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Wiley Interdisciplinary Reviews : RNA 
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ISSN (Online) 1757-7012
Published by John Wiley and Sons
[1587 journals]
Follow Subscription journalISSN (Online) 1757-7012
Published by John Wiley and Sons
[1587 journals]- Making ends meet: coordination between RNA 3′‐end processing and transcription initiation
- Authors: Pia K. Andersen; Torben Heick Jensen, Søren Lykke‐Andersen
Pages: n/a - n/a
Abstract: RNA polymerase II (RNAPII)‐mediated gene transcription initiates at promoters and ends at terminators. Transcription termination is intimately connected to 3′‐end processing of the produced RNA and already when loaded at the promoter, RNAPII starts to become configured for this downstream event. Conversely, RNAPII is ‘reset’ as part of the 3′‐end processing/termination event, thus preparing the enzyme for its next round of transcription—possibly on the same gene. There is both direct and circumstantial evidence for preferential recycling of RNAPII from the gene terminator back to its own promoter, which supposedly increases the efficiency of the transcription process under conditions where RNAPII levels are rate limiting. Here, we review differences and commonalities between initiation and 3′‐end processing/termination processes on various types of RNAPII transcribed genes. In doing so, we discuss the requirements for efficient 3′‐end processing/termination and how these may relate to proper recycling of RNAPII. WIREs RNA 2013. doi: 10.1002/wrna.1156 For further resources related to this article, please visit the WIREs website.
PubDate: 2013-02-28T11:07:37.706318-05:
DOI: 10.1002/wrna.1156
- Authors: Pia K. Andersen; Torben Heick Jensen, Søren Lykke‐Andersen
- Translation regulation gets its ‘omics’ moment
- Abstract: The fate of cellular RNA is largely determined by complex networks of protein–RNA interactions through ribonucleoprotein (RNP) complexes. Despite their relatively short half‐life, transcripts associate with many different proteins that process, modify, translate, and degrade the RNA. Following biogenesis some mRNPs are immediately directed to translation and produce proteins, but many are diverted and regulated by processes including miRNA‐mediated mechanisms, transport and localization, as well as turnover. Because of this complex interplay estimates of steady‐state expression by methods such as RNAseq alone cannot capture critical aspects of cellular fate, environmental response, tumorigenesis, or gene expression regulation. More selective and integrative tools are needed to measure protein–RNA complexes and the regulatory processes involved. One focus area is measurements of the transcriptome associated with ribosomes and translation. These so‐called polysome or ribosome profiling techniques can evaluate translation efficiency as well as the interplay between translation initiation, elongation, and termination—subject areas not well understood at a systems biology level. Ribosome profiling is a highly promising technique that provides mRNA positional information of ribosome occupancy, potentially bridging the gap between gene expression (i.e., RNAseq and microarray analysis) and protein quantification (i.e., mass spectrometry). In combination with methods such as RNA immunoprecipitation, miRNA profiling, or proteomics, we obtain a fresh view of global post‐transcriptional and translational gene regulation. In addition, these techniques also provide new insight into new regulatory elements, such as alternative open reading frames, and translation regulation under different conditions.WIREs RNA 2013. doi: 10.1002/wrna.1173
For further resources related to this article, please visit the WIREs website.
- Abstract: The fate of cellular RNA is largely determined by complex networks of protein–RNA interactions through ribonucleoprotein (RNP) complexes. Despite their relatively short half‐life, transcripts associate with many different proteins that process, modify, translate, and degrade the RNA. Following biogenesis some mRNPs are immediately directed to translation and produce proteins, but many are diverted and regulated by processes including miRNA‐mediated mechanisms, transport and localization, as well as turnover. Because of this complex interplay estimates of steady‐state expression by methods such as RNAseq alone cannot capture critical aspects of cellular fate, environmental response, tumorigenesis, or gene expression regulation. More selective and integrative tools are needed to measure protein–RNA complexes and the regulatory processes involved. One focus area is measurements of the transcriptome associated with ribosomes and translation. These so‐called polysome or ribosome profiling techniques can evaluate translation efficiency as well as the interplay between translation initiation, elongation, and termination—subject areas not well understood at a systems biology level. Ribosome profiling is a highly promising technique that provides mRNA positional information of ribosome occupancy, potentially bridging the gap between gene expression (i.e., RNAseq and microarray analysis) and protein quantification (i.e., mass spectrometry). In combination with methods such as RNA immunoprecipitation, miRNA profiling, or proteomics, we obtain a fresh view of global post‐transcriptional and translational gene regulation. In addition, these techniques also provide new insight into new regulatory elements, such as alternative open reading frames, and translation regulation under different conditions.WIREs RNA 2013. doi: 10.1002/wrna.1173
For further resources related to this article, please visit the WIREs website.
- Staufen‐mediated mRNA decay
- Abstract: Staufen1 (STAU1)‐mediated mRNA decay (SMD) is an mRNA degradation process in mammalian cells that is mediated by the binding of STAU1 to a STAU1‐binding site (SBS) within the 3′‐untranslated region (3′‐UTR) of target mRNAs. During SMD, STAU1, a double‐stranded (ds) RNA‐binding protein, recognizes dsRNA structures formed either by intramolecular base pairing of 3′‐UTR sequences or by intermolecular base pairing of 3′‐UTR sequences with a long‐noncoding RNA (lncRNA) via partially complementary Alu elements. Recently, STAU2, a paralog of STAU1, has also been reported to mediate SMD. Both STAU1 and STAU2 interact directly with the ATP‐dependent RNA helicase UPF1, a key SMD factor, enhancing its helicase activity to promote effective SMD. Moreover, STAU1 and STAU2 form homodimeric and heterodimeric interactions via domain‐swapping. Because both SMD and the mechanistically related nonsense‐mediated mRNA decay (NMD) employ UPF1; SMD and NMD are competitive pathways. Competition contributes to cellular differentiation processes, such as myogenesis and adipogenesis, placing SMD at the heart of various physiologically important mechanisms. WIREs RNA 2013. doi: 10.1002/wrna.1168
For further resources related to this article, please visit the WIREs website.
- Abstract: Staufen1 (STAU1)‐mediated mRNA decay (SMD) is an mRNA degradation process in mammalian cells that is mediated by the binding of STAU1 to a STAU1‐binding site (SBS) within the 3′‐untranslated region (3′‐UTR) of target mRNAs. During SMD, STAU1, a double‐stranded (ds) RNA‐binding protein, recognizes dsRNA structures formed either by intramolecular base pairing of 3′‐UTR sequences or by intermolecular base pairing of 3′‐UTR sequences with a long‐noncoding RNA (lncRNA) via partially complementary Alu elements. Recently, STAU2, a paralog of STAU1, has also been reported to mediate SMD. Both STAU1 and STAU2 interact directly with the ATP‐dependent RNA helicase UPF1, a key SMD factor, enhancing its helicase activity to promote effective SMD. Moreover, STAU1 and STAU2 form homodimeric and heterodimeric interactions via domain‐swapping. Because both SMD and the mechanistically related nonsense‐mediated mRNA decay (NMD) employ UPF1; SMD and NMD are competitive pathways. Competition contributes to cellular differentiation processes, such as myogenesis and adipogenesis, placing SMD at the heart of various physiologically important mechanisms. WIREs RNA 2013. doi: 10.1002/wrna.1168
For further resources related to this article, please visit the WIREs website.
- Mapping and significance of the mRNA methylome
- Abstract: Internal methylation of eukaryotic mRNAs in the form of N6‐methyladenosine (m6A) and 5‐methylcytidine (m5C) has long been known to exist, but progress in understanding its role was hampered by difficulties in identifying individual sites. This was recently overcome by high‐throughput sequencing‐based methods that mapped thousands of sites for both modifications throughout mammalian transcriptomes, with most sites found in mRNAs. The topology of m6A in mouse and human revealed both conserved and variable sites as well as plasticity in response to extracellular cues. Within mRNAs, m5C and m6A sites were relatively depleted in coding sequences and enriched in untranslated regions, suggesting functional interactions with post‐transcriptional gene control. Finer distribution analyses and preexisting literature point toward roles in the regulation of mRNA splicing, translation, or decay, through an interplay with RNA‐binding proteins and microRNAs. The methyltransferase (MTase) METTL3 ‘writes’ m6A marks on mRNA, whereas the demethylase FTO can ‘erase’ them. The RNA:m5C MTases NSUN2 and TRDMT1 have roles in tRNA methylation but they also act on mRNA. Proper functioning of these enzymes is important in development and there are clear links to human disease. For instance, a common variant of FTO is a risk allele for obesity carried by 1 billion people worldwide and mutations cause a lethal syndrome with growth retardation and brain deficits. NSUN2 is linked to cancer and stem cell biology and mutations cause intellectual disability. In this review, we summarize the advances, open questions, and intriguing possibilities in this emerging field that might be called RNA modomics or epitranscriptomics. WIREs RNA 2013. doi: 10.1002/wrna.1166
For further resources related to this article, please visit the WIREs website.
- Abstract: Internal methylation of eukaryotic mRNAs in the form of N6‐methyladenosine (m6A) and 5‐methylcytidine (m5C) has long been known to exist, but progress in understanding its role was hampered by difficulties in identifying individual sites. This was recently overcome by high‐throughput sequencing‐based methods that mapped thousands of sites for both modifications throughout mammalian transcriptomes, with most sites found in mRNAs. The topology of m6A in mouse and human revealed both conserved and variable sites as well as plasticity in response to extracellular cues. Within mRNAs, m5C and m6A sites were relatively depleted in coding sequences and enriched in untranslated regions, suggesting functional interactions with post‐transcriptional gene control. Finer distribution analyses and preexisting literature point toward roles in the regulation of mRNA splicing, translation, or decay, through an interplay with RNA‐binding proteins and microRNAs. The methyltransferase (MTase) METTL3 ‘writes’ m6A marks on mRNA, whereas the demethylase FTO can ‘erase’ them. The RNA:m5C MTases NSUN2 and TRDMT1 have roles in tRNA methylation but they also act on mRNA. Proper functioning of these enzymes is important in development and there are clear links to human disease. For instance, a common variant of FTO is a risk allele for obesity carried by 1 billion people worldwide and mutations cause a lethal syndrome with growth retardation and brain deficits. NSUN2 is linked to cancer and stem cell biology and mutations cause intellectual disability. In this review, we summarize the advances, open questions, and intriguing possibilities in this emerging field that might be called RNA modomics or epitranscriptomics. WIREs RNA 2013. doi: 10.1002/wrna.1166
For further resources related to this article, please visit the WIREs website.
- Metabolite sensing in eukaryotic mRNA biology
- Abstract: All living creatures change their gene expression program in response to nutrient availability and metabolic demands. Nutrients and metabolites can directly control transcription and activate second‐messenger systems. More recent studies reveal that metabolites also affect post‐transcriptional regulatory mechanisms. Here, we review the increasing number of connections between metabolism and post‐transcriptional regulation in eukaryotic organisms. First, we present evidence that riboswitches, a common mechanism of metabolite sensing in bacteria, also function in eukaryotes. Next, we review an example of a double stranded RNA modifying enzyme that directly interacts with a metabolite, suggesting a link between RNA editing and metabolic state. Finally, we discuss work that shows some metabolic enzymes bind directly to RNA to affect mRNA stability or translation efficiency. These examples were discovered through gene‐specific genetic, biochemical, and structural studies. A directed systems level approach will be necessary to determine whether they are anomalies of evolution or pioneer discoveries in what may be a broadly connected network of metabolism and post‐transcriptional regulation. WIREs RNA 2013. doi: 10.1002/wrna.1167
For further resources related to this article, please visit the WIREs website.
- Abstract: All living creatures change their gene expression program in response to nutrient availability and metabolic demands. Nutrients and metabolites can directly control transcription and activate second‐messenger systems. More recent studies reveal that metabolites also affect post‐transcriptional regulatory mechanisms. Here, we review the increasing number of connections between metabolism and post‐transcriptional regulation in eukaryotic organisms. First, we present evidence that riboswitches, a common mechanism of metabolite sensing in bacteria, also function in eukaryotes. Next, we review an example of a double stranded RNA modifying enzyme that directly interacts with a metabolite, suggesting a link between RNA editing and metabolic state. Finally, we discuss work that shows some metabolic enzymes bind directly to RNA to affect mRNA stability or translation efficiency. These examples were discovered through gene‐specific genetic, biochemical, and structural studies. A directed systems level approach will be necessary to determine whether they are anomalies of evolution or pioneer discoveries in what may be a broadly connected network of metabolism and post‐transcriptional regulation. WIREs RNA 2013. doi: 10.1002/wrna.1167
For further resources related to this article, please visit the WIREs website.
- Perturbations of RNA helicases in cancer
- Abstract: Helicases are implicated in most stages of the gene expression pathway, ranging from DNA replication, RNA transcription, splicing, RNA transport, ribosome biogenesis, mRNA translation, RNA storage and decay. These enzymes utilize energy derived from nucleotide triphosphate hydrolysis to remodel ribonucleoprotein complexes, RNA, or DNA and in this manner affect the information content or output of RNA. Several RNA helicases have been implicated in the oncogenic process—either through altered expression levels, mutations, or due to their role in pathways required for tumor initiation, progression, maintenance, or chemosensitivity. The purpose of this review is to highlight those RNA helicases for which there is significant evidence implicating them in cancer biology. WIREs RNA 2013. doi: 10.1002/wrna.1163
For further resources related to this article, please visit the WIREs website.
- Abstract: Helicases are implicated in most stages of the gene expression pathway, ranging from DNA replication, RNA transcription, splicing, RNA transport, ribosome biogenesis, mRNA translation, RNA storage and decay. These enzymes utilize energy derived from nucleotide triphosphate hydrolysis to remodel ribonucleoprotein complexes, RNA, or DNA and in this manner affect the information content or output of RNA. Several RNA helicases have been implicated in the oncogenic process—either through altered expression levels, mutations, or due to their role in pathways required for tumor initiation, progression, maintenance, or chemosensitivity. The purpose of this review is to highlight those RNA helicases for which there is significant evidence implicating them in cancer biology. WIREs RNA 2013. doi: 10.1002/wrna.1163
For further resources related to this article, please visit the WIREs website.
- Perturbations of RNA helicases in cancer
- Abstract: Helicases are implicated in most stages of the gene expression pathway, ranging from DNA replication, RNA transcription, splicing, RNA transport, ribosome biogenesis, mRNA translation, RNA storage and decay. These enzymes utilize energy derived from nucleotide triphosphate hydrolysis to remodel ribonucleoprotein complexes, RNA, or DNA and in this manner affect the information content or output of RNA. Several RNA helicases have been implicated in the oncogenic process—either through altered expression levels, mutations, or due to their role in pathways required for tumor initiation, progression, maintenance, or chemosensitivity. The purpose of this review is to highlight those RNA helicases for which there is significant evidence implicating them in cancer biology. WIREs RNA 2013. doi: 10.1002/wrna.1163
For further resources related to this article, please visit the WIREs website.
- Abstract: Helicases are implicated in most stages of the gene expression pathway, ranging from DNA replication, RNA transcription, splicing, RNA transport, ribosome biogenesis, mRNA translation, RNA storage and decay. These enzymes utilize energy derived from nucleotide triphosphate hydrolysis to remodel ribonucleoprotein complexes, RNA, or DNA and in this manner affect the information content or output of RNA. Several RNA helicases have been implicated in the oncogenic process—either through altered expression levels, mutations, or due to their role in pathways required for tumor initiation, progression, maintenance, or chemosensitivity. The purpose of this review is to highlight those RNA helicases for which there is significant evidence implicating them in cancer biology. WIREs RNA 2013. doi: 10.1002/wrna.1163
For further resources related to this article, please visit the WIREs website.
- Issue information
- The role of the DEAD‐box RNA helicase DDX3 in mRNA metabolism
- Abstract: DDX3 belongs to the DEAD‐box proteins, a large family of ATP‐dependent RNA helicases that participate in all aspects of RNA metabolism. Human DDX3 is a component of several messenger ribonucleoproteins that are found in the spliceosome, the export and the translation initiation machineries but also in different cytoplasmic mRNA granules. DDX3 has been involved in several cellular processes such as cell cycle progression, apoptosis, cancer, innate immune response, and also as a host factor for viral replication. Interestingly, not all these functions require the catalytic activities of DDX3 and thus, the precise roles of this apparently multifaceted protein remain largely obscure. The aim of this review is to provide a rapid and critical overview of the structure and functions of DDX3 with a particular emphasis on its role during mRNA metabolism. WIREs RNA 2013. doi: 10.1002/wrna.1165
For further resources related to this article, please visit the WIREs website.
Conflict of interest: The authors have declared no conflicts of interest for this article.
- Abstract: DDX3 belongs to the DEAD‐box proteins, a large family of ATP‐dependent RNA helicases that participate in all aspects of RNA metabolism. Human DDX3 is a component of several messenger ribonucleoproteins that are found in the spliceosome, the export and the translation initiation machineries but also in different cytoplasmic mRNA granules. DDX3 has been involved in several cellular processes such as cell cycle progression, apoptosis, cancer, innate immune response, and also as a host factor for viral replication. Interestingly, not all these functions require the catalytic activities of DDX3 and thus, the precise roles of this apparently multifaceted protein remain largely obscure. The aim of this review is to provide a rapid and critical overview of the structure and functions of DDX3 with a particular emphasis on its role during mRNA metabolism. WIREs RNA 2013. doi: 10.1002/wrna.1165
For further resources related to this article, please visit the WIREs website.
Conflict of interest: The authors have declared no conflicts of interest for this article.
- RNA synthetic mechanisms employed by diverse families of RNA viruses
- Abstract: RNA viruses are ubiquitous in nature, infecting every known organism on the planet. These viruses can also be notorious human pathogens with significant medical and economic burdens. Central to the lifecycle of an RNA virus is the synthesis of new RNA molecules, a process that is mediated by specialized virally encoded enzymes called RNA‐dependent RNA polymerases (RdRps). RdRps directly catalyze phosphodiester bond formation between nucleoside triphosphates in an RNA‐templated manner. These enzymes are strikingly conserved in their structural and functional features, even among diverse RNA viruses belonging to different families. During host cell infection, the activities of viral RdRps are often regulated by viral cofactor proteins. Cofactors can modulate the type and timing of RNA synthesis by directly engaging the RdRp and/or by indirectly affecting its capacity to recognize template RNA. High‐resolution structures of RdRps as apoenzymes, bound to RNA templates, in the midst of catalysis, and/or interacting with regulatory cofactor proteins, have dramatically increased our understanding of viral RNA synthetic mechanisms. Combined with elegant biochemical studies, such structures are providing a scientific platform for the rational design of antiviral agents aimed at preventing and treating RNA virus‐induced diseases. WIREs RNA 2013. doi: 10.1002/wrna.1164
For further resources related to this article, please visit the WIREs website.
Conflict of interest: The author has declared no conflicts of interest for this article.
- Abstract: RNA viruses are ubiquitous in nature, infecting every known organism on the planet. These viruses can also be notorious human pathogens with significant medical and economic burdens. Central to the lifecycle of an RNA virus is the synthesis of new RNA molecules, a process that is mediated by specialized virally encoded enzymes called RNA‐dependent RNA polymerases (RdRps). RdRps directly catalyze phosphodiester bond formation between nucleoside triphosphates in an RNA‐templated manner. These enzymes are strikingly conserved in their structural and functional features, even among diverse RNA viruses belonging to different families. During host cell infection, the activities of viral RdRps are often regulated by viral cofactor proteins. Cofactors can modulate the type and timing of RNA synthesis by directly engaging the RdRp and/or by indirectly affecting its capacity to recognize template RNA. High‐resolution structures of RdRps as apoenzymes, bound to RNA templates, in the midst of catalysis, and/or interacting with regulatory cofactor proteins, have dramatically increased our understanding of viral RNA synthetic mechanisms. Combined with elegant biochemical studies, such structures are providing a scientific platform for the rational design of antiviral agents aimed at preventing and treating RNA virus‐induced diseases. WIREs RNA 2013. doi: 10.1002/wrna.1164
For further resources related to this article, please visit the WIREs website.
Conflict of interest: The author has declared no conflicts of interest for this article.
- Regulation of stress granules and P‐bodies during RNA virus infection
- Abstract: RNA granules are structures within cells that play major roles in gene expression and homeostasis. Two principle kinds of RNA granules are conserved from yeast to mammals: stress granules (SGs), which contain stalled translation initiation complexes, and processing bodies (P‐bodies, PBs), which are enriched with factors involved in RNA turnover. Since RNA granules are associated with silenced transcripts, viruses subvert RNA granule function for replicative advantages. This review, focusing on RNA viruses, discusses mechanisms that manipulate stress granules and P‐bodies to promote synthesis of viral proteins. Three main themes have emerged for how viruses manipulate RNA granules; (1) cleavage of key host factors, (2) control of protein kinase R (PKR) activation, and (3) redirecting RNA granule components for new or parallel roles in viral reproduction, at the same time disrupting RNA granules. Viruses utilize one or more of these routes to achieve robust and productive infection. WIREs RNA 2013. doi: 10.1002/wrna.1162
For further resources related to this article, please visit the WIREs website.
Conflict of interest: The author has declared no conflicts of interest for this article.
- Abstract: RNA granules are structures within cells that play major roles in gene expression and homeostasis. Two principle kinds of RNA granules are conserved from yeast to mammals: stress granules (SGs), which contain stalled translation initiation complexes, and processing bodies (P‐bodies, PBs), which are enriched with factors involved in RNA turnover. Since RNA granules are associated with silenced transcripts, viruses subvert RNA granule function for replicative advantages. This review, focusing on RNA viruses, discusses mechanisms that manipulate stress granules and P‐bodies to promote synthesis of viral proteins. Three main themes have emerged for how viruses manipulate RNA granules; (1) cleavage of key host factors, (2) control of protein kinase R (PKR) activation, and (3) redirecting RNA granule components for new or parallel roles in viral reproduction, at the same time disrupting RNA granules. Viruses utilize one or more of these routes to achieve robust and productive infection. WIREs RNA 2013. doi: 10.1002/wrna.1162
For further resources related to this article, please visit the WIREs website.
Conflict of interest: The author has declared no conflicts of interest for this article.
- Intercellular and systemic spread of RNA and RNAi in plants
- Abstract: Plants possess dynamic networks of intercellular communication that are crucial for plant development and physiology. In plants, intercellular communication involves a combination of ligand–receptor‐based apoplasmic signaling, and plasmodesmata and phloem‐mediated symplasmic signaling. The intercellular trafficking of macromolecules, including RNAs and proteins, has emerged as a novel mechanism of intercellular communication in plants. Various forms of regulatory RNAs move over distinct cellular boundaries through plasmodesmata and phloem. This plant‐specific, non‐cell‐autonomous RNA trafficking network is also involved in development, nutrient homeostasis, gene silencing, pathogen defense, and many other physiological processes. However, the mechanism underlying macromolecular trafficking in plants remains poorly understood. Current progress made in RNA trafficking research and its biological relevance to plant development will be summarized. Diverse plant regulatory mechanisms of cell‐to‐cell and systemic long‐distance transport of RNAs, including mRNAs, viral RNAs, and small RNAs, will also be discussed. WIREs RNA 2013. doi: 10.1002/wrna.1160
For further resources related to this article, please visit the WIREs website.
The authors have declared no conflicts of interest for this article.
- Abstract: Plants possess dynamic networks of intercellular communication that are crucial for plant development and physiology. In plants, intercellular communication involves a combination of ligand–receptor‐based apoplasmic signaling, and plasmodesmata and phloem‐mediated symplasmic signaling. The intercellular trafficking of macromolecules, including RNAs and proteins, has emerged as a novel mechanism of intercellular communication in plants. Various forms of regulatory RNAs move over distinct cellular boundaries through plasmodesmata and phloem. This plant‐specific, non‐cell‐autonomous RNA trafficking network is also involved in development, nutrient homeostasis, gene silencing, pathogen defense, and many other physiological processes. However, the mechanism underlying macromolecular trafficking in plants remains poorly understood. Current progress made in RNA trafficking research and its biological relevance to plant development will be summarized. Diverse plant regulatory mechanisms of cell‐to‐cell and systemic long‐distance transport of RNAs, including mRNAs, viral RNAs, and small RNAs, will also be discussed. WIREs RNA 2013. doi: 10.1002/wrna.1160
For further resources related to this article, please visit the WIREs website.
The authors have declared no conflicts of interest for this article.
- RNA processing and decay in plastids
- Abstract: Plastids were derived through endosymbiosis from a cyanobacterial ancestor, whose uptake was followed by massive gene transfer to the nucleus, resulting in the compact size and modest coding capacity of the extant plastid genome. Plastid gene expression is essential for plant development, but depends on nucleus‐encoded proteins recruited from cyanobacterial or host‐cell origins. The plastid genome is heavily transcribed from numerous promoters, giving posttranscriptional events a critical role in determining the quantity and sizes of accumulating RNA species. The major events reviewed here are RNA editing, which restores protein conservation or creates correct open reading frames by converting C residues to U, RNA splicing, which occurs both in cis and trans, and RNA cleavage, which relies on a variety of exoribonucleases and endoribonucleases. Because the RNases have little sequence specificity, they are collectively able to remove extraneous RNAs whose ends are not protected by RNA secondary structures or sequence‐specific RNA‐binding proteins (RBPs). Other plastid RBPs, largely members of the helical‐repeat superfamily, confer specificity to editing and splicing reactions. The enzymes that catalyze RNA processing are also the main actors in RNA decay, implying that these antagonistic roles are optimally balanced. We place the actions of RBPs and RNases in the context of a recent proteomic analysis that identifies components of the plastid nucleoid, a protein–DNA complex with multiple roles in gene expression. These results suggest that sublocalization and/or concentration gradients of plastid proteins could underpin the regulation of RNA maturation and degradation. WIREs RNA 2013. doi: 10.1002/wrna.1161
For further resources related to this article, please visit the WIREs website.
The authors have declared no conflicts of interest for this article.
- Abstract: Plastids were derived through endosymbiosis from a cyanobacterial ancestor, whose uptake was followed by massive gene transfer to the nucleus, resulting in the compact size and modest coding capacity of the extant plastid genome. Plastid gene expression is essential for plant development, but depends on nucleus‐encoded proteins recruited from cyanobacterial or host‐cell origins. The plastid genome is heavily transcribed from numerous promoters, giving posttranscriptional events a critical role in determining the quantity and sizes of accumulating RNA species. The major events reviewed here are RNA editing, which restores protein conservation or creates correct open reading frames by converting C residues to U, RNA splicing, which occurs both in cis and trans, and RNA cleavage, which relies on a variety of exoribonucleases and endoribonucleases. Because the RNases have little sequence specificity, they are collectively able to remove extraneous RNAs whose ends are not protected by RNA secondary structures or sequence‐specific RNA‐binding proteins (RBPs). Other plastid RBPs, largely members of the helical‐repeat superfamily, confer specificity to editing and splicing reactions. The enzymes that catalyze RNA processing are also the main actors in RNA decay, implying that these antagonistic roles are optimally balanced. We place the actions of RBPs and RNases in the context of a recent proteomic analysis that identifies components of the plastid nucleoid, a protein–DNA complex with multiple roles in gene expression. These results suggest that sublocalization and/or concentration gradients of plastid proteins could underpin the regulation of RNA maturation and degradation. WIREs RNA 2013. doi: 10.1002/wrna.1161
For further resources related to this article, please visit the WIREs website.
The authors have declared no conflicts of interest for this article.
- CRISPR‐Cas systems and RNA‐guided interference
- Abstract: Clustered regularly interspaced short palindromic repeats (CRISPR) together with associated sequences (cas) form the CRISPR‐Cas system, which provides adaptive immunity against viruses and plasmids in bacteria and archaea. Immunity is built through acquisition of short stretches of invasive nucleic acids into CRISPR loci as ‘spacers'. These immune markers are transcribed and processed into small noncoding interfering CRISPR RNAs (crRNAs) that guide Cas proteins toward target nucleic acids for specific cleavage of homologous sequences. Mechanistically, CRISPR‐Cas systems function in three distinct stages, namely: (1) adaptation, where new spacers are acquired from invasive elements for immunization; (2) crRNA biogenesis, where CRISPR loci are transcribed and processed into small interfering crRNAs; and (3) interference, where crRNAs guide the Cas machinery to specifically cleave homologous invasive nucleic acids. A number of studies have shown that CRISPR‐mediated immunity can readily increase the breadth and depth of virus resistance in bacteria and archaea. CRISPR interference can also target plasmid sequences and provide a barrier against the uptake of undesirable mobile genetic elements. These inheritable hypervariable loci provide phylogenetic information that can be insightful for typing purposes, epidemiological studies, and ecological surveys of natural habitats and environmental samples. More recently, the ability to reprogram CRISPR‐directed endonuclease activity using customizable small noncoding interfering RNAs has set the stage for novel genome editing and engineering avenues. This review highlights recent studies that revealed the molecular basis of CRISPR‐mediated immunity, and discusses applications of crRNA‐guided interference. WIREs RNA 2013. doi: 10.1002/wrna.1159
For further resources related to this article, please visit the WIREs website.
Conflict of interest: RB is a co‐inventor on several patents related to CRISPR use and applications.
- Abstract: Clustered regularly interspaced short palindromic repeats (CRISPR) together with associated sequences (cas) form the CRISPR‐Cas system, which provides adaptive immunity against viruses and plasmids in bacteria and archaea. Immunity is built through acquisition of short stretches of invasive nucleic acids into CRISPR loci as ‘spacers'. These immune markers are transcribed and processed into small noncoding interfering CRISPR RNAs (crRNAs) that guide Cas proteins toward target nucleic acids for specific cleavage of homologous sequences. Mechanistically, CRISPR‐Cas systems function in three distinct stages, namely: (1) adaptation, where new spacers are acquired from invasive elements for immunization; (2) crRNA biogenesis, where CRISPR loci are transcribed and processed into small interfering crRNAs; and (3) interference, where crRNAs guide the Cas machinery to specifically cleave homologous invasive nucleic acids. A number of studies have shown that CRISPR‐mediated immunity can readily increase the breadth and depth of virus resistance in bacteria and archaea. CRISPR interference can also target plasmid sequences and provide a barrier against the uptake of undesirable mobile genetic elements. These inheritable hypervariable loci provide phylogenetic information that can be insightful for typing purposes, epidemiological studies, and ecological surveys of natural habitats and environmental samples. More recently, the ability to reprogram CRISPR‐directed endonuclease activity using customizable small noncoding interfering RNAs has set the stage for novel genome editing and engineering avenues. This review highlights recent studies that revealed the molecular basis of CRISPR‐mediated immunity, and discusses applications of crRNA‐guided interference. WIREs RNA 2013. doi: 10.1002/wrna.1159
For further resources related to this article, please visit the WIREs website.
Conflict of interest: RB is a co‐inventor on several patents related to CRISPR use and applications.
- Targeting RNA splicing for disease therapy
- Abstract: Splicing of pre‐messenger RNA into mature messenger RNA is an essential step for the expression of most genes in higher eukaryotes. Defects in this process typically affect cellular function and can have pathological consequences. Many human genetic diseases are caused by mutations that cause splicing defects. Furthermore, a number of diseases are associated with splicing defects that are not attributed to overt mutations. Targeting splicing directly to correct disease‐associated aberrant splicing is a logical approach to therapy. Splicing is a favorable intervention point for disease therapeutics, because it is an early step in gene expression and does not alter the genome. Significant advances have been made in the development of approaches to manipulate splicing for therapy. Splicing can be manipulated with a number of tools including antisense oligonucleotides, modified small nuclear RNAs (snRNAs), trans‐splicing, and small molecule compounds, all of which have been used to increase specific alternatively spliced isoforms or to correct aberrant gene expression resulting from gene mutations that alter splicing. Here we describe clinically relevant splicing defects in disease states, the current tools used to target and alter splicing, specific mutations and diseases that are being targeted using splice‐modulating approaches, and emerging therapeutics. WIREs RNA 2013. doi: 10.1002/wrna.1158
For further resources related to this article, please visit the WIREs website.
The authors have declared no conflicts of interest for this article.
- Abstract: Splicing of pre‐messenger RNA into mature messenger RNA is an essential step for the expression of most genes in higher eukaryotes. Defects in this process typically affect cellular function and can have pathological consequences. Many human genetic diseases are caused by mutations that cause splicing defects. Furthermore, a number of diseases are associated with splicing defects that are not attributed to overt mutations. Targeting splicing directly to correct disease‐associated aberrant splicing is a logical approach to therapy. Splicing is a favorable intervention point for disease therapeutics, because it is an early step in gene expression and does not alter the genome. Significant advances have been made in the development of approaches to manipulate splicing for therapy. Splicing can be manipulated with a number of tools including antisense oligonucleotides, modified small nuclear RNAs (snRNAs), trans‐splicing, and small molecule compounds, all of which have been used to increase specific alternatively spliced isoforms or to correct aberrant gene expression resulting from gene mutations that alter splicing. Here we describe clinically relevant splicing defects in disease states, the current tools used to target and alter splicing, specific mutations and diseases that are being targeted using splice‐modulating approaches, and emerging therapeutics. WIREs RNA 2013. doi: 10.1002/wrna.1158
For further resources related to this article, please visit the WIREs website.
The authors have declared no conflicts of interest for this article.
