451
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Hierarchical rules for Argonaute loading in Drosophila. Mol Cell 2010; 36:445-56. [PMID: 19917252 DOI: 10.1016/j.molcel.2009.09.028] [Citation(s) in RCA: 197] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2009] [Revised: 08/20/2009] [Accepted: 08/28/2009] [Indexed: 11/23/2022]
Abstract
Drosophila Argonaute-1 and Argonaute-2 differ in function and small RNA content. AGO2 binds to siRNAs, whereas AGO1 is almost exclusively occupied by microRNAs. MicroRNA duplexes are intrinsically asymmetric, with one strand, the miR strand, preferentially entering AGO1 to recognize and regulate the expression of target mRNAs. The other strand, miR*, has been viewed as a byproduct of microRNA biogenesis. Here, we show that miR*s are often loaded as functional species into AGO2. This indicates that each microRNA precursor can potentially produce two mature small RNA strands that are differentially sorted within the RNAi pathway. miR* biogenesis depends upon the canonical microRNA pathway, but loading into AGO2 is mediated by factors traditionally dedicated to siRNAs. By inferring and validating hierarchical rules that predict differential AGO loading, we find that intrinsic determinants, including structural and thermodynamic properties of the processed duplex, regulate the fate of each RNA strand within the RNAi pathway.
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452
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Ghildiyal M, Xu J, Seitz H, Weng Z, Zamore PD. Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA (NEW YORK, N.Y.) 2010; 16:43-56. [PMID: 19917635 PMCID: PMC2802036 DOI: 10.1261/rna.1972910] [Citation(s) in RCA: 254] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 10/22/2009] [Indexed: 05/19/2023]
Abstract
In flies, small silencing RNAs are sorted between Argonaute1 (Ago1), the central protein component of the microRNA (miRNA) pathway, and Argonaute2 (Ago2), which mediates RNA interference. Extensive double-stranded character-as is found in small interfering RNAs (siRNAs)-directs duplexes into Ago2, whereas central mismatches, like those found in miRNA/miRNA* duplexes, direct duplexes into Ago1. Central to this sorting decision is the affinity of the small RNA duplex for the Dcr-2/R2D2 heterodimer, which loads small RNAs into Ago2. Here, we show that while most Drosophila miRNAs are bound to Ago1, miRNA* strands accumulate bound to Ago2. Like siRNA loading, efficient loading of miRNA* strands in Ago2 favors duplexes with a paired central region and requires both Dcr-2 and R2D2. Those miRNA and miRNA* sequences bound to Ago2, like siRNAs diced in vivo from long double-stranded RNA, typically begin with cytidine, whereas Ago1-bound miRNA and miRNA* disproportionately begin with uridine. Consequently, some pre-miRNA generate two or more isoforms from the same side of the stem that differentially partition between Ago1 and Ago2. Our findings provide the first genome-wide test for the idea that Drosophila small RNAs are sorted between Ago1 and Ago2 according to their duplex structure and the identity of their first nucleotide.
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Affiliation(s)
- Megha Ghildiyal
- Howard Hughes Medical Institute, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School,Worcester, Massachusetts 01605, USA
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453
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Marques JT, Kim K, Wu PH, Alleyne TM, Jafari N, Carthew RW. Loqs and R2D2 act sequentially in the siRNA pathway in Drosophila. Nat Struct Mol Biol 2009; 17:24-30. [PMID: 20037596 DOI: 10.1038/nsmb.1735] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 11/13/2009] [Indexed: 12/26/2022]
Abstract
In Drosophila melanogaster, the small interfering RNA (siRNA) pathway is triggered by exogenous double-stranded RNA (dsRNA) or upon viral infection. This pathway requires Dicer-2 (Dcr-2) in association with a dsRNA-binding protein (dsRBP) called R2D2. A potentially distinct siRNA pathway, which requires Dcr-2 in association with a different dsRBP, called Loquacious (Loqs), is activated by endogenous dsRNA derived from transposons, structured loci and overlapping transcripts. Here we show that different sources of dsRNA enter a common siRNA pathway that requires R2D2 and Loqs. R2D2 and loqs mutants show impaired silencing triggered by injection of exogenous dsRNA or by artificial and natural expression of endogenous dsRNA. In addition, we show that these dsRBPs function sequentially and nonredundantly in collaboration with Dcr-2. Loqs is primarily required for dsRNA processing, whereas R2D2 is essential for the subsequent loading of siRNAs into effector Ago-RISC complexes.
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Affiliation(s)
- João Trindade Marques
- Department of Biochemistry, Molecular Biology and Cell Biology, Northwestern University, Evanston, Illinois, USA
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454
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Alu and b1 repeats have been selectively retained in the upstream and intronic regions of genes of specific functional classes. PLoS Comput Biol 2009; 5:e1000610. [PMID: 20019790 PMCID: PMC2784220 DOI: 10.1371/journal.pcbi.1000610] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 11/13/2009] [Indexed: 11/20/2022] Open
Abstract
Alu and B1 repeats are mobile elements that originated in an initial duplication of the 7SL RNA gene prior to the primate-rodent split about 80 million years ago and currently account for a substantial fraction of the human and mouse genome, respectively. Following the primate-rodent split, Alu and B1 elements spread independently in each of the two genomes in a seemingly random manner, and, according to the prevailing hypothesis, negative selection shaped their final distribution in each genome by forcing the selective loss of certain Alu and B1 copies. In this paper, contrary to the prevailing hypothesis, we present evidence that Alu and B1 elements have been selectively retained in the upstream and intronic regions of genes belonging to specific functional classes. At the same time, we found no evidence for selective loss of these elements in any functional class. A subset of the functional links we discovered corresponds to functions where Alu involvement has actually been experimentally validated, whereas the majority of the functional links we report are novel. Finally, the unexpected finding that Alu and B1 elements show similar biases in their distribution across functional classes, despite having spread independently in their respective genomes, further supports our claim that the extant instances of Alu and B1 elements are the result of positive selection. Despite their fundamental role in cell regulation, genes account for less than 1% of the human genome. Recent studies have shown that non-genic regions of our DNA may also play an important functional role in human cells. In this paper, we study Alu and B elements, a specific class of such non-genic elements that account for ∼10% of the human genome and ∼7% of the mouse genome respectively. We show that, contrary to the prevailing hypothesis, Alu and B elements have been preferentially retained in the proximity of genes that perform specific functions in the cell. In contrast, we found no evidence for selective loss of these elements in any functional class. Several of the functional classes that we have linked to Alu and B elements are central to the proper working of the cell, and their disruption has previously been shown to lead to the onset of disease. Interestingly, the DNA sequences of Alu and B elements differ substantially between human and mouse, thus hinting at the existence of a potentially large number of non-conserved regulatory elements.
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455
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Yang JH, Shao P, Zhou H, Chen YQ, Qu LH. deepBase: a database for deeply annotating and mining deep sequencing data. Nucleic Acids Res 2009; 38:D123-30. [PMID: 19966272 PMCID: PMC2808990 DOI: 10.1093/nar/gkp943] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Advances in high-throughput next-generation sequencing technology have reshaped the transcriptomic research landscape. However, exploration of these massive data remains a daunting challenge. In this study, we describe a novel database, deepBase, which we have developed to facilitate the comprehensive annotation and discovery of small RNAs from transcriptomic data. The current release of deepBase contains deep sequencing data from 185 small RNA libraries from diverse tissues and cell lines of seven organisms: human, mouse, chicken, Ciona intestinalis, Drosophila melanogaster, Caenhorhabditis elegans and Arabidopsis thaliana. By analyzing ∼14.6 million unique reads that perfectly mapped to more than 284 million genomic loci, we annotated and identified ∼380 000 unique ncRNA-associated small RNAs (nasRNAs), ∼1.5 million unique promoter-associated small RNAs (pasRNAs), ∼4.0 million unique exon-associated small RNAs (easRNAs) and ∼6 million unique repeat-associated small RNAs (rasRNAs). Furthermore, 2038 miRNA and 1889 snoRNA candidates were predicted by miRDeep and snoSeeker. All of the mapped reads can be grouped into about 1.2 million RNA clusters. For the purpose of comparative analysis, deepBase provides an integrative, interactive and versatile display. A convenient search option, related publications and other useful information are also provided for further investigation. deepBase is available at: http://deepbase.sysu.edu.cn/.
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Affiliation(s)
- Jian-Hua Yang
- Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510275, PR China
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456
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Cole C, Sobala A, Lu C, Thatcher SR, Bowman A, Brown JWS, Green PJ, Barton GJ, Hutvagner G. Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA (NEW YORK, N.Y.) 2009; 15:2147-60. [PMID: 19850906 PMCID: PMC2779667 DOI: 10.1261/rna.1738409] [Citation(s) in RCA: 465] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Deep sequencing technologies such as Illumina, SOLiD, and 454 platforms have become very powerful tools in discovering and quantifying small RNAs in diverse organisms. Sequencing small RNA fractions always identifies RNAs derived from abundant RNA species such as rRNAs, tRNAs, snRNA, and snoRNA, and they are widely considered to be random degradation products. We carried out bioinformatic analysis of deep sequenced HeLa RNA and after quality filtering, identified highly abundant small RNA fragments, derived from mature tRNAs that are likely produced by specific processing rather than from random degradation. Moreover, we showed that the processing of small RNAs derived from tRNA(Gln) is dependent on Dicer in vivo and that Dicer cleaves the tRNA in vitro.
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Affiliation(s)
- Christian Cole
- Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, Dundee DD1 5EH, United Kingdom
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457
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Lu J, Clark AG. Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila. Genome Res 2009; 20:212-27. [PMID: 19948818 DOI: 10.1101/gr.095406.109] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Transposable elements (TEs) are mobile DNA sequences that make up a large fraction of eukaryotic genomes. Recently it was discovered that PIWI-interacting RNAs (piRNAs), a class of small RNA molecules that are mainly generated from transposable elements, are crucial repressors of active TEs in the germline of fruit flies. By quantifying expression levels of 32 TE families in piRNA pathway mutants relative to wild-type fruit flies, we provide evidence that piRNAs can severely silence the activities of retrotransposons. We incorporate piRNAs into a population genetic framework for retrotransposons and perform forward simulations to model the population dynamics of piRNA loci and their targets. Using parameters optimized for Drosophila melanogaster, our simulation results indicate that (1) piRNAs can significantly reduce the fitness cost of retrotransposons; (2) retrotransposons that generate piRNAs (piRTs) are selectively more advantageous, and such retrotransposon insertions more easily attain high frequency or fixation; (3) retrotransposons that are repressed by piRNAs (targetRTs), however, also have an elevated probability of reaching high frequency or fixation in the population because their deleterious effects are attenuated. By surveying the polymorphisms of piRT and targetRT insertions across nine strains of D. melanogaster, we verified these theoretical predictions with population genomic data. Our theoretical and empirical analysis suggests that piRNAs can significantly increase the fitness of individuals that bear them; however, piRNAs may provide a shelter or Trojan horse for retrotransposons, allowing them to increase in frequency in a population by shielding the host from the deleterious consequences of retrotransposition.
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Affiliation(s)
- Jian Lu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
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458
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The endogenous siRNA pathway is involved in heterochromatin formation in Drosophila. Proc Natl Acad Sci U S A 2009; 106:21258-63. [PMID: 19948966 DOI: 10.1073/pnas.0809208105] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A new class of small RNAs (endo-siRNAs) produced from endogenous double-stranded RNA (dsRNA) precursors was recently shown to mediate transposable element (TE) silencing in the Drosophila soma. These endo-siRNAs might play a role in heterochromatin formation, as has been shown in S. pombe for siRNAs derived from repetitive sequences in chromosome pericentromeres. To address this possibility, we used the viral suppressors of RNA silencing B2 and P19. These proteins normally counteract the RNAi host defense by blocking the biogenesis or activity of virus-derived siRNAs. We hypothesized that both proteins would similarly block endo-siRNA processing or function, thereby revealing the contribution of endo-siRNA to heterochromatin formation. Accordingly, P19 as well as a nuclear form of P19 expressed in Drosophila somatic cells were found to sequester TE-derived siRNAs whereas B2 predominantly bound their longer precursors. Strikingly, B2 or the nuclear form of P19, but not P19, suppressed silencing of heterochromatin gene markers in adult flies, and altered histone H3-K9 methylation as well as chromosomal distribution of histone methyl transferase Su(var)3-9 and Heterochromatin Protein 1 in larvae. Similar effects were observed in dcr2, r2d2, and ago2 mutants. Our findings provide evidence that a nuclear pool of TE-derived endo-siRNAs is involved in heterochromatin formation in somatic tissues in Drosophila.
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459
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Pepper ASR, Beerman RW, Bhogal B, Jongens TA. Argonaute2 suppresses Drosophila fragile X expression preventing neurogenesis and oogenesis defects. PLoS One 2009; 4:e7618. [PMID: 19888420 PMCID: PMC2770736 DOI: 10.1371/journal.pone.0007618] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 10/01/2009] [Indexed: 01/05/2023] Open
Abstract
Fragile X Syndrome is caused by the silencing of the Fragile X Mental Retardation gene (FMR1). Regulating dosage of FMR1 levels is critical for proper development and function of the nervous system and germ line, but the pathways responsible for maintaining normal expression levels are less clearly defined. Loss of Drosophila Fragile X protein (dFMR1) causes several behavioral and developmental defects in the fly, many of which are analogous to those seen in Fragile X patients. Over-expression of dFMR1 also causes specific neuronal and behavioral abnormalities. We have found that Argonaute2 (Ago2), the core component of the small interfering RNA (siRNA) pathway, regulates dfmr1 expression. Previously, the relationship between dFMR1 and Ago2 was defined by their physical interaction and co-regulation of downstream targets. We have found that Ago2 and dFMR1 are also connected through a regulatory relationship. Ago2 mediated repression of dFMR1 prevents axon growth and branching defects of the Drosophila neuromuscular junction (NMJ). Consequently, the neurogenesis defects in larvae mutant for both dfmr1 and Ago2 mirror those in dfmr1 null mutants. The Ago2 null phenotype at the NMJ is rescued in animals carrying an Ago2 genomic rescue construct. However, animals carrying a mutant Ago2 allele that produces Ago2 with significantly reduced endoribonuclease catalytic activity are normal with respect to the NMJ phenotypes examined. dFMR1 regulation by Ago2 is also observed in the germ line causing a multiple oocyte in a single egg chamber mutant phenotype. We have identified Ago2 as a regulator of dfmr1 expression and have clarified an important developmental role for Ago2 in the nervous system and germ line that requires dfmr1 function.
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Affiliation(s)
- Anita S.-R. Pepper
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Rebecca W. Beerman
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Balpreet Bhogal
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
| | - Thomas A. Jongens
- Department of Genetics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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460
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Lucchetta EM, Carthew RW, Ismagilov RF. The endo-siRNA pathway is essential for robust development of the Drosophila embryo. PLoS One 2009; 4:e7576. [PMID: 19851503 PMCID: PMC2761733 DOI: 10.1371/journal.pone.0007576] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Accepted: 08/03/2009] [Indexed: 11/20/2022] Open
Abstract
Background Robustness to natural temperature fluctuations is critical to proper development in embryos and to cellular functions in adult organisms. However, mechanisms and pathways which govern temperature compensation remain largely unknown beyond circadian rhythms. Pathways which ensure robustness against temperature fluctuations may appear to be nonessential under favorable, uniform environmental conditions used in conventional laboratory experiments where there is little variation for which to compensate. The endo-siRNA pathway, which produces small double-stranded RNAs in Drosophila, appears to be nonessential for robust development of the embryo under ambient uniform temperature and to be necessary only for viral defense. Embryos lacking a functional endo-siRNA pathway develop into phenotypically normal adults. However, we hypothesized that small RNAs may regulate the embryo's response to temperature, as a ribonucleoprotein complex has been previously shown to mediate mammalian cell response to heat shock. Principal Findings Here, we show that the genes DICER-2 and ARGONAUTE2, which code for integral protein components of the endo-siRNA pathway, are essential for robust development and temperature compensation in the Drosophila embryo when exposed to temperature perturbations. The regulatory functions of DICER-2 and ARGONAUTE2 were uncovered by using microfluidics to expose developing Drosophila embryos to a temperature step, in which each half of the embryo develops at a different temperature through developmental cycle 14. Under this temperature perturbation, dicer-2 or argonaute2 embryos displayed abnormal segmentation. The abnormalities in segmentation are presumably due to the inability of the embryo to compensate for temperature-induced differences in rate of development and to coordinate developmental timing in the anterior and posterior halves. A deregulation of the length of nuclear division cycles 10–14 is also observed in dicer-2 embryos at high temperatures. Conclusions Results presented herein uncover a novel function of the endo-siRNA pathway in temperature compensation and cell cycle regulation, and we hypothesize that the endo-siRNA pathway may regulate the degradation of maternal cell cycle regulators. Endo-siRNAs may have a more general role buffering against environmental perturbations in other organisms.
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Affiliation(s)
- Elena M Lucchetta
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois, United States of America.
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461
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Obbard DJ, Welch JJ, Kim KW, Jiggins FM. Quantifying adaptive evolution in the Drosophila immune system. PLoS Genet 2009; 5:e1000698. [PMID: 19851448 PMCID: PMC2759075 DOI: 10.1371/journal.pgen.1000698] [Citation(s) in RCA: 203] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Accepted: 09/23/2009] [Indexed: 11/28/2022] Open
Abstract
It is estimated that a large proportion of amino acid substitutions in Drosophila have been fixed by natural selection, and as organisms are faced with an ever-changing array of pathogens and parasites to which they must adapt, we have investigated the role of parasite-mediated selection as a likely cause. To quantify the effect, and to identify which genes and pathways are most likely to be involved in the host–parasite arms race, we have re-sequenced population samples of 136 immunity and 287 position-matched non-immunity genes in two species of Drosophila. Using these data, and a new extension of the McDonald-Kreitman approach, we estimate that natural selection fixes advantageous amino acid changes in immunity genes at nearly double the rate of other genes. We find the rate of adaptive evolution in immunity genes is also more variable than other genes, with a small subset of immune genes evolving under intense selection. These genes, which are likely to represent hotspots of host–parasite coevolution, tend to share similar functions or belong to the same pathways, such as the antiviral RNAi pathway and the IMD signalling pathway. These patterns appear to be general features of immune system evolution in both species, as rates of adaptive evolution are correlated between the D. melanogaster and D. simulans lineages. In summary, our data provide quantitative estimates of the elevated rate of adaptive evolution in immune system genes relative to the rest of the genome, and they suggest that adaptation to parasites is an important force driving molecular evolution. All organisms are attacked by an ever-changing array of pathogens and parasites, and it is widely supposed that the ensuing host–parasite “arms race” must drive extensive adaptive evolution in genes of the immune system. Here we have taken advantage of new sequencing technologies and analytical approaches to quantify the amount of adaptation that is occurring in immunity genes relative to the rest of the genome. We sampled two species of fruit fly (D. melanogaster and D. simulans) from eight different populations around the world, and sequenced 136 immunity and 287 non-immunity genes from these samples. Based on the differences in the sequences between the two species, and the genetic diversity within each species, we have estimated that natural selection drives twice as much change in immune-related proteins as in proteins with no immune function. Interestingly, the rate of adaptation is also more variable among immunity genes than among other genes in the genome, with a small subset of immunity genes evolving under intense natural selection. We suggest that these genes may represent hotspots of host–parasite coevolution within the genome.
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Affiliation(s)
- Darren J Obbard
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK.
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462
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26G endo-siRNAs regulate spermatogenic and zygotic gene expression in Caenorhabditis elegans. Proc Natl Acad Sci U S A 2009; 106:18674-9. [PMID: 19846761 DOI: 10.1073/pnas.0906378106] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Endogenous small interfering RNAs (endo-siRNAs) regulate diverse gene expression programs in eukaryotes by either binding and cleaving mRNA targets or mediating heterochromatin formation; however, the mechanisms of endo-siRNA biogenesis, sorting, and target regulation remain poorly understood. Here we report the identification and function of a specific class of germline-generated endo-siRNAs in Caenorhabditis elegans that are 26 nt in length and contain a guanine at the first nucleotide position (i.e., 26G RNAs). 26G RNAs regulate gene expression during spermatogenesis and zygotic development, and their biogenesis requires the ERI-1 exonuclease and the RRF-3 RNA-dependent RNA polymerase (RdRP). Remarkably, we identified two nonoverlapping subclasses of 26G RNAs that sort into specific RNA-induced silencing complexes (RISCs) and differentially regulate distinct mRNA targets. Class I 26G RNAs target genes are expressed during spermatogenesis, whereas class II 26G RNAs are maternally inherited and silence gene expression during zygotic development. These findings implicate a class of endo-siRNAs in the global regulation of transcriptional programs required for fertility and development.
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463
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Saito K, Inagaki S, Mituyama T, Kawamura Y, Ono Y, Sakota E, Kotani H, Asai K, Siomi H, Siomi MC. A regulatory circuit for piwi by the large Maf gene traffic jam in Drosophila. Nature 2009; 461:1296-9. [PMID: 19812547 DOI: 10.1038/nature08501] [Citation(s) in RCA: 332] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 09/16/2009] [Indexed: 12/24/2022]
Abstract
PIWI-interacting RNAs (piRNAs) silence retrotransposons in Drosophila germ lines by associating with the PIWI proteins Argonaute 3 (AGO3), Aubergine (Aub) and Piwi. piRNAs in Drosophila are produced from intergenic repetitive genes and piRNA clusters by two systems: the primary processing pathway and the amplification loop. The amplification loop occurs in a Dicer-independent, PIWI-Slicer-dependent manner. However, primary piRNA processing remains elusive. Here we analysed piRNA processing in a Drosophila ovarian somatic cell line where Piwi, but not Aub or AGO3, is expressed; thus, only the primary piRNAs exist. In addition to flamenco, a Piwi-specific piRNA cluster, traffic jam (tj), a large Maf gene, was determined as a new piRNA cluster. piRNAs arising from tj correspond to the untranslated regions of tj messenger RNA and are sense-oriented. piRNA loading on to Piwi may occur in the cytoplasm. zucchini, a gene encoding a putative cytoplasmic nuclease, is required for tj-derived piRNA production. In tj and piwi mutant ovaries, somatic cells fail to intermingle with germ cells and Fasciclin III is overexpressed. Loss of tj abolishes Piwi expression in gonadal somatic cells. Thus, in gonadal somatic cells, tj gives rise simultaneously to two different molecules: the TJ protein, which activates Piwi expression, and piRNAs, which define the Piwi targets for silencing.
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Affiliation(s)
- Kuniaki Saito
- Keio University School of Medicine, Tokyo 160-8582, Japan
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464
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Abstract
Recently identified small (20 to 40 bases) RNAs, such as microRNAs (miRNAs) and endogenous small interfering RNAs (siRNAs) participate in important cellular pathways. In this report, we systematically characterized several novel features of human and viral RNA products smaller than miRNAs. We found that Kaposi sarcoma-associated herpesvirus K12-1 miRNA (23 bases) associates with a distinct, unusually small (17-base) RNA (usRNA) that can effectively downregulate a K12-1 miRNA target, human RAD21, suggesting that stable degradation-like products may also contribute to gene regulation. High-throughput sequencing reveals a diverse set of human miRNA-derived usRNAs and other non-miRNA-derived usRNAs. Human miRNA-derived usRNAs preferentially match to 5' ends of miRNAs and are also more likely to associate with the siRNA effector protein Ago2 than with Ago1. Many non-miRNA-derived usRNAs associate with Ago proteins and also frequently contain C-rich 3'-specific motifs that are overrepresented in comparison to Piwi-interacting RNAs and transcription start site-associated RNAs. We postulate that approximately 30% of usRNAs could have evolved to participate in biological processes, including gene silencing.
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465
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Okamura K, Lai EC. [Diversity and complexity of dicer dependent small RNA networks in animals]. SEIKAGAKU. THE JOURNAL OF JAPANESE BIOCHEMICAL SOCIETY 2009; 81:904-909. [PMID: 19928532 PMCID: PMC4515750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Affiliation(s)
- Katsutomo Okamura
- Memorial Sloan-Kettering Cancer Center, Department of Developmental Biology, 1275 York Ave, Box 252, New York, NY 10065, 212-639-5578
| | - Eric C. Lai
- Memorial Sloan-Kettering Cancer Center, Department of Developmental Biology, 1275 York Ave, Box 252, New York, NY 10065, 212-639-5578
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466
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Zhou R, Czech B, Brennecke J, Sachidanandam R, Wohlschlegel JA, Perrimon N, Hannon GJ. Processing of Drosophila endo-siRNAs depends on a specific Loquacious isoform. RNA (NEW YORK, N.Y.) 2009; 15:1886-95. [PMID: 19635780 PMCID: PMC2743050 DOI: 10.1261/rna.1611309] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Accepted: 06/30/2009] [Indexed: 05/20/2023]
Abstract
Drosophila melanogaster expresses three classes of small RNAs, which are classified according to their mechanisms of biogenesis. MicroRNAs are approximately 22-23 nucleotides (nt), ubiquitously expressed small RNAs that are sequentially processed from hairpin-like precursors by Drosha/Pasha and Dcr-1/Loquacious complexes. MicroRNAs usually associate with AGO1 and regulate the expression of protein-coding genes. Piwi-interacting RNAs (piRNAs) of approximately 24-28 nt associate with Piwi-family proteins and can arise from single-stranded precursors. piRNAs function in transposon silencing and are mainly restricted to gonadal tissues. Endo-siRNAs are found in both germline and somatic tissues. These approximately 21-nt RNAs are produced by a distinct Dicer, Dcr-2, and do not depend on Drosha/Pasha complexes. They predominantly bind to AGO2 and target both mobile elements and protein-coding genes. Surprisingly, a subset of endo-siRNAs strongly depend for their production on the dsRNA-binding protein Loquacious (Loqs), thought generally to be a partner for Dcr-1 and a cofactor for miRNA biogenesis. Endo-siRNA production depends on a specific Loqs isoform, Loqs-PD, which is distinct from the one, Loqs-PB, required for the production of microRNAs. Paralleling their roles in the biogenesis of distinct small RNA classes, Loqs-PD and Loqs-PB bind to different Dicer proteins, with Dcr-1/Loqs-PB complexes and Dcr-2/Loqs-PD complexes driving microRNA and endo-siRNA biogenesis, respectively.
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Affiliation(s)
- Rui Zhou
- Harvard Medical School, Department of Genetics, Howard Hughes Medical Institute, Boston, Massachusetts 02115, USA
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467
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Distinct argonaute-mediated 22G-RNA pathways direct genome surveillance in the C. elegans germline. Mol Cell 2009; 36:231-44. [PMID: 19800275 DOI: 10.1016/j.molcel.2009.09.020] [Citation(s) in RCA: 356] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2009] [Revised: 08/29/2009] [Accepted: 09/15/2009] [Indexed: 01/01/2023]
Abstract
Endogenous small RNAs (endo-siRNAs) interact with Argonaute (AGO) proteins to mediate sequence-specific regulation of diverse biological processes. Here, we combine deep-sequencing and genetic approaches to explore the biogenesis and function of endo-siRNAs in C. elegans. We describe conditional alleles of the Dicer-related helicase, drh-3, that abrogate both RNA interference and the biogenesis of endo-siRNAs, called 22G-RNAs. DRH-3 is a core component of RNA-dependent RNA polymerase (RdRP) complexes essential for several distinct 22G-RNA systems. We show that, in the germline, one system is dependent on worm-specific AGOs, including WAGO-1, which localizes to germline nuage structures called P granules. WAGO-1 silences certain genes, transposons, pseudogenes, and cryptic loci. Finally, we demonstrate that components of the nonsense-mediated decay pathway function in at least one WAGO-mediated surveillance pathway. These findings broaden our understanding of the biogenesis and diversity of 22G-RNAs and suggest additional regulatory functions for small RNAs.
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468
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Requirement for the ERI/DICER complex in endogenous RNA interference and sperm development in Caenorhabditis elegans. Genetics 2009; 183:1283-95. [PMID: 19797044 DOI: 10.1534/genetics.109.108134] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Small regulatory RNAs are key regulators of gene expression. One class of small regulatory RNAs, termed the endogenous small interfering RNAs (endo siRNAs), is thought to negatively regulate cellular transcripts via an RNA interference (RNAi)-like mechanism termed endogenous RNAi (endo RNAi). A complex of proteins composed of ERI-1/3/5, RRF-3, and DICER (the ERI/DICER complex) mediates endo RNAi processes in Caenorhabditis elegans. We conducted a genetic screen to identify additional components of the endo RNAi machinery. Our screen recovered alleles of eri-9, which encodes a novel DICER-interacting protein, and a missense mutation within the helicase domain of DICER [DCR-1(G492R)]. ERI-9(-) and DCR-1(G492) animals exhibit defects in endo siRNA expression and a concomitant failure to regulate mRNAs that exhibit sequence homology to these endo siRNAs, indicating that ERI-9 and the DCR-1 helicase domain function in the C. elegans endo RNAi pathway. We define a subset of Eri mutant animals (including eri-1, rrf-3, eri-3, and dcr-1, but not eri-9 or ergo-1) that exhibit temperature-sensitive, sperm-specific sterility and defects in X chromosome segregation. Among these mutants we find multiple aberrations in sperm development beginning with cytokinesis and extending through terminal differentiation. These results identify novel components of the endo RNAi machinery, demonstrate differential requirements for the Eri factors in the sperm-producing germline, and begin to delineate the functional requirement for the ERI/DICER complex in sperm development.
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469
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Morozova O, Hirst M, Marra MA. Applications of new sequencing technologies for transcriptome analysis. Annu Rev Genomics Hum Genet 2009; 10:135-51. [PMID: 19715439 DOI: 10.1146/annurev-genom-082908-145957] [Citation(s) in RCA: 340] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Transcriptome analysis has been a key area of biological inquiry for decades. Over the years, research in the field has progressed from candidate gene-based detection of RNAs using Northern blotting to high-throughput expression profiling driven by the advent of microarrays. Next-generation sequencing technologies have revolutionized transcriptomics by providing opportunities for multidimensional examinations of cellular transcriptomes in which high-throughput expression data are obtained at a single-base resolution.
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Affiliation(s)
- Olena Morozova
- BC Cancer Agency, Genome Sciences Center, Vancouver, BC V5Z 4S6, Canada.
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470
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Sabin LR, Zhou R, Gruber JJ, Lukinova N, Bambina S, Berman A, Lau CK, Thompson CB, Cherry S. Ars2 regulates both miRNA- and siRNA- dependent silencing and suppresses RNA virus infection in Drosophila. Cell 2009; 138:340-51. [PMID: 19632183 DOI: 10.1016/j.cell.2009.04.045] [Citation(s) in RCA: 171] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2008] [Revised: 03/02/2009] [Accepted: 04/20/2009] [Indexed: 11/25/2022]
Abstract
Intrinsic immune responses autonomously inhibit viral replication and spread. One pathway that restricts viral infection in plants and insects is RNA interference (RNAi), which targets and degrades viral RNA to limit infection. To identify additional genes involved in intrinsic antiviral immunity, we screened Drosophila cells for modulators of viral infection using an RNAi library. We identified Ars2 as a key component of Drosophila antiviral immunity. Loss of Ars2 in cells, or in flies, increases susceptibility to RNA viruses. Consistent with its antiviral properties, we found that Ars2 physically interacts with Dcr-2, modulates its activity in vitro, and is required for siRNA-mediated silencing. Furthermore, we show that Ars2 plays an essential role in miRNA-mediated silencing, interacting with the Microprocessor and stabilizing pri-miRNAs. The identification of Ars2 as a player in these small RNA pathways provides new insight into the biogenesis of small RNAs that may be extended to other systems.
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Affiliation(s)
- Leah R Sabin
- Department of Microbiology, Penn Genome Frontiers Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
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471
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Regulatory divergence in Drosophila melanogaster and D. simulans, a genomewide analysis of allele-specific expression. Genetics 2009; 183:547-61, 1SI-21SI. [PMID: 19667135 DOI: 10.1534/genetics.109.105957] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Species-specific regulation of gene expression contributes to the development and maintenance of reproductive isolation and to species differences in ecologically important traits. A better understanding of the evolutionary forces that shape regulatory variation and divergence can be developed by comparing expression differences among species and interspecific hybrids. Once expression differences are identified, the underlying genetics of regulatory variation or divergence can be explored. With the goal of associating cis and/or trans components of regulatory divergence with differences in gene expression, overall and allele-specific expression levels were assayed genomewide in female adult heads of Drosophila melanogaster, D. simulans, and their F1 hybrids. A greater proportion of cis differences than trans differences were identified for genes expressed in heads and, in accordance with previous studies, cis differences also explained a larger number of species differences in overall expression level. Regulatory divergence was found to be prevalent among genes associated with defense, olfaction, and among genes downstream of the Drosophila sex determination hierarchy. In addition, two genes, with critical roles in sex determination and micro RNA processing, Sxl and loqs, were identified as misexpressed in hybrid female heads, potentially contributing to hybrid incompatibility.
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472
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Couvillion MT, Lee SR, Hogstad B, Malone CD, Tonkin LA, Sachidanandam R, Hannon GJ, Collins K. Sequence, biogenesis, and function of diverse small RNA classes bound to the Piwi family proteins of Tetrahymena thermophila. Genes Dev 2009; 23:2016-32. [PMID: 19656801 DOI: 10.1101/gad.1821209] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
PAZ/PIWI domain (PPD) proteins carrying small RNAs (sRNAs) function in gene and genome regulation. The ciliate Tetrahymena thermophila encodes numerous PPD proteins exclusively of the Piwi clade. We show that the three Tetrahymena Piwi family proteins (Twis) preferentially expressed in growing cells differ in their genetic essentiality and subcellular localization. Affinity purification of all eight distinct Twi proteins revealed unique properties of their bound sRNAs. Deep sequencing of Twi-bound and total sRNAs in strains disrupted for various silencing machinery uncovered an unanticipated diversity of 23- to 24-nt sRNA classes in growing cells, each with distinct genetic requirements for accumulation. Altogether, Twis distinguish sRNAs derived from loci of pseudogene families, three types of DNA repeats, structured RNAs, and EST-supported loci with convergent or paralogous transcripts. Most surprisingly, Twi7 binds complementary strands of unequal length, while Twi10 binds a specific permutation of the guanosine-rich telomeric repeat. These studies greatly expand the structural and functional repertoire of endogenous sRNAs and RNPs.
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Affiliation(s)
- Mary T Couvillion
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA
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473
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Hartig JV, Esslinger S, Böttcher R, Saito K, Förstemann K. Endo-siRNAs depend on a new isoform of loquacious and target artificially introduced, high-copy sequences. EMBO J 2009; 28:2932-44. [PMID: 19644447 DOI: 10.1038/emboj.2009.220] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 07/09/2009] [Indexed: 12/20/2022] Open
Abstract
Colonization of genomes by a new selfish genetic element is detrimental to the host species and must lead to an efficient, repressive response. In vertebrates as well as in Drosophila, piRNAs repress transposons in the germ line, whereas endogenous siRNAs take on this role in somatic cells. We show that their biogenesis depends on a new isoform of the Drosophila TRBP homologue loquacious, which arises by alternative polyadenylation and is distinct from the one that functions during the biogenesis of miRNAs. For endo-siRNAs and piRNAs, it is unclear how an efficient response can be initiated de novo. Our experiments establish that the endo-siRNA pathway will target artificially introduced sequences without the need for a pre-existing template in the genome. This response is also triggered in transiently transfected cells, thus genomic integration is not essential. Deep sequencing showed that corresponding endo-siRNAs are generated throughout the sequence, but preferentially from transcribed regions. One strand of the dsRNA precursor can come from spliced mRNA, whereas the opposite strand derives from independent transcripts in antisense orientation.
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Affiliation(s)
- Julia Verena Hartig
- Department of Chemistry and Biochemistry, Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
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474
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Schwach F, Moxon S, Moulton V, Dalmay T. Deciphering the diversity of small RNAs in plants: the long and short of it. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:472-81. [PMID: 19641088 DOI: 10.1093/bfgp/elp024] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
RNA silencing is a complex and highly conserved regulatory mechanism that is now known to be involved in such diverse processes as development, pathogen control, genome maintenance and response to environmental changes. Since its recent discovery, RNA silencing has become a fast moving key area of research in plant and animal molecular biology. Research in this field has greatly profited from recent developments in novel sequencing technologies that allow massive parallel sequencing of small RNA (sRNA) molecules, the key players of all RNA silencing phenomena. As researchers are beginning to decipher the complexity of RNA silencing, novel methodologies have to be developed to make sense of the large amounts of data that are currently being generated. In this review we present an overview of RNA silencing pathways in plants and the current challenges in analysing sRNA data, with a special focus on computational approaches.
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Affiliation(s)
- Frank Schwach
- School of Computing Sciences, University of East Anglia, Norwich, UK.
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475
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Faghihi MA, Wahlestedt C. Regulatory roles of natural antisense transcripts. Nat Rev Mol Cell Biol 2009; 10:637-43. [PMID: 19638999 DOI: 10.1038/nrm2738] [Citation(s) in RCA: 558] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mammalian genomes encode numerous natural antisense transcripts, but the function of these transcripts is not well understood. Functional validation studies indicate that antisense transcripts are not a uniform group of regulatory RNAs but instead belong to multiple categories with some common features. Recent evidence indicates that antisense transcripts are frequently functional and use diverse transcriptional and post-transcriptional gene regulatory mechanisms to carry out a wide variety of biological roles.
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Affiliation(s)
- Mohammad Ali Faghihi
- Molecular and Integrative Neurosciences Department, The Scripps Research Institute, Jupiter, Florida 33458, USA
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476
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Glazov EA, Kongsuwan K, Assavalapsakul W, Horwood PF, Mitter N, Mahony TJ. Repertoire of bovine miRNA and miRNA-like small regulatory RNAs expressed upon viral infection. PLoS One 2009; 4:e6349. [PMID: 19633723 PMCID: PMC2713767 DOI: 10.1371/journal.pone.0006349] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Accepted: 06/17/2009] [Indexed: 12/21/2022] Open
Abstract
MicroRNA (miRNA) and other types of small regulatory RNAs play a crucial role in the regulation of gene expression in eukaryotes. Several distinct classes of small regulatory RNAs have been discovered in recent years. To extend the repertoire of small RNAs characterized in mammals and to examine relationship between host miRNA expression and viral infection we used Illumina's ultrahigh throughput sequencing approach. We sequenced three small RNA libraries prepared from cell line derived from the adult bovine kidney under normal conditions and upon infection of the cell line with Bovine herpesvirus 1. We used a bioinformatics approach to distinguish authentic mature miRNA sequences from other classes of small RNAs and short RNA fragments represented in the sequencing data. Using this approach we detected 219 out of 356 known bovine miRNAs and 115 respective miRNA* sequences. In addition we identified five new bovine orthologs of known mammalian miRNAs and discovered 268 new cow miRNAs many of which are not identifiable in other mammalian genomes and thus might be specific to the ruminant lineage. In addition we found seven new bovine mirtron candidates. We also discovered 10 small nucleolar RNA (snoRNA) loci that give rise to small RNA with possible miRNA-like function. Results presented in this study extend our knowledge of the biology and evolution of small regulatory RNAs in mammals and illuminate mechanisms of small RNA biogenesis and function. New miRNA sequences and the original sequencing data have been submitted to miRNA repository (miRBase) and NCBI GEO archive respectively. We envisage that these resources will facilitate functional annotation of the bovine genome and promote further functional and comparative genomics studies of small regulatory RNA in mammals.
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Affiliation(s)
- Evgeny A. Glazov
- Diamantina Institute for Cancer, Immunology and Metabolic Medicine, The University of Queensland, Princess Alexandra Hospital, Woolloongabba, Queensland, Australia
- * E-mail: (EAG); (TJM)
| | - Kritaya Kongsuwan
- CSIRO Livestock Industries, Queensland Bioscience Precinct, St Lucia, Queensland, Australia
| | - Wanchai Assavalapsakul
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai, Bangkok, Thailand
| | - Paul F. Horwood
- Department of Primary Industries and Fisheries, Ritchie Building, Brisbane, Queensland, Australia
| | - Neena Mitter
- Department of Primary Industries and Fisheries, Ritchie Building, Brisbane, Queensland, Australia
| | - Timothy J. Mahony
- Department of Primary Industries and Fisheries, Ritchie Building, Brisbane, Queensland, Australia
- School of Veterinary Sciences, University of Queensland, St Lucia, Queensland, Australia
- * E-mail: (EAG); (TJM)
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477
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Armisen J, Gilchrist MJ, Wilczynska A, Standart N, Miska EA. Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis. Genome Res 2009; 19:1766-75. [PMID: 19628731 DOI: 10.1101/gr.093054.109] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Small regulatory RNAs have recently emerged as key regulators of eukaryotic gene expression. Here we used high-throughput sequencing to determine small RNA populations in the germline and soma of the African clawed frog Xenopus tropicalis. We identified a number of miRNAs that were expressed in the female germline. miRNA expression profiling revealed that miR-202-5p is an oocyte-enriched miRNA. We identified two novel miRNAs that were expressed in the soma. In addition, we sequenced large numbers of Piwi-associated RNAs (piRNAs) and other endogenous small RNAs, likely representing endogenous siRNAs (endo-siRNAs). Of these, only piRNAs were restricted to the germline, suggesting that endo-siRNAs are an abundant class of small RNAs in the vertebrate soma. In the germline, both endogenous small RNAs and piRNAs mapped to many high copy number loci. Furthermore, endogenous small RNAs mapped to the same specific subsets of repetitive elements in both the soma and the germline, suggesting that these RNAs might act to silence repetitive elements in both compartments. Data presented here suggest a conserved role for miRNAs in the vertebrate germline. Furthermore, this study provides a basis for the functional analysis of small regulatory RNAs in an important vertebrate model system.
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Affiliation(s)
- Javier Armisen
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, United Kingdom
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478
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Abstract
MicroRNAs (miRNA) are small RNAs that regulate the translation of thousands of message RNAs and play a profound role in mammalian biology. Over the past 5 years, significant advances have been made towards understanding the pathways that generate miRNAs and the mechanisms by which miRNAs exert their regulatory functions. An emerging theme is that miRNAs are both generated by and utilized by large and complex macromolecular assemblies. Here, we review the biology of mammalian miRNAs with a focus on the macromolecular complexes that generate and control the biogenesis of miRNAs.
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Affiliation(s)
- Pick-Wei Lau
- Department of Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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479
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Drosophila RISC component VIG and its homolog Vig2 impact heterochromatin formation. PLoS One 2009; 4:e6182. [PMID: 19584931 PMCID: PMC2703606 DOI: 10.1371/journal.pone.0006182] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2009] [Accepted: 05/29/2009] [Indexed: 11/19/2022] Open
Abstract
Heterochromatin formation plays an important role in gene regulation and the maintenance of genome integrity. Here we present results from a study of the D. melanogaster gene vig, encoding an RNAi complex component and its homolog vig2 (CG11844) that support their involvement in heterochromatin formation and/or maintenance. Protein null mutations vig(EP812) and vig2(PL470) act as modifiers of Position Effect Variegation (PEV). VIG and Vig2 are present in polytene chromosomes and partially overlap with HP1. Quantitative immunoblots show depletion of HP1 and HP2 (large isoform) in isolated nuclei from the vig(EP812) mutant. The vig2(PL470) mutant strain demonstrates a decreased level of H3K9me2. Pull-down experiments using antibodies specific to HP1 recovered both VIG and Vig2. The association between HP1 and both VIG and Vig2 proteins depends on an RNA component. The above data and the developmental profiles of the two genes suggest that Vig2 may be involved in heterochromatin targeting and establishment early in development, while VIG may have a role in stabilizing HP1/HP2 chromatin binding during later stages.
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480
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Wilusz JE, Sunwoo H, Spector DL. Long noncoding RNAs: functional surprises from the RNA world. Genes Dev 2009; 23:1494-504. [PMID: 19571179 DOI: 10.1101/gad.1800909] [Citation(s) in RCA: 1811] [Impact Index Per Article: 120.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Most of the eukaryotic genome is transcribed, yielding a complex network of transcripts that includes tens of thousands of long noncoding RNAs with little or no protein-coding capacity. Although the vast majority of long noncoding RNAs have yet to be characterized thoroughly, many of these transcripts are unlikely to represent transcriptional "noise" as a significant number have been shown to exhibit cell type-specific expression, localization to subcellular compartments, and association with human diseases. Here, we highlight recent efforts that have identified a myriad of molecular functions for long noncoding RNAs. In some cases, it appears that simply the act of noncoding RNA transcription is sufficient to positively or negatively affect the expression of nearby genes. However, in many cases, the long noncoding RNAs themselves serve key regulatory roles that were assumed previously to be reserved for proteins, such as regulating the activity or localization of proteins and serving as organizational frameworks of subcellular structures. In addition, many long noncoding RNAs are processed to yield small RNAs or, conversely, modulate how other RNAs are processed. It is thus becoming increasingly clear that long noncoding RNAs can function via numerous paradigms and are key regulatory molecules in the cell.
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Affiliation(s)
- Jeremy E Wilusz
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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481
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Taft RJ, Glazov EA, Lassmann T, Hayashizaki Y, Carninci P, Mattick JS. Small RNAs derived from snoRNAs. RNA (NEW YORK, N.Y.) 2009; 15:1233-40. [PMID: 19474147 PMCID: PMC2704076 DOI: 10.1261/rna.1528909] [Citation(s) in RCA: 337] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Small nucleolar RNAs (snoRNAs) guide RNA modification and are localized in nucleoli and Cajal bodies in eukaryotic cells. Components of the RNA silencing pathway associate with these structures, and two recent reports have revealed that a human and a protozoan snoRNA can be processed into miRNA-like RNAs. Here we show that small RNAs with evolutionary conservation of size and position are derived from the vast majority of snoRNA loci in animals (human, mouse, chicken, fruit fly), Arabidopsis, and fission yeast. In animals, sno-derived RNAs (sdRNAs) from H/ACA snoRNAs are predominantly 20-24 nucleotides (nt) in length and originate from the 3' end. Those derived from C/D snoRNAs show a bimodal size distribution at approximately 17-19 nt and >27 nt and predominantly originate from the 5' end. SdRNAs are associated with AGO7 in Arabidopsis and Ago1 in fission yeast with characteristic 5' nucleotide biases and show altered expression patterns in fly loquacious and Dicer-2 and mouse Dicer1 and Dgcr8 mutants. These findings indicate that there is interplay between the RNA silencing and snoRNA-mediated RNA processing systems, and that sdRNAs comprise a novel and ancient class of small RNAs in eukaryotes.
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Affiliation(s)
- Ryan J Taft
- Australian Research Council Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia
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482
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Lau NC, Robine N, Martin R, Chung WJ, Niki Y, Berezikov E, Lai EC. Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line. Genome Res 2009; 19:1776-85. [PMID: 19541914 DOI: 10.1101/gr.094896.109] [Citation(s) in RCA: 154] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Piwi proteins, a subclass of Argonaute-family proteins, carry approximately 24-30-nt Piwi-interacting RNAs (piRNAs) that mediate gonadal defense against transposable elements (TEs). We analyzed the Drosophila ovary somatic sheet (OSS) cell line and found that it expresses miRNAs, endogenous small interfering RNAs (endo-siRNAs), and piRNAs in abundance. In contrast to intact gonads, which contain mixtures of germline and somatic cell types that express different Piwi-class proteins, OSS cells are a homogenous somatic cell population that expresses only PIWI and primary piRNAs. Detailed examination of its TE-derived piRNAs and endo-siRNAs revealed aspects of TE defense that do not rely upon ping-pong amplification. In particular, we provide evidence that a subset of piRNA master clusters, including flamenco, are specifically expressed in OSS and ovarian follicle cells. These data indicate that the restriction of certain TEs in somatic gonadal cells is largely mediated by a primary piRNA pathway.
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Affiliation(s)
- Nelson C Lau
- Department of Molecular Biology, Massachusetts General Hospital, Boston, 02114, USA.
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483
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Berry B, Deddouche S, Kirschner D, Imler JL, Antoniewski C. Viral suppressors of RNA silencing hinder exogenous and endogenous small RNA pathways in Drosophila. PLoS One 2009; 4:e5866. [PMID: 19516905 PMCID: PMC2689938 DOI: 10.1371/journal.pone.0005866] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2009] [Accepted: 05/13/2009] [Indexed: 12/19/2022] Open
Abstract
Background In plants and insects, RNA interference (RNAi) is the main responder against viruses and shapes the basis of antiviral immunity. Viruses counter this defense by expressing viral suppressors of RNAi (VSRs). While VSRs in Drosophila melanogaster were shown to inhibit RNAi through different modes of action, whether they act on other silencing pathways remained unexplored. Methodology/Principal Findings Here we show that expression of various plant and insect VSRs in transgenic flies does not perturb the Drosophila microRNA (miRNA) pathway; but in contrast, inhibits antiviral RNAi and the RNA silencing response triggered by inverted repeat transcripts, and injection of dsRNA or siRNA. Strikingly, these VSRs also suppressed transposon silencing by endogenous siRNAs (endo-siRNAs). Conclusions/Significance Our findings identify VSRs as tools to unravel small RNA pathways in insects and suggest a cosuppression of antiviral RNAi and endo-siRNA silencing by viruses during fly infections.
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Affiliation(s)
- Bassam Berry
- Institut Pasteur, Drosophila Genetics and Epigenetics, CNRS-URA2578, Paris, France
| | | | - Doris Kirschner
- Institut Pasteur, Drosophila Genetics and Epigenetics, CNRS-URA2578, Paris, France
| | | | - Christophe Antoniewski
- Institut Pasteur, Drosophila Genetics and Epigenetics, CNRS-URA2578, Paris, France
- * E-mail:
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484
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Zeller G, Henz SR, Widmer CK, Sachsenberg T, Rätsch G, Weigel D, Laubinger S. Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2009; 58:1068-82. [PMID: 19222804 DOI: 10.1111/j.1365-313x.2009.03835.x] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The responses of plants to abiotic stresses are accompanied by massive changes in transcriptome composition. To provide a comprehensive view of stress-induced changes in the Arabidopsis thaliana transcriptome, we have used whole-genome tiling arrays to analyze the effects of salt, osmotic, cold and heat stress as well as application of the hormone abscisic acid (ABA), an important mediator of stress responses. Among annotated genes in the reference strain Columbia we have found many stress-responsive genes, including several transcription factor genes as well as pseudogenes and transposons that have been missed in previous analyses with standard expression arrays. In addition, we report hundreds of newly identified, stress-induced transcribed regions. These often overlap with known, annotated genes. The results are accessible through the Arabidopsis thaliana Tiling Array Express (At-TAX) homepage, which provides convenient tools for displaying expression values of annotated genes, as well as visualization of unannotated transcribed regions along each chromosome.
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Affiliation(s)
- Georg Zeller
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
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485
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Brosnan CA, Voinnet O. The long and the short of noncoding RNAs. Curr Opin Cell Biol 2009; 21:416-25. [PMID: 19447594 DOI: 10.1016/j.ceb.2009.04.001] [Citation(s) in RCA: 275] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Accepted: 04/06/2009] [Indexed: 12/27/2022]
Abstract
Controlling protein-coding gene expression can no longer be attributed purely to proteins involved in transcription, RNA processing, and translation. The role that noncoding RNAs (ncRNAs) play as potent and specific regulators of gene expression is now widely recognized in almost all species studied to date. Long ncRNAs can both upregulate and downregulate gene expression in both eukaryotes and prokaryotes and are essential in processes such as dosage compensation, genomic imprinting, developmental patterning and differentiation, and stress response. Small ncRNAs also play essential roles in diverse organisms, although are limited to eukaryotes. Different small RNA classes regulate diverse processes such as transposon and virus suppression, as well as many key developmental processes.
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Affiliation(s)
- Christopher A Brosnan
- Institut de Biologie Moléculaire des Plantes, CNRS UPR2357-Université de Strasbourg, Strasbourg, France
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486
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Dimitri P, Caizzi R, Giordano E, Carmela Accardo M, Lattanzi G, Biamonti G. Constitutive heterochromatin: a surprising variety of expressed sequences. Chromosoma 2009; 118:419-35. [PMID: 19412619 DOI: 10.1007/s00412-009-0211-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 03/30/2009] [Accepted: 04/01/2009] [Indexed: 10/20/2022]
Abstract
The organization of chromosomes into euchromatin and heterochromatin is amongst the most important and enigmatic aspects of genome evolution. Constitutive heterochromatin is a basic yet still poorly understood component of eukaryotic chromosomes, and its molecular characterization by means of standard genomic approaches is intrinsically difficult. Although recent evidence indicates that the presence of transcribed genes in constitutive heterochromatin is a conserved trait that accompanies the evolution of eukaryotic genomes, the term heterochromatin is still considered by many as synonymous of gene silencing. In this paper, we comprehensively review data that provide a clearer picture of transcribed sequences within constitutive heterochromatin, with a special emphasis on Drosophila and humans.
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Affiliation(s)
- Patrizio Dimitri
- Laboratorio di Genomica Funzionale e Proteomica di Sistemi modello and Istituto Pasteur-Fondazione Bolognetti, Dipartimento di Genetica e Biologia Molecolare Charles Darwin, Università La Sapienza, 00185, Italy.
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487
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Fahlgren N, Sullivan CM, Kasschau KD, Chapman EJ, Cumbie JS, Montgomery TA, Gilbert SD, Dasenko M, Backman TWH, Givan SA, Carrington JC. Computational and analytical framework for small RNA profiling by high-throughput sequencing. RNA (NEW YORK, N.Y.) 2009; 15:992-1002. [PMID: 19307293 PMCID: PMC2673065 DOI: 10.1261/rna.1473809] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The advent of high-throughput sequencing (HTS) methods has enabled direct approaches to quantitatively profile small RNA populations. However, these methods have been limited by several factors, including representational artifacts and lack of established statistical methods of analysis. Furthermore, massive HTS data sets present new problems related to data processing and mapping to a reference genome. Here, we show that cluster-based sequencing-by-synthesis technology is highly reproducible as a quantitative profiling tool for several classes of small RNA from Arabidopsis thaliana. We introduce the use of synthetic RNA oligoribonucleotide standards to facilitate objective normalization between HTS data sets, and adapt microarray-type methods for statistical analysis of multiple samples. These methods were tested successfully using mutants with small RNA biogenesis (miRNA-defective dcl1 mutant and siRNA-defective dcl2 dcl3 dcl4 triple mutant) or effector protein (ago1 mutant) deficiencies. Computational methods were also developed to rapidly and accurately parse, quantify, and map small RNA data.
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Affiliation(s)
- Noah Fahlgren
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon 97331, USA
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488
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Taft RJ, Glazov EA, Cloonan N, Simons C, Stephen S, Faulkner GJ, Lassmann T, Forrest ARR, Grimmond SM, Schroder K, Irvine K, Arakawa T, Nakamura M, Kubosaki A, Hayashida K, Kawazu C, Murata M, Nishiyori H, Fukuda S, Kawai J, Daub CO, Hume DA, Suzuki H, Orlando V, Carninci P, Hayashizaki Y, Mattick JS. Tiny RNAs associated with transcription start sites in animals. Nat Genet 2009; 41:572-8. [PMID: 19377478 DOI: 10.1038/ng.312] [Citation(s) in RCA: 265] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2008] [Accepted: 12/06/2008] [Indexed: 12/13/2022]
Abstract
It has been reported that relatively short RNAs of heterogeneous sizes are derived from sequences near the promoters of eukaryotic genes. In conjunction with the FANTOM4 project, we have identified tiny RNAs with a modal length of 18 nt that map within -60 to +120 nt of transcription start sites (TSSs) in human, chicken and Drosophila. These transcription initiation RNAs (tiRNAs) are derived from sequences on the same strand as the TSS and are preferentially associated with G+C-rich promoters. The 5' ends of tiRNAs show peak density 10-30 nt downstream of TSSs, indicating that they are processed. tiRNAs are generally, although not exclusively, associated with highly expressed transcripts and sites of RNA polymerase II binding. We suggest that tiRNAs may be a general feature of transcription in metazoa and possibly all eukaryotes.
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Affiliation(s)
- Ryan J Taft
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Australia
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489
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Chang S, Wen S, Chen D, Jin P. Small regulatory RNAs in neurodevelopmental disorders. Hum Mol Genet 2009; 18:R18-26. [PMID: 19297398 DOI: 10.1093/hmg/ddp072] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Increasingly complex networks of small RNAs act through RNA interference pathway to regulate gene expression. Recent evidence suggests that both development and proper function of central nervous system require intricate spatiotemporal expression of a wide repertoire of small regulatory RNAs. Misregulation of these small regulatory RNAs could contribute to the abnormalities in brain development that are associated with neurodevelopmental disorders. Here, we will review recent progress made toward understanding roles of small regulatory RNAs in neurodevelopmental disorders and discuss the potential involvement of newly discovered classes of small RNAs in these disorders.
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Affiliation(s)
- Shuang Chang
- Department of Human Genetics, Emory University School of Medicine, Atlanta, GA 30322, USA
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490
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Dykxhoorn DM. RNA interference as an anticancer therapy: a patent perspective. Expert Opin Ther Pat 2009; 19:475-91. [DOI: 10.1517/13543770902838008] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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491
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Nimmo RA, Slack FJ. An elegant miRror: microRNAs in stem cells, developmental timing and cancer. Chromosoma 2009; 118:405-18. [PMID: 19340450 DOI: 10.1007/s00412-009-0210-z] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Revised: 03/17/2009] [Accepted: 03/17/2009] [Indexed: 12/27/2022]
Abstract
MicroRNAs (miRNAs) were first discovered in genetic screens for regulators of developmental timing in the stem-cell-like seam cell lineage in Caenorhabditis elegans. As members of the heterochronic pathway, the lin-4 and let-7 miRNAs are required in the seam cells for the correct progression of stage-specific events and to ensure that cell cycle exit and terminal differentiation occur at the correct time. Other heterochronic genes such as lin-28 and lin-41 are direct targets of the lin-4 and let-7 miRNAs. Recent findings on the functions of the let-7 and lin-4/mir-125 miRNA families and lin-28 and lin-41 orthologs from a variety of organisms suggest that core elements of the heterochronic pathway are retained in mammalian stem cells and development. In particular, these genes appear to form bistable switches via double-negative feedback loops in both nematode and mammalian stem cell development, the functional relevance of which is finally becoming clear. let-7 inhibits stem cell self-renewal in both normal and cancer stem cells of the breast and acts as a tumor suppressor in lung and breast cancer. let-7 also promotes terminal differentiation at the larval to adult transition in both nematode stem cells and fly wing imaginal discs and inhibits proliferation of human lung and liver cancer cells. Conversely, LIN-28 is a highly specific embryonic stem cell marker and is one of four "stemness" factors used to reprogram adult fibroblasts into induced pluripotent stem cells; furthermore, lin-28 is oncogenic in hepatocellular carcinomas. Therefore, a core module of heterochronic genes--lin-28, lin-41, let-7, and lin-4/mir-125-acts as an ancient regulatory switch for differentiation in stem cells (and in some cancers), illustrating that nematode seam cells mirror miRNA regulatory networks in mammalian stem cells during both normal development and cancer.
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Affiliation(s)
- Rachael A Nimmo
- Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, CT 06520, USA
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492
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Kadener S, Rodriguez J, Abruzzi KC, Khodor YL, Sugino K, Marr MT, Nelson S, Rosbash M. Genome-wide identification of targets of the drosha-pasha/DGCR8 complex. RNA (NEW YORK, N.Y.) 2009; 15:537-45. [PMID: 19223442 PMCID: PMC2661833 DOI: 10.1261/rna.1319309] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Accepted: 12/18/2008] [Indexed: 05/24/2023]
Abstract
Drosha is a type III RNase, which plays a critical role in miRNA biogenesis. Drosha and its double-stranded RNA-binding partner protein Pasha/DGCR8 likely recognize and cleave miRNA precursor RNAs or pri-miRNA hairpins cotranscriptionally. To identify RNAs processed by Drosha, we used tiling microarrays to examine transcripts after depletion of drosha mRNA with dsRNA in Drosophila Schneider S2 cells. This strategy identified 137 Drosha-regulated RNAs, including 11 putative pri-miRNAs comprising 15 annotated miRNAs. Most of the identified pri-miRNAs seem extremely large, >10 kb as revealed by both the Drosha knock-down strategy and by RNA PolII chromatin IP followed by Drosophila tiling microarrays. Surprisingly, more than a hundred additional RNAs not annotated as miRNAs are under Drosha control and are likely to be direct targets of Drosha action. This is because many of them encode annotated genes, and unlike bona fide pri-miRNAs, they are not affected by depletion of the miRNA processing factor, dicer-1. Moreover, application of the evofold analysis software indicates that at least 25 of the Drosha-regulated RNAs contain evolutionarily conserved hairpins similar to those recognized by the Drosha-Pasha/DGCR8 complex in pri-miRNAs. One of these hairpins is located in the 5' UTR of both pasha and mammalian DGCR8. These observations suggest that a negative feedback loop acting on pasha mRNA may regulate the miRNA-biogenesis pathway: i.e., excess Drosha cleaves pasha/DGCR8 primary transcripts and leads to a reduction in pasha/DGCR8 mRNA levels and Pasha/DGCR8 synthesis.
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Affiliation(s)
- Sebastian Kadener
- Howard Hughes Medical Institute, Brandeis University, Waltham, MA 02454, USA
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493
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Iwasaki S, Kawamata T, Tomari Y. Drosophila Argonaute1 and Argonaute2 Employ Distinct Mechanisms for Translational Repression. Mol Cell 2009; 34:58-67. [DOI: 10.1016/j.molcel.2009.02.010] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2008] [Revised: 11/21/2008] [Accepted: 02/12/2009] [Indexed: 10/21/2022]
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494
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Siomi MC, Kuramochi-Miyagawa S. RNA silencing in germlines--exquisite collaboration of Argonaute proteins with small RNAs for germline survival. Curr Opin Cell Biol 2009; 21:426-34. [PMID: 19303759 DOI: 10.1016/j.ceb.2009.02.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Revised: 02/02/2009] [Accepted: 02/13/2009] [Indexed: 10/21/2022]
Abstract
As the proper development of germlines is vital for species preservation, elaborative, regulatory systems for gene expression must operate in germlines. One such system is RNA silencing, sequence-specific gene silencing mechanisms mediated by small RNAs of 20-30 nucleotides long. Indeed, recent studies have revealed that various types of small RNAs are expressed germline-specifically. To preserve the germlines, they collaborate with Argonaute proteins, the catalytic engines in RNA silencing, to inhibit injurious, parasitic genes, transcriptionally or post-transcriptionally. This chapter summarizes the exquisite collaboration of Argonaute proteins with small RNAs in the RNA silencing mechanisms necessary for germline survival in Drosophila and mice.
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Affiliation(s)
- Mikiko C Siomi
- Keio University School of Medicine, Tokyo 160-8582, Japan.
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495
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van Rij RP, Berezikov E. Small RNAs and the control of transposons and viruses in Drosophila. Trends Microbiol 2009; 17:163-71. [PMID: 19299135 DOI: 10.1016/j.tim.2009.01.003] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 01/09/2009] [Accepted: 01/09/2009] [Indexed: 10/21/2022]
Abstract
RNA interference (RNAi) - post-transcriptional gene silencing guided by small interfering RNA (siRNA) - is an important antiviral defense mechanism in insects and plants. Several recent studies in Drosophila identified endogenous siRNAs corresponding to transposons, to structured cellular transcripts and to overlapping convergent transcripts. In addition, one of these studies detected a large pool of Argonaute-2 associated siRNAs that mapped to the genome of flock house virus, a (+) RNA virus. Our bioinformatic analyses indicate that these viral siRNAs mapped in roughly equal proportions to both (+) and (-) viral RNA strands. These reports attribute an important function to RNAi in the defense against parasitic nucleic acids (viruses and transposable elements) and provide a novel mechanism for RNAi-based regulation of cellular gene expression. Furthermore, the detection of viral siRNAs of both (+) and (-) polarity implicates double-stranded RNA replication intermediates as the Dicer substrates that mediate antiviral defense.
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Affiliation(s)
- Ronald P van Rij
- Department of Medical Microbiology, Radboud University Nijmegen Medical Centre, Nijmegen Centre for Molecular Life Sciences, 6500 HB Nijmegen, The Netherlands.
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496
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Abstract
Transposons populate the landscape of all eukaryotic genomes. Often considered purely genomic parasites, transposons can also benefit their hosts, playing roles in gene regulation and in genome organization and evolution. Peaceful coexistence with mobile elements depends upon adaptive control mechanisms, since unchecked transposon activity can impact long-term fitness and acutely reduce the fertility of progeny. Here, we review the conserved roles played by small RNAs in the adaptation of eukaryotes to coexist with their genomic colonists. An understanding of transposon-defense pathways has uncovered recurring themes in the mechanisms by which genomes distinguish "self" from "non-self" and selectively silence the latter.
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Affiliation(s)
- Colin D Malone
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
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497
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Abstract
Since the discovery in 1993 of the first small silencing RNA, a dizzying number of small RNA classes have been identified, including microRNAs (miRNAs), small interfering RNAs (siRNAs) and Piwi-interacting RNAs (piRNAs). These classes differ in their biogenesis, their modes of target regulation and in the biological pathways they regulate. There is a growing realization that, despite their differences, these distinct small RNA pathways are interconnected, and that small RNA pathways compete and collaborate as they regulate genes and protect the genome from external and internal threats.
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Affiliation(s)
- Megha Ghildiyal
- Department of Biochemistry and Molecular Pharmacology and Howard Hughes Medical Institute, University of Massachusetts Medical School, 364 Plantation Street, Worcester, Massachusetts 01605, USA
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498
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Dicing of viral replication intermediates during silencing of latent Drosophila viruses. Proc Natl Acad Sci U S A 2009; 106:5270-5. [PMID: 19251644 DOI: 10.1073/pnas.0813412106] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Previous studies revealed roles for RNA interference (RNAi) in the immediate cellular response to viral infection in plants, nematodes and flies. However, little is known about how RNAi combats viruses during persistent or latent infections. Our analysis of small RNAs cloned from Drosophila cells latently infected with Flock House Virus (FHV) failed to reveal signatures of bulk degradation of the viral genome. Instead, this + strand virus specifically generated Dicer-2-dependent, 21-nucleotide siRNAs that derived in equal proportion from + and - strands. Curiously, luciferase reporters that are fully complementary to abundant viral siRNAs were poorly repressed. Moreover, although the viral siRNAs that were incorporated into an effector complex associated with Argonaute2, bulk FHV siRNAs in latently infected cells were not loaded into any Argonaute protein. Together, these data suggest that direct dicing of viral replication intermediates plays an important role in maintaining the latent viral state. In addition, the denial of bulk viral siRNAs from effector complexes suggests that criteria beyond the structural competency of RNA duplexes influence the assembly of functional silencing complexes.
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499
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Cecere G, Cogoni C. Quelling targets the rDNA locus and functions in rDNA copy number control. BMC Microbiol 2009; 9:44. [PMID: 19243581 PMCID: PMC2650698 DOI: 10.1186/1471-2180-9-44] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2008] [Accepted: 02/25/2009] [Indexed: 03/09/2023] Open
Abstract
Background RNA silencing occurs in a broad range of organisms. Although its ancestral function is probably related to the genome defense mechanism against repetitive selfish elements, it has been found that RNA silencing regulates different cellular processes such as gene expression and chromosomal segregation. In Neurospora crassa, a RNA silencing mechanism, called quelling, acts to repress the expression of transgenes and transposons, but until now no other cellular functions have been shown to be regulated by this mechanism. Results Here, we detected by northern blotting endogenous short interfering RNA (siRNAs) from the repetitive ribosomal DNA locus (rDNA) that are loaded onto the argonaute protein QDE-2. Moreover, we found a bidirectional transcription that can generate double strand RNA (dsRNA) molecules. Interestingly, quelling mutants have a reduced rDNA gene copy number. Conclusion Our finding could suggest a new biological function for RNA silencing in the maintenance of the integrity and stability of the Neurospora rDNA locus.
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Affiliation(s)
- Germano Cecere
- Dipartimento di Biotecnologie Cellulari ed Ematologia, Università La Sapienza, Rome, Italy.
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500
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Castanotto D, Rossi JJ. The promises and pitfalls of RNA-interference-based therapeutics. Nature 2009; 457:426-33. [PMID: 19158789 DOI: 10.1038/nature07758] [Citation(s) in RCA: 933] [Impact Index Per Article: 62.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The discovery that gene expression can be controlled by the Watson-Crick base-pairing of small RNAs with messenger RNAs containing complementary sequence - a process known as RNA interference - has markedly advanced our understanding of eukaryotic gene regulation and function. The ability of short RNA sequences to modulate gene expression has provided a powerful tool with which to study gene function and is set to revolutionize the treatment of disease. Remarkably, despite being just one decade from its discovery, the phenomenon is already being used therapeutically in human clinical trials, and biotechnology companies that focus on RNA-interference-based therapeutics are already publicly traded.
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Affiliation(s)
- Daniela Castanotto
- Department of Molecular Biology and City of Hope Graduate School of Biological Sciences, Beckman Research Institute of the City of Hope, Duarte, California 91010, USA
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