JournalTOCs

Epigenomes
Number of Followers: 0

This is an Open Access Journal

Open Access journal
ISSN (Online) 2075-4655
Published by MDPI

[84 journals]

Epigenomes, Vol. 6, Pages 16: Global m6A RNA Methylation in SARS-CoV-2
Positive Nasopharyngeal Samples in a Mexican Population: A First
Approximation Study
- Authors: Jorge Luis Batista-Roche, Bruno Gómez-Gil, Gertrud Lund, César Alejandro Berlanga-Robles, Alejandra García-Gasca
  First page: 16
  Abstract: The Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) is the causal agent of COVID-19 (Coronavirus Disease-19). Both mutation and/or recombination events in the SARS-CoV-2 genome have resulted in variants that differ in transmissibility and severity. Furthermore, RNA methylation of the N6 position of adenosine (m6A) is known to be altered in cells infected with SARS-CoV-2. However, it is not known whether this epitranscriptomic modification differs across individuals dependent on the presence of infection with distinct SARS-CoV-2 variants, the viral load, or the vaccination status. To address this issue, we selected RNAs (n = 60) from SARS-CoV-2 sequenced nasopharyngeal samples (n = 404) of 30- to 60-year-old outpatients or hospitalized individuals from the city of Mazatlán (Mexico) between February 2021 and March 2022. Control samples were non-infected individuals (n = 10). SARS-CoV-2 was determined with real-time PCR, viral variants were determined with sequencing, and global m6A levels were determined by using a competitive immunoassay method. We identified variants of concern (VOC; alpha, gamma, delta, omicron), the variant of interest (VOI; epsilon), and the lineage B.1.1.519. Global m6A methylation differed significantly across viral variants (p = 3.2 × 10−7). In particular, we found that m6A levels were significantly lower in the VOC delta- and omicron-positive individuals compared to non-infected individuals (p = 2.541236 × 10−2 and 1.134411 × 10−4, respectively). However, we uncovered no significant correlation between global m6A levels and viral nucleocapsid (N) gene expression or age. Furthermore, individuals with complete vaccination schemes showed significantly lower m6A levels than unvaccinated individuals (p = 2.6 × 10−4), and differences in methylation levels across variants in unvaccinated individuals were significant (p = 3.068 × 10−3). These preliminary results suggest that SARS-CoV-2 variants show differences in global m6A levels.
  Citation: Epigenomes
  PubDate: 2022-06-29
  DOI: 10.3390/epigenomes6030016
  Issue No: Vol. 6, No. 3 (2022)
Epigenomes, Vol. 6, Pages 11: Sex-Specific Expression of Non-Coding RNA
Fragments in Frontal Cortex, Hippocampus and Cerebellum of Rats
- Authors: Anna Fiselier, Boseon Byeon, Yaroslav Ilnytskyy, Igor Kovalchuk, Olga Kovalchuk
  First page: 11
  Abstract: Non-coding RNA fragments (ncRFs) are processed from various non-coding RNAs (ncRNAs), with the most abundant being those produced from tRNAs. ncRFs were reported in many animal and plant species. Many ncRFs exhibit tissue specificity or/and are affected by stress. There is, however, only a handful of reports that describe differential expression of ncRFs in the brain regions. In this work, we analyzed the abundance of ncRFs processed from four major ncRNAs, including tRNA (tRFs), snoRNA (snoRFs), snRNA (snRFs), and rRNA (rRFs) in the frontal cortex (FC), hippocampus (HIP), and cerebellum (CER) of male and female rats. We found brain-specific and sex-specific differences. Reads mapping to lincRNAs were significantly larger in CER as compared to HIP and CER, while those mapping to snRNAs and tRNA were smaller in HIP than in FC and CER. tRF reads were the most abundant among all ncRF reads, and FC had more reads than HIP and CER. Reads mapping to antisense ncRNAs were significantly larger in females than in males in FC. Additionally, males consistently had more tRF, snRF, and snoRF reads in all brain regions. rRFs were more abundant in males in FC and females in HIP. Several tRFs were significantly underrepresented, including tRF-ValCAC, tRF-ValACC, and tRF-LysCTT in all brain regions. We also found brain- and sex-specific differences in the number of brain function-related mRNA targets. To summarize, we found sex-specific differences in the expression of several ncRNA fragments in various brain regions of healthy rats.
  Citation: Epigenomes
  PubDate: 2022-04-02
  DOI: 10.3390/epigenomes6020011
  Issue No: Vol. 6, No. 2 (2022)
Epigenomes, Vol. 6, Pages 12: The Transmission of Intergenerational
Epigenetic Information by Sperm microRNAs
- Authors: Grace S. Lee, Colin C. Conine
  First page: 12
  Abstract: Epigenetic information is transmitted from one generation to the next, modulating the phenotype of offspring non-genetically in organisms ranging from plants to mammals. For intergenerational non-genetic inheritance to occur, epigenetic information must accumulate in germ cells. The three main carriers of epigenetic information—histone post-translational modifications, DNA modifications, and RNAs—all exhibit dynamic patterns of regulation during germ cell development. For example, histone modifications and DNA methylation are extensively reprogrammed and often eliminated during germ cell maturation and after fertilization during embryogenesis. Consequently, much attention has been given to RNAs, specifically small regulatory RNAs, as carriers of inherited epigenetic information. In this review, we discuss examples in which microRNAs have been implicated as key players in transmitting paternal epigenetic information intergenerationally.
  Citation: Epigenomes
  PubDate: 2022-04-07
  DOI: 10.3390/epigenomes6020012
  Issue No: Vol. 6, No. 2 (2022)
Epigenomes, Vol. 6, Pages 13: Insights into Cardiovascular Defects and
Cardiac Epigenome in the Context of COVID-19
- Authors: Shreya Sarkar, Rwik Sen
  First page: 13
  Abstract: Although few in number, studies on epigenome of the heart of COVID-19 patients show that epigenetic signatures such as DNA methylation are significantly altered, leading to changes in expression of several genes. It contributes to pathogenic cardiac phenotypes of COVID-19, e.g., low heart rate, myocardial edema, and myofibrillar disarray. DNA methylation studies reveal changes which likely contribute to cardiac disease through unknown mechanisms. The incidence of severe COVID-19 disease, including hospitalization, requiring respiratory support, morbidity, and mortality, is disproportionately higher in individuals with co-morbidities. This poses unprecedented strains on the global healthcare system. While their underlying conditions make patients more susceptible to severe COVID-19 disease, strained healthcare systems, lack of adequate support, or sedentary lifestyles from ongoing lockdowns have proved detrimental to their underlying health conditions, thus pushing them to severe risk of congenital heart disease (CHD) itself. Prophylactic vaccines against COVID-19 have ushered new hope for CHD. A common connection between COVID-19 and CHD is SARS-CoV-2’s host receptor ACE2, because ACE2 regulates and protects organs, including the heart, in various ways. ACE2 is a common therapeutic target against cardiovascular disease and COVID-19 which damages organs. Hence, this review explores the above regarding CHDs, cardiovascular damage, and cardiac epigenetics, in COVID-19 patients.
  Citation: Epigenomes
  PubDate: 2022-04-21
  DOI: 10.3390/epigenomes6020013
  Issue No: Vol. 6, No. 2 (2022)
Epigenomes, Vol. 6, Pages 14: Epigenetic Signatures of Centrosomes Are
Novel Targets in Cancer Diagnosis: Insights from an Analysis of the Cancer
Genome Atlas
- Authors: Zhou Zhang, Wei Zhang
  First page: 14
  Abstract: The centrosome plays a central role for cellular signaling and is critical for several fundamental cellular processes in human cells. Centrosome abnormalities have been linked to multiple solid tumors and hematological malignancies. We sought to explore the potential role of the DNA methylation, a critical epigenetic modification, of centrosome-related genes in different cancers. The 450K array DNA methylation data and RNA-seq data were downloaded for ~4000 tumor samples and ~500 normal controls from The Cancer Genome Atlas (TCGA) project, covering 11 major cancer types. Cancers with more than 30 normal controls were retained for analysis. Differentially modified CpGs of centrosome genes were identified, and cancer-specific epigenetic models were developed using a machine-learning algorithm for each cancer type. The association between the methylation level of differential CpGs and the corresponding gene expression, as well as the co-localization of the differential CpGs and cis-regulatory elements were evaluated. In total, 2761 CpGs located on 160 centrosome genes for 6 cancers were included in the analysis. Cancer-specific models demonstrated a high accuracy in terms of the area under the receiver operating characteristic (ROC) curve (AUC > 0.9) in five cancers and showed tissue specificity. This study enhanced our understanding of the epigenetic mechanisms underlying the DNA methylation of centrosome-related genes in cancers, and showed the potential of these epigenetic modifications as novel cancer biomarkers.
  Citation: Epigenomes
  PubDate: 2022-06-02
  DOI: 10.3390/epigenomes6020014
  Issue No: Vol. 6, No. 2 (2022)
Epigenomes, Vol. 6, Pages 15: The Role of Genetics, Epigenetics, and the
Environment in ASD: A Mini Review
- Authors: Asim A. Khogeer, Iman S. AboMansour, Dia A. Mohammed
  First page: 15
  Abstract: According to recent findings, variances in autism spectrum disorder (ASD) risk factors might be determined by several factors, including molecular genetic variants. Accumulated evidence has also revealed the important role of biological and chemical pathways in ASD aetiology. In this paper, we assess several reviews with regard to their quality of evidence and provide a brief outline of the presumed mechanisms of the genetic, epigenetic, and environmental risk factors of ASD. We also review some of the critical literature, which supports the basis of each factor in the underlying and specific risk patterns of ASD. Finally, we consider some of the implications of recent research regarding potential molecular targets for future investigations.
  Citation: Epigenomes
  PubDate: 2022-06-19
  DOI: 10.3390/epigenomes6020015
  Issue No: Vol. 6, No. 2 (2022)
Epigenomes, Vol. 6, Pages 2: Chromatin Unlimited: An Evolutionary View of
Chromatin
- Authors: Yasushi Hiraoka
  First page: 2
  Abstract: Chromatin is a fundamental and highly conserved structure that carries genetic and epigenetic information in eukaryotic cells [...]
  Citation: Epigenomes
  PubDate: 2022-01-02
  DOI: 10.3390/epigenomes6010002
  Issue No: Vol. 6, No. 1 (2022)
Epigenomes, Vol. 6, Pages 3: Polycomb Repressive Complex 2 in
Eukaryotes—An Evolutionary Perspective
- Authors: Mallika Vijayanathan, María Guadalupe Trejo-Arellano, Iva Mozgová
  First page: 3
  Abstract: Polycomb repressive complex 2 (PRC2) represents a group of evolutionarily conserved multi-subunit complexes that repress gene transcription by introducing trimethylation of lysine 27 on histone 3 (H3K27me3). PRC2 activity is of key importance for cell identity specification and developmental phase transitions in animals and plants. The composition, biochemistry, and developmental function of PRC2 in animal and flowering plant model species are relatively well described. Recent evidence demonstrates the presence of PRC2 complexes in various eukaryotic supergroups, suggesting conservation of the complex and its function. Here, we provide an overview of the current understanding of PRC2-mediated repression in different representatives of eukaryotic supergroups with a focus on the green lineage. By comparison of PRC2 in different eukaryotes, we highlight the possible common and diverged features suggesting evolutionary implications and outline emerging questions and directions for future research of polycomb repression and its evolution.
  Citation: Epigenomes
  PubDate: 2022-01-17
  DOI: 10.3390/epigenomes6010003
  Issue No: Vol. 6, No. 1 (2022)
Epigenomes, Vol. 6, Pages 4: Biochemical Principles in Prion-Based
Inheritance
- Authors: Emily M. Dennis, David M. Garcia
  First page: 4
  Abstract: Prions are proteins that can stably fold into alternative structures that frequently alter their activities. They can self-template their alternate structures and are inherited across cell divisions and generations. While they have been studied for more than four decades, their enigmatic nature has limited their discovery. In the last decade, we have learned just how widespread they are in nature, the many beneficial phenotypes that they confer, while also learning more about their structures and modes of inheritance. Here, we provide a brief review of the biochemical principles of prion proteins, including their sequences, characteristics and structures, and what is known about how they self-template, citing examples from multiple organisms. Prion-based inheritance is the most understudied segment of epigenetics. Here, we lay a biochemical foundation and share a framework for how to define these molecules, as new examples are unearthed throughout nature.
  Citation: Epigenomes
  PubDate: 2022-01-25
  DOI: 10.3390/epigenomes6010004
  Issue No: Vol. 6, No. 1 (2022)
Epigenomes, Vol. 6, Pages 5: Acknowledgment to Reviewers of Epigenomes in
2021
- Authors: Epigenomes Editorial Office Epigenomes Editorial Office
  First page: 5
  Abstract: Rigorous peer-reviews are the basis of high-quality academic publishing [...]
  Citation: Epigenomes
  PubDate: 2022-01-26
  DOI: 10.3390/epigenomes6010005
  Issue No: Vol. 6, No. 1 (2022)
Epigenomes, Vol. 6, Pages 6: Opportunities for Early Cancer Detection: The
Rise of ctDNA Methylation-Based Pan-Cancer Screening Technologies
- Authors: Nicolas Constantin, Abu Ali Ibn Sina, Darren Korbie, Matt Trau
  First page: 6
  Abstract: The efficiency of conventional screening programs to identify early-stage malignancies can be limited by the low number of cancers recommended for screening as well as the high cumulative false-positive rate, and associated iatrogenic burden, resulting from repeated multimodal testing. The opportunity to use minimally invasive liquid biopsy testing to screen asymptomatic individuals at-risk for multiple cancers simultaneously could benefit from the aggregated diseases prevalence and a fixed specificity. Increasing both latter parameters is paramount to mediate high positive predictive value—a useful metric to evaluate a screening test accuracy and its potential harm-benefit. Thus, the use of a single test for multi-cancer early detection (stMCED) has emerged as an appealing strategy for increasing early cancer detection rate efficiency and benefit population health. A recent flurry of these stMCED technologies have been reported for clinical potential; however, their development is facing unique challenges to effectively improve clinical cost–benefit. One promising avenue is the analysis of circulating tumour DNA (ctDNA) for detecting DNA methylation biomarker fingerprints of malignancies—a hallmark of disease aetiology and progression holding the potential to be tissue- and cancer-type specific. Utilizing panels of epigenetic biomarkers could potentially help to detect earlier stages of malignancies as well as identify a tumour of origin from blood testing, useful information for follow-up clinical decision making and subsequent patient care improvement. Overall, this review collates the latest and most promising stMCED methodologies, summarizes their clinical performances, and discusses the specific requirements multi-cancer tests should meet to be successfully implemented into screening guidelines.
  Citation: Epigenomes
  PubDate: 2022-02-04
  DOI: 10.3390/epigenomes6010006
  Issue No: Vol. 6, No. 1 (2022)
Epigenomes, Vol. 6, Pages 7: Methylation Status of Exon IV of the
Brain-Derived Neurotrophic Factor (BDNF)-Encoding Gene in Patients with
Non-Diabetic Hyperglycaemia (NDH) before and after a Lifestyle
Intervention
- Authors: Helene A. Fachim, Nagaraj Malipatil, Kirk Siddals, Rachelle Donn, Gabriela Y. Cortés, Caroline F. Dalton, J. Martin Gibson, Adrian H. Heald
  First page: 7
  Abstract: BDNF signalling in hypothalamic neuronal circuits is thought to regulate mammalian food intake. In light of this, we investigated how a lifestyle intervention influenced serum levels and DNA methylation of BDNF gene in fat tissue and buffy coat of NDH individuals. In total, 20 participants underwent anthropometric measurements/fasting blood tests and adipose tissue biopsy pre-/post-lifestyle (6 months) intervention. DNA was extracted from adipose tissue and buffy coat, bisulphite converted, and pyrosequencing was used to determine methylation levels in exon IV of the BDNF gene. RNA was extracted from buffy coat for gene expression analysis and serum BDNF levels were measured by ELISA. No differences were found in BDNF serum levels, but buffy coat mean BDNF gene methylation decreased post-intervention. There were correlations between BDNF serum levels and/or methylation and cardiometabolic markers. (i) Pre-intervention: for BDNF methylation, we found positive correlations between mean methylation in fat tissue and waist-hip ratio, and negative correlations between mean methylation in buffy coat and weight. (ii) Post-intervention: we found correlations between BDNF mean methylation in buffy coat and HbA1c, BDNF methylation in buffy coat and circulating IGFBP-2, and BDNF serum and insulin. Higher BDNF % methylation levels are known to reduce BNDF expression. The fall in buffy coat mean BDNF methylation plus the association between lower BDNF methylation (so potentially higher BDNF) and higher HbA1c and serum IGFBP-2 (as a marker of insulin sensitivity) and between lower serum BDNF and higher circulating insulin are evidence for the degree of BDNF gene methylation being implicated in insulinisation and glucose homeostasis, particularly after lifestyle change in NDH individuals.
  Citation: Epigenomes
  PubDate: 2022-02-18
  DOI: 10.3390/epigenomes6010007
  Issue No: Vol. 6, No. 1 (2022)
Epigenomes, Vol. 6, Pages 8: The Importance of Networking: Plant Polycomb
Repressive Complex 2 and Its Interactors
- Authors: James Godwin, Sara Farrona
  First page: 8
  Abstract: Polycomb Repressive Complex 2 (PRC2) is arguably the best-known plant complex of the Polycomb Group (PcG) pathway, formed by a group of proteins that epigenetically represses gene expression. PRC2-mediated deposition of H3K27me3 has amply been studied in Arabidopsis and, more recently, data from other plant model species has also been published, allowing for an increasing knowledge of PRC2 activities and target genes. How PRC2 molecular functions are regulated and how PRC2 is recruited to discrete chromatin regions are questions that have brought more attention in recent years. A mechanism to modulate PRC2-mediated activity is through its interaction with other protein partners or accessory proteins. Current evidence for PRC2 interactors has demonstrated the complexity of its protein network and how far we are from fully understanding the impact of these interactions on the activities of PRC2 core subunits and on the formation of new PRC2 versions. This review presents a list of PRC2 interactors, emphasizing their mechanistic action upon PRC2 functions and their effects on transcriptional regulation.
  Citation: Epigenomes
  PubDate: 2022-03-03
  DOI: 10.3390/epigenomes6010008
  Issue No: Vol. 6, No. 1 (2022)
Epigenomes, Vol. 6, Pages 9: Genetic and Epigenetic Inheritance at
Telomeres
- Authors: Evan H. Lister-Shimauchi, Benjamin McCarthy, Michael Lippincott, Shawn Ahmed
  First page: 9
  Abstract: Transgenerational inheritance can occur at telomeres in distinct contexts. Deficiency for telomerase or telomere-binding proteins in germ cells can result in shortened or lengthened chromosome termini that are transmitted to progeny. In human families, altered telomere lengths can result in stem cell dysfunction or tumor development. Genetic inheritance of altered telomeres as well as mutations that alter telomeres can result in progressive telomere length changes over multiple generations. Telomeres of yeast can modulate the epigenetic state of subtelomeric genes in a manner that is mitotically heritable, and the effects of telomeres on subtelomeric gene expression may be relevant to senescence or other human adult-onset disorders. Recently, two novel epigenetic states were shown to occur at C. elegans telomeres, where very low or high levels of telomeric protein foci can be inherited for multiple generations through a process that is regulated by histone methylation.Together, these observations illustrate that information relevant to telomere biology can be inherited via genetic and epigenetic mechanisms, although the broad impact of epigenetic inheritance to human biology remains unclear.
  Citation: Epigenomes
  PubDate: 2022-03-16
  DOI: 10.3390/epigenomes6010009
  Issue No: Vol. 6, No. 1 (2022)
Epigenomes, Vol. 6, Pages 10: SWI/SNF Chromatin Remodeling Enzymes in
Melanoma
- Authors: Megan R. Dreier, Ivana L. de la Serna
  First page: 10
  Abstract: Melanoma is an aggressive malignancy that arises from the transformation of melanocytes on the skin, mucosal membranes, and uvea of the eye. SWI/SNF chromatin remodeling enzymes are multi-subunit complexes that play important roles in the development of the melanocyte lineage and in the response to ultraviolet radiation, a key environmental risk factor for developing cutaneous melanoma. Exome sequencing has revealed frequent loss of function mutations in genes encoding SWI/SNF subunits in melanoma. However, some SWI/SNF subunits have also been demonstrated to have pro-tumorigenic roles in melanoma and to affect sensitivity to therapeutics. This review summarizes studies that have implicated SWI/SNF components in melanomagenesis and have evaluated how SWI/SNF subunits modulate the response to current therapeutics.
  Citation: Epigenomes
  PubDate: 2022-03-18
  DOI: 10.3390/epigenomes6010010
  Issue No: Vol. 6, No. 1 (2022)