12151
      Abstract: AbstractA central component of the epigenome is the pattern of histone post-translational modifications that play a critical role in the formation of specific chromatin states. Following DNA replication, nascent chromatin is a 1:1 mixture of parental and newly synthesized histones and the transfer of modification patterns from parental histones to new histones is a fundamental step in epigenetic inheritance. Here we report that loss of HAT1, which acetylates lysines 5 and 12 of newly synthesized histone H4 during replication-coupled chromatin assembly, results in the loss of accessibility of large domains of heterochromatin, termed HAT1-dependent Accessibility Domains (HADs). HADs are mega base-scale domains that comprise ∼10% of the mouse genome. HAT1 globally represses H3 K9 me3 levels and HADs correspond to the regions of the genome that display HAT1-dependent increases in H3 K9me3 peak density. HADs display a high degree of overlap with a subset of Lamin-Associated Domains (LADs). HAT1 is required to maintain nuclear structure and integrity. These results indicate that HAT1 and the acetylation of newly synthesized histones may be critical regulators of the epigenetic inheritance of heterochromatin and suggest a new mechanism for the epigenetic regulation of nuclear lamina-heterochromatin interactions.
      PubDate: Fri, 12 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1044
      Issue No: Vol. 49, No. 21 (2021)
       
  • Chromatin loading of MCM hexamers is associated with di-/tri-methylation
           of histone H4K20 toward S phase entry

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      Authors: Hayashi-Takanaka Y; Hayashi Y, Hirano Y, et al.
      Pages: 12152 - 12166
      Abstract: AbstractDNA replication is a key step in initiating cell proliferation. Loading hexameric complexes of minichromosome maintenance (MCM) helicase onto DNA replication origins during the G1 phase is essential for initiating DNA replication. Here, we examined MCM hexamer states during the cell cycle in human hTERT-RPE1 cells using multicolor immunofluorescence-based, single-cell plot analysis, and biochemical size fractionation. Experiments involving cell-cycle arrest at the G1 phase and release from the arrest revealed that a double MCM hexamer was formed via a single hexamer during G1 progression. A single MCM hexamer was recruited to chromatin in the early G1 phase. Another single hexamer was recruited to form a double hexamer in the late G1 phase. We further examined relationship between the MCM hexamer states and the methylation levels at lysine 20 of histone H4 (H4K20) and found that the double MCM hexamer state was correlated with di/trimethyl-H4K20 (H4K20me2/3). Inhibiting the conversion from monomethyl-H4K20 (H4K20me1) to H4K20me2/3 retained the cells in the single MCM hexamer state. Non-proliferative cells, including confluent cells or Cdk4/6 inhibitor-treated cells, also remained halted in the single MCM hexamer state. We propose that the single MCM hexamer state is a halting step in the determination of cell cycle progression.
      PubDate: Fri, 19 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1068
      Issue No: Vol. 49, No. 21 (2021)
       
  • Relaxed 3D genome conformation facilitates the pluripotent to
           totipotent-like state transition in embryonic stem cells

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      Authors: Zhu Y; Yu J, Gu J, et al.
      Pages: 12167 - 12177
      Abstract: AbstractThe 3D genome organization is crucial for gene regulation. Although recent studies have revealed a uniquely relaxed genome conformation in totipotent early blastomeres of both fertilized and cloned embryos, how weakened higher-order chromatin structure is functionally linked to totipotency acquisition remains elusive. Using low-input Hi-C, ATAC-seq and ChIP-seq, we systematically examined the dynamics of 3D genome and epigenome during pluripotent to totipotent-like state transition in mouse embryonic stem cells (ESCs). The spontaneously converted 2-cell-embryo-like cells (2CLCs) exhibited more relaxed chromatin architecture compared to ESCs, including global weakening of both enhancer-promoter interactions and TAD insulation. While the former correlated with inactivation of ESC enhancers and down-regulation of pluripotent genes, the latter might facilitate contacts between the putative new enhancers arising in 2CLCs and neighboring 2C genes. Importantly, disruption of chromatin organization by depleting CTCF or the cohesin complex promoted the ESC to 2CLC transition. Our results thus establish a critical role of 3D genome organization in totipotency acquisition.
      PubDate: Wed, 17 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1069
      Issue No: Vol. 49, No. 21 (2021)
       
  • Assessing genome-wide dynamic changes in enhancer activity during early
           mESC differentiation by FAIRE-STARR-seq

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      Authors: Glaser L; Steiger M, Fuchs A, et al.
      Pages: 12178 - 12195
      Abstract: AbstractEmbryonic stem cells (ESCs) can differentiate into any given cell type and therefore represent a versatile model to study the link between gene regulation and differentiation. To quantitatively assess the dynamics of enhancer activity during the early stages of murine ESC differentiation, we analyzed accessible genomic regions using STARR-seq, a massively parallel reporter assay. This resulted in a genome-wide quantitative map of active mESC enhancers, in pluripotency and during the early stages of differentiation. We find that only a minority of accessible regions is active and that such regions are enriched near promoters, characterized by specific chromatin marks, enriched for distinct sequence motifs, and modeling shows that active regions can be predicted from sequence alone. Regions that change their activity upon retinoic acid-induced differentiation are more prevalent at distal intergenic regions when compared to constitutively active enhancers. Further, analysis of differentially active enhancers verified the contribution of individual TF motifs toward activity and inducibility as well as their role in regulating endogenous genes. Notably, the activity of retinoic acid receptor alpha (RARα) occupied regions can either increase or decrease upon the addition of its ligand, retinoic acid, with the direction of the change correlating with spacing and orientation of the RARα consensus motif and the co-occurrence of additional sequence motifs. Together, our genome-wide enhancer activity map elucidates features associated with enhancer activity levels, identifies regulatory regions disregarded by computational prediction tools, and provides a resource for future studies into regulatory elements in mESCs.
      PubDate: Wed, 24 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1100
      Issue No: Vol. 49, No. 21 (2021)
       
  • Master lineage transcription factors anchor trans mega transcriptional
           complexes at highly accessible enhancer sites to promote long-range
           chromatin clustering and transcription of distal target genes

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      Authors: White S; Snyder M, Yi C.
      Pages: 12196 - 12210
      Abstract: AbstractThe term ‘super enhancers’ (SE) has been widely used to describe stretches of closely localized enhancers that are occupied collectively by large numbers of transcription factors (TFs) and co-factors, and control the transcription of highly-expressed genes. Through integrated analysis of >600 DNase-seq, ChIP-seq, GRO-seq, STARR-seq, RNA-seq, Hi-C and ChIA-PET data in five human cancer cell lines, we identified a new class of autonomous SEs (aSEs) that are excluded from classic SE calls by the widely used Rank Ordering of Super-Enhancers (ROSE) method. TF footprint analysis revealed that compared to classic SEs and regular enhancers, aSEs are tightly bound by a dense array of master lineage TFs, which serve as anchors to recruit additional TFs and co-factors in trans. In addition, aSEs are preferentially enriched for Cohesins, which likely involve in stabilizing long-distance interactions between aSEs and their distal target genes. Finally, we showed that aSEs can be reliably predicted using a single DNase-seq data or combined with Mediator and/or P300 ChIP-seq. Overall, our study demonstrates that aSEs represent a unique class of functionally important enhancer elements that distally regulate the transcription of highly expressed genes.
      PubDate: Wed, 24 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1105
      Issue No: Vol. 49, No. 21 (2021)
       
  • BAF155 methylation drives metastasis by hijacking super-enhancers and
           subverting anti-tumor immunity

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      Authors: Kim E; Liu P, Zhang S, et al.
      Pages: 12211 - 12233
      Abstract: AbstractSubunits of the chromatin remodeler SWI/SNF are the most frequently disrupted genes in cancer. However, how post-translational modifications (PTM) of SWI/SNF subunits elicit epigenetic dysfunction remains unknown. Arginine-methylation of BAF155 by coactivator-associated arginine methyltransferase 1 (CARM1) promotes triple-negative breast cancer (TNBC) metastasis. Herein, we discovered the dual roles of methylated-BAF155 (me-BAF155) in promoting tumor metastasis: activation of super-enhancer-addicted oncogenes by recruiting BRD4, and repression of interferon α/γ pathway genes to suppress host immune response. Pharmacological inhibition of CARM1 and BAF155 methylation not only abrogated the expression of an array of oncogenes, but also boosted host immune responses by enhancing the activity and tumor infiltration of cytotoxic T cells. Moreover, strong me-BAF155 staining was detected in circulating tumor cells from metastatic cancer patients. Despite low cytotoxicity, CARM1 inhibitors strongly inhibited TNBC cell migration in vitro, and growth and metastasis in vivo. These findings illustrate a unique mechanism of arginine methylation of a SWI/SNF subunit that drives epigenetic dysregulation, and establishes me-BAF155 as a therapeutic target to enhance immunotherapy efficacy.
      PubDate: Fri, 19 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1122
      Issue No: Vol. 49, No. 21 (2021)
       
  • TRF2-mediated ORC recruitment underlies telomere stability upon DNA
           replication stress

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      Authors: Higa M; Matsuda Y, Fujii J, et al.
      Pages: 12234 - 12251
      Abstract: AbstractTelomeres are intrinsically difficult-to-replicate region of eukaryotic chromosomes. Telomeric repeat binding factor 2 (TRF2) binds to origin recognition complex (ORC) to facilitate the loading of ORC and the replicative helicase MCM complex onto DNA at telomeres. However, the biological significance of the TRF2–ORC interaction for telomere maintenance remains largely elusive. Here, we employed a TRF2 mutant with mutations in two acidic acid residues (E111A and E112A) that inhibited the TRF2–ORC interaction in human cells. The TRF2 mutant was impaired in ORC recruitment to telomeres and showed increased replication stress-associated telomeric DNA damage and telomere instability. Furthermore, overexpression of an ORC1 fragment (amino acids 244–511), which competitively inhibited the TRF2–ORC interaction, increased telomeric DNA damage under replication stress conditions. Taken together, these findings suggest that TRF2-mediated ORC recruitment contributes to the suppression of telomere instability.
      PubDate: Thu, 11 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1004
      Issue No: Vol. 49, No. 21 (2021)
       
  • Genome-wide analysis of 8-oxo-7,8-dihydro-2'-deoxyguanosine at
           single-nucleotide resolution unveils reduced occurrence of oxidative
           damage at G-quadruplex sites

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      Authors: An J; Yin M, Yin J, et al.
      Pages: 12252 - 12267
      Abstract: Abstract8-Oxo-7,8-dihydro-2′-deoxyguanosine (OG), one of the most common oxidative DNA damages, causes genome instability and is associated with cancer, neurological diseases and aging. In addition, OG and its repair intermediates can regulate gene transcription, and thus play a role in sensing cellular oxidative stress. However, the lack of methods to precisely map OG has hindered the study of its biological roles. Here, we developed a single-nucleotide resolution OG-sequencing method, named CLAPS-seq (Chemical Labeling And Polymerase Stalling Sequencing), to measure the genome-wide distribution of both exogenous and endogenous OGs with high specificity. Our data identified decreased OG occurrence at G-quadruplexes (G4s), in association with underrepresentation of OGs in promoters which have high GC content. Furthermore, we discovered that potential quadruplex sequences (PQSs) were hotspots of OGs, implying a role of non-G4-PQSs in OG-mediated oxidative stress response.
      PubDate: Fri, 12 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1022
      Issue No: Vol. 49, No. 21 (2021)
       
  • The chromatin remodeler RSF1 coordinates epigenetic marks for
           transcriptional repression and DSB repair

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      Authors: Min S; Lee H, Ji J, et al.
      Pages: 12268 - 12283
      Abstract: AbstractDNA lesions impact on local transcription and the damage-induced transcriptional repression facilitates efficient DNA repair. However, how chromatin dynamics cooperates with these two events remained largely unknown. We here show that histone H2A acetylation at K118 is enriched in transcriptionally active regions. Under DNA damage, the RSF1 chromatin remodeling factor recruits HDAC1 to DSB sites. The RSF1-HDAC1 complex induces the deacetylation of H2A(X)-K118 and its deacetylation is indispensable for the ubiquitination of histone H2A at K119. Accordingly, the acetylation mimetic H2A-K118Q suppressed the H2A-K119ub level, perturbing the transcriptional repression at DNA lesions. Intriguingly, deacetylation of H2AX at K118 also licenses the propagation of γH2AX and recruitment of MDC1. Consequently, the H2AX-K118Q limits DNA repair. Together, the RSF1-HDAC1 complex controls the traffic of the DNA damage response and transcription simultaneously in transcriptionally active chromatins. The interplay between chromatin remodelers and histone modifiers highlights the importance of chromatin versatility in the maintenance of genome integrity.
      PubDate: Thu, 25 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1093
      Issue No: Vol. 49, No. 21 (2021)
       
  • Loss of full-length hnRNP R isoform impairs DNA damage response in
           motoneurons by inhibiting Yb1 recruitment to chromatin

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      Authors: Ghanawi H; Hennlein L, Zare A, et al.
      Pages: 12284 - 12305
      Abstract: AbstractNeurons critically rely on the functions of RNA-binding proteins to maintain their polarity and resistance to neurotoxic stress. HnRNP R has a diverse range of post-transcriptional regulatory functions and is important for neuronal development by regulating axon growth. Hnrnpr pre-mRNA undergoes alternative splicing giving rise to a full-length protein and a shorter isoform lacking its N-terminal acidic domain. To investigate functions selectively associated with the full-length hnRNP R isoform, we generated a Hnrnpr knockout mouse (Hnrnprtm1a/tm1a) in which expression of full-length hnRNP R was abolished while production of the truncated hnRNP R isoform was retained. Motoneurons cultured from Hnrnprtm1a/tm1a mice did not show any axonal growth defects but exhibited enhanced accumulation of double-strand breaks and an impaired DNA damage response upon exposure to genotoxic agents. Proteomic analysis of the hnRNP R interactome revealed the multifunctional protein Yb1 as a top interactor. Yb1-depleted motoneurons were defective in DNA damage repair. We show that Yb1 is recruited to chromatin upon DNA damage where it interacts with γ-H2AX, a mechanism that is dependent on full-length hnRNP R. Our findings thus suggest a novel role of hnRNP R in maintaining genomic integrity and highlight the function of its N-terminal acidic domain in this context.
      PubDate: Thu, 25 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1120
      Issue No: Vol. 49, No. 21 (2021)
       
  • Nucleosomes enter cells by clathrin- and caveolin-dependent endocytosis

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      Authors: Wang H; Shan X, Ren M, et al.
      Pages: 12306 - 12319
      Abstract: AbstractDNA damage and apoptosis lead to the release of free nucleosomes—the basic structural repeating units of chromatin—into the blood circulation system. We recently reported that free nucleosomes that enter the cytoplasm of mammalian cells trigger immune responses by activating cGMP-AMP synthase (cGAS). In the present study, we designed experiments to reveal the mechanism of nucleosome uptake by human cells. We showed that nucleosomes are first absorbed on the cell membrane through nonspecific electrostatic interactions between positively charged histone N-terminal tails and ligands on the cell surface, followed by internalization via clathrin- or caveolae-dependent endocytosis. After cellular internalization, endosomal escape occurs rapidly, and nucleosomes are released into the cytosol, maintaining structural integrity for an extended period. The efficient endocytosis of extracellular nucleosomes suggests that circulating nucleosomes may lead to cellular disorders as well as immunostimulation, and thus, the biological effects exerted by endocytic nucleosomes should be addressed in the future.
      PubDate: Fri, 19 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1121
      Issue No: Vol. 49, No. 21 (2021)
       
  • Cellular heterogeneity in DNA alkylation repair increases population
           genetic plasticity

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      Authors: Vincent M; Uphoff S.
      Pages: 12320 - 12331
      Abstract: AbstractDNA repair mechanisms fulfil a dual role, as they are essential for cell survival and genome maintenance. Here, we studied how cells regulate the interplay between DNA repair and mutation. We focused on the adaptive response that increases the resistance of Escherichia coli cells to DNA alkylation damage. Combination of single-molecule imaging and microfluidic-based single-cell microscopy showed that noise in the gene activation timing of the master regulator Ada is accurately propagated to generate a distinct subpopulation of cells in which all proteins of the adaptive response are essentially absent. Whereas genetic deletion of these proteins causes extreme sensitivity to alkylation stress, a temporary lack of expression is tolerated and increases genetic plasticity of the whole population. We demonstrated this by monitoring the dynamics of nascent DNA mismatches during alkylation stress as well as the frequency of fixed mutations that are generated by the distinct subpopulations of the adaptive response. We propose that stochastic modulation of DNA repair capacity by the adaptive response creates a viable hypermutable subpopulation of cells that acts as a source of genetic diversity in a clonal population.
      PubDate: Thu, 25 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1143
      Issue No: Vol. 49, No. 21 (2021)
       
  • The hyperthermophilic archaeon Thermococcus kodakarensis is resistant to
           pervasive negative supercoiling activity of DNA gyrase

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      Authors: Villain P; da Cunha V, Villain E, et al.
      Pages: 12332 - 12347
      Abstract: AbstractIn all cells, DNA topoisomerases dynamically regulate DNA supercoiling allowing essential DNA processes such as transcription and replication to occur. How this complex system emerged in the course of evolution is poorly understood. Intriguingly, a single horizontal gene transfer event led to the successful establishment of bacterial gyrase in Archaea, but its emergent function remains a mystery. To better understand the challenges associated with the establishment of pervasive negative supercoiling activity, we expressed the gyrase of the bacterium Thermotoga maritima in a naïve archaeon Thermococcus kodakarensis which naturally has positively supercoiled DNA. We found that the gyrase was catalytically active in T. kodakarensis leading to strong negative supercoiling of plasmid DNA which was stably maintained over at least eighty generations. An increased sensitivity of gyrase-expressing T. kodakarensis to ciprofloxacin suggested that gyrase also modulated chromosomal topology. Accordingly, global transcriptome analyses revealed large scale gene expression deregulation and identified a subset of genes responding to the negative supercoiling activity of gyrase. Surprisingly, the artificially introduced dominant negative supercoiling activity did not have a measurable effect on T. kodakarensis growth rate. Our data suggest that gyrase can become established in Thermococcales archaea without critically interfering with DNA transaction processes.
      PubDate: Wed, 10 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab869
      Issue No: Vol. 49, No. 21 (2021)
       
  • Fast interaction dynamics of G-quadruplex and RGG-rich peptides unveiled
           in zero-mode waveguides

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      Authors: Patra S; Claude J, Naubron J, et al.
      Pages: 12348 - 12357
      Abstract: AbstractG-quadruplexes (GQs), a non-canonical form of DNA, are receiving a huge interest as target sites for potential applications in antiviral and anticancer drug treatments. The biological functions of GQs can be controlled by specifically binding proteins known as GQs binding proteins. Some of the GQs binding proteins contain an arginine and glycine-rich sequence known as RGG peptide. Despite the important role of RGG, the GQs-RGG interaction remains poorly understood. By single molecule measurements, the interaction dynamics can be determined in principle. However, the RGG–GQs interaction occurs at micromolar concentrations, making conventional single-molecule experiments impossible with a diffraction-limited confocal microscope. Here, we use a 120 nm zero-mode waveguide (ZMW) nanoaperture to overcome the diffraction limit. The combination of dual-color fluorescence cross-correlation spectroscopy (FCCS) with FRET is used to unveil the interaction dynamics and measure the association and dissociation rates. Our data show that the RGG–GQs interaction is predominantly driven by electrostatics but that a specific affinity between the RGG sequence and the GQs structure is preserved. The single molecule approach at micromolar concentration is the key to improve our understanding of GQs function and develop its therapeutic applications by screening a large library of GQs-targeting peptides and proteins.
      PubDate: Wed, 17 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1002
      Issue No: Vol. 49, No. 21 (2021)
       
  • Cyclophilin acts as a ribosome biogenesis factor by chaperoning the
           ribosomal protein (PlRPS15) in filamentous fungi

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      Authors: Mo C; Xie C, Wang G, et al.
      Pages: 12358 - 12376
      Abstract: AbstractThe rapid transport of ribosomal proteins (RPs) into the nucleus and their efficient assembly into pre-ribosomal particles are prerequisites for ribosome biogenesis. Proteins that act as dedicated chaperones for RPs to maintain their stability and facilitate their assembly have not been identified in filamentous fungi. PlCYP5 is a nuclear cyclophilin in the nematophagous fungus Purpureocillium lilacinum, whose expression is up-regulated during abiotic stress and nematode egg-parasitism. Here, we found that PlCYP5 co-translationally interacted with the unassembled small ribosomal subunit protein, PlRPS15 (uS19). PlRPS15 contained an eukaryote-specific N-terminal extension that mediated the interaction with PlCYP5. PlCYP5 increased the solubility of PlRPS15 independent of its catalytic peptide-prolyl isomerase function and supported the integration of PlRPS15 into pre-ribosomes. Consistently, the phenotypes of the PlCYP5 loss-of-function mutant were similar to those of the PlRPS15 knockdown mutant (e.g. growth and ribosome biogenesis defects). PlCYP5 homologs in Arabidopsis thaliana, Homo sapiens, Schizosaccharomyces pombe, Sclerotinia sclerotiorum, Botrytis cinerea and Metarhizium anisopliae were identified. Notably, PlCYP5-PlRPS15 homologs from three filamentous fungi interacted with each other but not those from other species. In summary, our data disclosed a unique dedicated chaperone system for RPs by cyclophilin in filamentous fungi.
      PubDate: Thu, 18 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1102
      Issue No: Vol. 49, No. 21 (2021)
       
  • TRF2 promotes dynamic and stepwise looping of POT1 bound telomeric
           overhang

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      Authors: Paul T; Liou W, Cai X, et al.
      Pages: 12377 - 12393
      Abstract: AbstractHuman telomeres are protected by shelterin proteins, but how telomeres maintain a dynamic structure remains elusive. Here, we report an unexpected activity of POT1 in imparting conformational dynamics of the telomere overhang, even at a monomer level. Strikingly, such POT1-induced overhang dynamics is greatly enhanced when TRF2 engages with the telomere duplex. Interestingly, TRF2, but not TRF2ΔB, recruits POT1-bound overhangs to the telomere ds/ss junction and induces a discrete stepwise movement up and down the axis of telomere duplex. The same steps are observed regardless of the length of the POT1-bound overhang, suggesting a tightly regulated conformational dynamic coordinated by TRF2 and POT1. TPP1 and TIN2 which physically connect POT1 and TRF2 act to generate a smooth movement along the axis of the telomere duplex. Our results suggest a plausible mechanism wherein telomeres maintain a dynamic structure orchestrated by shelterin.
      PubDate: Thu, 25 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1123
      Issue No: Vol. 49, No. 21 (2021)
       
  • A new RNA–DNA interaction required for integration of group II intron
           retrotransposons into DNA targets

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      Authors: Monachello D; Lauraine M, Gillot S, et al.
      Pages: 12394 - 12410
      Abstract: AbstractMobile group II introns are site-specific retrotransposable elements abundant in bacterial and organellar genomes. They are composed of a large and highly structured ribozyme and an intron-encoded reverse transcriptase that binds tightly to its intron to yield a ribonucleoprotein (RNP) particle. During the first stage of the mobility pathway, the intron RNA catalyses its own insertion directly into the DNA target site. Recognition of the proper target rests primarily on multiple base-pairing interactions between the intron RNA and the target DNA, while the protein makes contacts with only a few target positions by yet-unidentified mechanisms. Using a combination of comparative sequence analyses and in vivo mobility assays we demonstrate the existence of a new base-pairing interaction named EBS2a–IBS2a between the intron RNA and its DNA target site. This pairing adopts a Watson–Crick geometry and is essential for intron mobility, most probably by driving unwinding of the DNA duplex. Importantly, formation of EBS2a–IBS2a also requires the reverse transcriptase enzyme which stabilizes the pairing in a non-sequence-specific manner. In addition to bringing to light a new structural device that allows subgroup IIB1 and IIB2 introns to invade their targets with high efficiency and specificity our work has important implications for the biotechnological applications of group II introns in bacterial gene targeting.
      PubDate: Wed, 17 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1031
      Issue No: Vol. 49, No. 21 (2021)
       
  • Probing the stability of the SpCas9–DNA complex after cleavage

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      Authors: Aldag P; Welzel F, Jakob L, et al.
      Pages: 12411 - 12421
      Abstract: AbstractCRISPR–Cas9 is a ribonucleoprotein complex that sequence-specifically binds and cleaves double-stranded DNA. Wildtype Cas9 and its nickase and cleavage-incompetent mutants have been used in various biological techniques due to their versatility and programmable specificity. Cas9 has been shown to bind very stably to DNA even after cleavage of the individual DNA strands, inhibiting further turnovers and considerably slowing down in-vivo repair processes. This poses an obstacle in genome editing applications. Here, we employed single-molecule magnetic tweezers to investigate the binding stability of different Streptococcus pyogenes Cas9 variants after cleavage by challenging them with supercoiling. We find that different release mechanisms occur depending on which DNA strand is cleaved. After initial target strand cleavage, supercoils are only removed after the collapse of the R-loop. We identified several states with different stabilities of the R-loop. Most importantly, we find that the post-cleavage state of Cas9 exhibits a higher stability than the pre-cleavage state. After non-target strand cleavage, supercoils are immediately but slowly released by swiveling of the non-target strand around Cas9 bound to the target strand. Consequently, Cas9 and its non-target strand nicking mutant stay stably bound to the DNA for many hours even at elevated torsional stress.
      PubDate: Thu, 18 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1072
      Issue No: Vol. 49, No. 21 (2021)
       
  • Discovery of highly reactive self-splicing group II introns within the
           mitochondrial genomes of human pathogenic fungi

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      Authors: Liu T; Pyle A.
      Pages: 12422 - 12432
      Abstract: AbstractFungal pathogens represent an expanding global health threat for which treatment options are limited. Self-splicing group II introns have emerged as promising drug targets, but their development has been limited by a lack of information on their distribution and architecture in pathogenic fungi. To meet this challenge, we developed a bioinformatic workflow for scanning sequence data to identify unique RNA structural signatures within group II introns. Using this approach, we discovered a set of ubiquitous introns within thermally dimorphic fungi (genera of Blastomyces, Coccidioides and Histoplasma). These introns are the most biochemically reactive group II introns ever reported, and they self-splice rapidly under near-physiological conditions without protein cofactors. Moreover, we demonstrated the small molecule targetability of these introns by showing that they can be inhibited by the FDA-approved drug mitoxantrone in vitro. Taken together, our results highlight the utility of structure-based informatic searches for identifying riboregulatory elements in pathogens, revealing a striking diversity of reactive self-splicing introns with great promise as antifungal drug targets.
      PubDate: Thu, 25 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1077
      Issue No: Vol. 49, No. 21 (2021)
       
  • Efficient DNA interrogation of SpCas9 governed by its electrostatic
           interaction with DNA beyond the PAM and protospacer

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      Authors: Zhang Q; Chen Z, Wang F, et al.
      Pages: 12433 - 12444
      Abstract: AbstractStreptococcus pyogenes Cas9 (SpCas9), a programmable RNA-guided DNA endonuclease, has been widely repurposed for biological and medical applications. Critical interactions between SpCas9 and DNA confer the high specificity of the enzyme in genome engineering. Here, we unveil that an essential SpCas9–DNA interaction located beyond the protospacer adjacent motif (PAM) is realized through electrostatic forces between four positively charged lysines among SpCas9 residues 1151–1156 and the negatively charged DNA backbone. Modulating this interaction by substituting lysines with amino acids that have distinct charges revealed a strong dependence of DNA target binding and cleavage activities of SpCas9 on the charge. Moreover, the SpCas9 mutants show markedly distinguishable DNA interaction sites beyond the PAM compared with wild-type SpCas9. Functionally, this interaction governs DNA sampling and participates in protospacer DNA unwinding during DNA interrogation. Overall, a mechanistic and functional understanding of this vital interaction explains how SpCas9 carries out efficient DNA interrogation.
      PubDate: Thu, 25 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1139
      Issue No: Vol. 49, No. 21 (2021)
       
  • In vivo architecture of the telomerase RNA catalytic core in Trypanosoma
           brucei

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      Authors: Dey A; Monroy-Eklund A, Klotz K, et al.
      Pages: 12445 - 12466
      Abstract: AbstractTelomerase is a unique ribonucleoprotein (RNP) reverse transcriptase that utilizes its cognate RNA molecule as a template for telomere DNA repeat synthesis. Telomerase contains the reverse transcriptase protein, TERT and the template RNA, TR, as its core components. The 5’-half of TR forms a highly conserved catalytic core comprising of the template region and adjacent domains necessary for telomere synthesis. However, how telomerase RNA folding takes place in vivo has not been fully understood due to low abundance of the native RNP. Here, using unicellular pathogen Trypanosoma brucei as a model, we reveal important regional folding information of the native telomerase RNA core domains, i.e. TR template, template boundary element, template proximal helix and Helix IV (eCR4-CR5) domain. For this purpose, we uniquely combined in-cell probing with targeted high-throughput RNA sequencing and mutational mapping under three conditions: in vivo (in WT and TERT−/− cells), in an immunopurified catalytically active telomerase RNP complex and ex vivo (deproteinized). We discover that TR forms at least two different conformers with distinct folding topologies in the insect and mammalian developmental stages of T. brucei. Also, TERT does not significantly affect the RNA folding in vivo, suggesting that the telomerase RNA in T. brucei exists in a conformationally preorganized stable structure. Our observed differences in RNA (TR) folding at two distinct developmental stages of T. brucei suggest that important conformational changes are a key component of T. brucei development.
      PubDate: Wed, 24 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1042
      Issue No: Vol. 49, No. 21 (2021)
       
  • Evolutionary repair reveals an unexpected role of the tRNA modification
           m1G37 in aminoacylation

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      Authors: Clifton B; Fariz M, Uechi G, et al.
      Pages: 12467 - 12485
      Abstract: AbstractThe tRNA modification m1G37, introduced by the tRNA methyltransferase TrmD, is thought to be essential for growth in bacteria because it suppresses translational frameshift errors at proline codons. However, because bacteria can tolerate high levels of mistranslation, it is unclear why loss of m1G37 is not tolerated. Here, we addressed this question through experimental evolution of trmD mutant strains of Escherichia coli. Surprisingly, trmD mutant strains were viable even if the m1G37 modification was completely abolished, and showed rapid recovery of growth rate, mainly via duplication or mutation of the proline-tRNA ligase gene proS. Growth assays and in vitro aminoacylation assays showed that G37-unmodified tRNAPro is aminoacylated less efficiently than m1G37-modified tRNAPro, and that growth of trmD mutant strains can be largely restored by single mutations in proS that restore aminoacylation of G37-unmodified tRNAPro. These results show that inefficient aminoacylation of tRNAPro is the main reason for growth defects observed in trmD mutant strains and that proS may act as a gatekeeper of translational accuracy, preventing the use of error-prone unmodified tRNAPro in translation. Our work shows the utility of experimental evolution for uncovering the hidden functions of essential genes and has implications for the development of antibiotics targeting TrmD.
      PubDate: Thu, 11 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1067
      Issue No: Vol. 49, No. 21 (2021)
       
  • G-quadruplex RNA motifs influence gene expression in the malaria parasite
           Plasmodium falciparum

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      Authors: Dumetz F; Chow E, Harris L, et al.
      Pages: 12486 - 12501
      Abstract: AbstractG-quadruplexes are non-helical secondary structures that can fold in vivo in both DNA and RNA. In human cells, they can influence replication, transcription and telomere maintenance in DNA, or translation, transcript processing and stability of RNA. We have previously showed that G-quadruplexes are detectable in the DNA of the malaria parasite Plasmodium falciparum, despite a very highly A/T-biased genome with unusually few guanine-rich sequences. Here, we show that RNA G-quadruplexes can also form in P. falciparum RNA, using rG4-seq for transcriptome-wide structure-specific RNA probing. Many of the motifs, detected here via the rG4seeker pipeline, have non-canonical forms and would not be predicted by standard in silico algorithms. However, in vitro biophysical assays verified formation of non-canonical motifs. The G-quadruplexes in the P. falciparum transcriptome are frequently clustered in certain genes and associated with regions encoding low-complexity peptide repeats. They are overrepresented in particular classes of genes, notably those that encode PfEMP1 virulence factors, stress response genes and DNA binding proteins. In vitro translation experiments and in vivo measures of translation efficiency showed that G-quadruplexes can influence the translation of P. falciparum mRNAs. Thus, the G-quadruplex is a novel player in post-transcriptional regulation of gene expression in this major human pathogen.
      PubDate: Thu, 18 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1095
      Issue No: Vol. 49, No. 21 (2021)
       
  • Inhibition of SARS-CoV-2 coronavirus proliferation by designer
           antisense-circRNAs

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      Authors: Pfafenrot C; Schneider T, Müller C, et al.
      Pages: 12502 - 12516
      Abstract: AbstractCircular RNAs (circRNAs) are noncoding RNAs that exist in all eukaryotes investigated and are derived from back-splicing of certain pre-mRNA exons. Here, we report the application of artificial circRNAs designed to act as antisense-RNAs. We systematically tested a series of antisense-circRNAs targeted to the SARS-CoV-2 genome RNA, in particular its structurally conserved 5′-untranslated region. Functional assays with both reporter transfections as well as with SARS-CoV-2 infections revealed that specific segments of the SARS-CoV-2 5′-untranslated region can be efficiently accessed by specific antisense-circRNAs, resulting in up to 90% reduction of virus proliferation in cell culture, and with a durability of at least 48 h. Presenting the antisense sequence within a circRNA clearly proved more efficient than in the corresponding linear configuration and is superior to modified antisense oligonucleotides. The activity of the antisense-circRNA is surprisingly robust towards point mutations in the target sequence. This strategy opens up novel applications for designer circRNAs and promising therapeutic strategies in molecular medicine.
      PubDate: Wed, 24 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1096
      Issue No: Vol. 49, No. 21 (2021)
       
  • The pioneer round of translation ensures proper targeting of ER and
           mitochondrial proteins

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      Authors: Park J; Chang J, Hwang H, et al.
      Pages: 12517 - 12534
      Abstract: AbstractThe pioneer (or first) round of translation of newly synthesized mRNAs is largely mediated by a nuclear cap-binding complex (CBC). In a transcriptome-wide analysis of polysome-associated and CBC-bound transcripts, we identify RN7SL1, a noncoding RNA component of a signal recognition particle (SRP), as an interaction partner of the CBC. The direct CBC–SRP interaction safeguards against abnormal expression of polypeptides from a ribosome–nascent chain complex (RNC)–SRP complex until the latter is properly delivered to the endoplasmic reticulum. Failure of this surveillance causes abnormal expression of misfolded proteins at inappropriate intracellular locations, leading to a cytosolic stress response. This surveillance pathway also blocks protein synthesis through RNC–SRP misassembled on an mRNA encoding a mitochondrial protein. Thus, our results reveal a surveillance pathway in which pioneer translation ensures proper targeting of endoplasmic reticulum and mitochondrial proteins.
      PubDate: Thu, 25 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1098
      Issue No: Vol. 49, No. 21 (2021)
       
  • Broken symmetry between RNA enantiomers in a crystal lattice

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      Authors: Kiliszek A; Błaszczyk L, Bejger M, et al.
      Pages: 12535 - 12539
      Abstract: Explaining the origin of the homochirality of biological molecules requires a mechanism of disrupting the natural equilibrium between enantiomers and amplifying the initial imbalance to significant levels.
      Authors of existing models have sought an explanation in the parity-breaking weak nuclear force, in some selectively acting external factor, or in random fluctuations that subsequently became amplified by an autocatalytic process. We have obtained crystals in which l- and d-enantiomers of short RNA duplexes assemble in an asymmetric manner. These enantiomers make different lattice contacts and have different exposures to water and metal ions present in the crystal. Apparently, asymmetry between enantiomers can arise upon their mutual interactions and then propagate via crystallization. Asymmetric racemic compounds are worth considering as possible factors in symmetry breaking and enantioenrichment that took place in the early biosphere.
      PubDate: Wed, 09 Jun 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab480
      Issue No: Vol. 49, No. 21 (2021)
       
  • Revealing A-T and G-C Hoogsteen base pairs in stressed protein-bound
           duplex DNA

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      Authors: Shi H; Kimsey I, Gu S, et al.
      Pages: 12540 - 12555
      Abstract: AbstractWatson–Crick base pairs (bps) are the fundamental unit of genetic information and the building blocks of the DNA double helix. However, A-T and G-C can also form alternative ‘Hoogsteen’ bps, expanding the functional complexity of DNA. We developed ‘Hoog-finder’, which uses structural fingerprints to rapidly screen Hoogsteen bps, which may have been mismodeled as Watson–Crick in crystal structures of protein–DNA complexes. We uncovered 17 Hoogsteen bps, 7 of which were in complex with 6 proteins never before shown to bind Hoogsteen bps. The Hoogsteen bps occur near mismatches, nicks and lesions and some appear to participate in recognition and damage repair. Our results suggest a potentially broad role for Hoogsteen bps in stressed regions of the genome and call for a community-wide effort to identify these bps in current and future crystal structures of DNA and its complexes.
      PubDate: Thu, 18 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab936
      Issue No: Vol. 49, No. 21 (2021)
       
  • Functional asymmetry and chemical reactivity of CsoR family persulfide
           sensors

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      Authors: Fakhoury J; Zhang Y, Edmonds K, et al.
      Pages: 12556 - 12576
      Abstract: AbstractCstR is a persulfide-sensing member of the functionally diverse copper-sensitive operon repressor (CsoR) superfamily. While CstR regulates the bacterial response to hydrogen sulfide (H2S) and more oxidized reactive sulfur species (RSS) in Gram-positive pathogens, other dithiol-containing CsoR proteins respond to host derived Cu(I) toxicity, sometimes in the same bacterial cytoplasm, but without regulatory crosstalk in cells. It is not clear what prevents this crosstalk, nor the extent to which RSS sensors exhibit specificity over other oxidants. Here, we report a sequence similarity network (SSN) analysis of the entire CsoR superfamily, which together with the first crystallographic structure of a CstR and comprehensive mass spectrometry-based kinetic profiling experiments, reveal new insights into the molecular basis of RSS specificity in CstRs. We find that the more N-terminal cysteine is the attacking Cys in CstR and is far more nucleophilic than in a CsoR. Moreover, our CstR crystal structure is markedly asymmetric and chemical reactivity experiments reveal the functional impact of this asymmetry. Substitution of the Asn wedge between the resolving and the attacking thiol with Ala significantly decreases asymmetry in the crystal structure and markedly impacts the distribution of species, despite adopting the same global structure as the parent repressor. Companion NMR, SAXS and molecular dynamics simulations reveal that the structural and functional asymmetry can be traced to fast internal dynamics of the tetramer. Furthermore, this asymmetry is preserved in all CstRs and with all oxidants tested, giving rise to markedly distinct distributions of crosslinked products. Our exploration of the sequence, structural, and kinetic features that determine oxidant-specificity suggest that the product distribution upon RSS exposure is determined by internal flexibility.
      PubDate: Wed, 10 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1040
      Issue No: Vol. 49, No. 21 (2021)
       
  • Structural basis of cyclic oligoadenylate degradation by ancillary Type
           III CRISPR-Cas ring nucleases

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      Authors: Molina R; Jensen A, Marchena-Hurtado J, et al.
      Pages: 12577 - 12590
      Abstract: AbstractType III CRISPR-Cas effector systems detect foreign RNA triggering DNA and RNA cleavage and synthesizing cyclic oligoadenylate molecules (cA) in their Cas10 subunit. cAs act as a second messenger activating auxiliary nucleases, leading to an indiscriminate RNA degradation that can end in cell dormancy or death. Standalone ring nucleases are CRISPR ancillary proteins which downregulate the strong immune response of Type III systems by degrading cA. These enzymes contain a CRISPR-associated Rossman-fold (CARF) domain, which binds and cleaves the cA molecule. Here, we present the structures of the standalone ring nuclease from Sulfolobus islandicus (Sis) 0811 in its apo and post-catalytic states. This enzyme is composed by a N-terminal CARF and a C-terminal wHTH domain. Sis0811 presents a phosphodiester hydrolysis metal-independent mechanism, which cleaves cA4 rings to generate linear adenylate species, thus reducing the levels of the second messenger and switching off the cell antiviral state. The structural and biochemical analysis revealed the coupling of a cork-screw conformational change with the positioning of key catalytic residues to proceed with cA4 phosphodiester hydrolysis in a non-concerted manner.
      PubDate: Fri, 26 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1130
      Issue No: Vol. 49, No. 21 (2021)
       
  • Modulating the chemo-mechanical response of structured DNA assemblies
           through binding molecules

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      Authors: Lee C; Kim Y, Kim K, et al.
      Pages: 12591 - 12599
      Abstract: AbstractRecent advances in DNA nanotechnology led the fabrication and utilization of various DNA assemblies, but the development of a method to control their global shapes and mechanical flexibilities with high efficiency and repeatability is one of the remaining challenges for the realization of the molecular machines with on-demand functionalities. DNA-binding molecules with intercalation and groove binding modes are known to induce the perturbation on the geometrical and mechanical characteristics of DNA at the strand level, which might be effective in structured DNA assemblies as well. Here, we demonstrate that the chemo-mechanical response of DNA strands with binding ligands can change the global shape and stiffness of DNA origami nanostructures, thereby enabling the systematic modulation of them by selecting a proper ligand and its concentration. Multiple DNA-binding drugs and fluorophores were applied to straight and curved DNA origami bundles, which demonstrated a fast, recoverable, and controllable alteration of the bending persistence length and the radius of curvature of DNA nanostructures. This chemo-mechanical modulation of DNA nanostructures would provide a powerful tool for reconfigurable and dynamic actuation of DNA machineries.
      PubDate: Thu, 25 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1119
      Issue No: Vol. 49, No. 21 (2021)
       
  • Correction to ‘Binding of DNA origami to lipids: maximizing yield and
           switching via strand displacement’

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      Authors: Singh J; Darley E, Ridone P, et al.
      Pages: 12600 - 12600
      Abstract: Australian Research Council10.13039/501100000923DE180101635DP210101892Commonwealth Scientific and Industrial Research Organisation10.13039/501100000943Westpac Bicentennial Foundation10.13039/100013787Medical Advances Without Animals Trust10.13039/501100001220
      PubDate: Fri, 12 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1163
      Issue No: Vol. 49, No. 21 (2021)
       
  • Correction to ‘Molecular structure, DNA binding mode, photophysical
           properties and recommendations for use of SYBR Gold’

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      Authors: Kolbeck P; Vanderlinden W, Gemmecker G, et al.
      Pages: 12601 - 12602
      Abstract: The published version of our article (1) contains two errors that we would like to correct. The full name of the compound SYBR Gold was incorrectly stated in the Abstract (page 5143) and in the Results section (on page 5148). The correct name is 2-(4-{[diethyl(methyl)ammonio]methyl}phenyl)-6-methoxy-1-methyl-4-{[(2Z)-3-methyl-1,3-benzoxazol-2-ylidene]methyl}quinolin-1-ium
      PubDate: Wed, 24 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1164
      Issue No: Vol. 49, No. 21 (2021)
       
  • Correction to ‘DNA repair factor XPC is modified by SUMO-1 and ubiquitin
           following UV irradiation’

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      Authors: Wang Q; Zhu Q, Wani G, et al.
      Pages: 12603 - 12604
      Abstract: The authors regret the presence of undisclosed image splicing in the western blots shown in Figure 4A of their article (1).
      PubDate: Wed, 24 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1165
      Issue No: Vol. 49, No. 21 (2021)
       
  • Correction to ‘Structural insights into chromosome attachment to the
           nuclear envelope by an inner nuclear membrane protein Bqt4 in fission
           yeast’

    • Free pre-print version: Loading...

      Authors: Hu C; Inoue H, Sun W, et al.
      Pages: 12605 - 12605
      Abstract: Nucleic Acids Research, Volume 47, Issue 3, 20 February 2019, Pages 1573–1584, https://doi.org/10.1093/nar/gky1186
      PubDate: Wed, 24 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1181
      Issue No: Vol. 49, No. 21 (2021)
       
  • Retraction of ‘Interplay between REST and nucleolin transcription
           factors: a key mechanism in the overexpression of genes upon increased
           phosphorylation’

    • Free pre-print version: Loading...

      Pages: 12606 - 12606
      Abstract: Nucleic Acids Research, Volume 38, Issue 9, 1 May 2010, Pages 2799–2812, https://doi.org/10.1093/nar/gkq013
      PubDate: Wed, 17 Nov 2021 00:00:00 GMT
      DOI: 10.1093/nar/gkab1151
      Issue No: Vol. 49, No. 21 (2021)
       
 
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