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Shatskikh AS, Fefelova EA, Klenov MS. Functions of RNAi Pathways in Ribosomal RNA Regulation. Noncoding RNA 2024; 10:19. [PMID: 38668377 PMCID: PMC11054153 DOI: 10.3390/ncrna10020019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/19/2024] [Accepted: 03/27/2024] [Indexed: 04/29/2024] Open
Abstract
Argonaute proteins, guided by small RNAs, play crucial roles in gene regulation and genome protection through RNA interference (RNAi)-related mechanisms. Ribosomal RNAs (rRNAs), encoded by repeated rDNA units, constitute the core of the ribosome being the most abundant cellular transcripts. rDNA clusters also serve as sources of small RNAs, which are loaded into Argonaute proteins and are able to regulate rDNA itself or affect other gene targets. In this review, we consider the impact of small RNA pathways, specifically siRNAs and piRNAs, on rRNA gene regulation. Data from diverse eukaryotic organisms suggest the potential involvement of small RNAs in various molecular processes related to the rDNA transcription and rRNA fate. Endogenous siRNAs are integral to the chromatin-based silencing of rDNA loci in plants and have been shown to repress rDNA transcription in animals. Small RNAs also play a role in maintaining the integrity of rDNA clusters and may function in the cellular response to rDNA damage. Studies on the impact of RNAi and small RNAs on rRNA provide vast opportunities for future exploration.
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Affiliation(s)
- Aleksei S. Shatskikh
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 26 Vavilov Street, 119334 Moscow, Russia;
| | - Elena A. Fefelova
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
| | - Mikhail S. Klenov
- Institute of Molecular Genetics, Russian Academy of Sciences, 2 Kurchatov Sq., 123182 Moscow, Russia
- RNA Therapeutics Institute, University of Massachusetts Chan Medical School, 368 Plantation Street, Worcester, MA 01605, USA
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2
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Wahba L, Hansen L, Fire AZ. An essential role for the piRNA pathway in regulating the ribosomal RNA pool in C. elegans. Dev Cell 2021; 56:2295-2312.e6. [PMID: 34388368 DOI: 10.1016/j.devcel.2021.07.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 06/11/2021] [Accepted: 07/15/2021] [Indexed: 01/08/2023]
Abstract
Piwi-interacting RNAs (piRNAs) are RNA effectors with key roles in maintaining genome integrity and promoting fertility in metazoans. In Caenorhabditis elegans loss of piRNAs leads to a transgenerational sterility phenotype. The plethora of piRNAs and their ability to silence transcripts with imperfect complementarity have raised several (non-exclusive) models for the underlying drivers of sterility. Here, we report the extranuclear and transferable nature of the sterility driver, its suppression via mutations disrupting the endogenous RNAi and poly-uridylation machinery, and copy-number amplification at the ribosomal DNA locus. In piRNA-deficient animals, several small interfering RNA (siRNA) populations become increasingly overabundant in the generations preceding loss of germline function, including ribosomal siRNAs (risiRNAs). A concomitant increase in uridylated sense rRNA fragments suggests that poly-uridylation may potentiate RNAi-mediated gene silencing of rRNAs. We conclude that loss of the piRNA machinery allows for unchecked amplification of siRNA populations, originating from abundant highly structured RNAs, to deleterious levels.
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Affiliation(s)
- Lamia Wahba
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Loren Hansen
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Andrew Z Fire
- Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA.
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3
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Audoynaud C, Vagner S, Lambert S. Non-homologous end-joining at challenged replication forks: an RNA connection? Trends Genet 2021; 37:973-985. [PMID: 34238592 DOI: 10.1016/j.tig.2021.06.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 05/20/2021] [Accepted: 06/11/2021] [Indexed: 12/29/2022]
Abstract
Defective DNA replication, known as 'replication stress', is a source of DNA damage, a hallmark of numerous human diseases, including cancer, developmental defect, neurological disorders, and premature aging. Recent work indicates that non-homologous end-joining (NHEJ) is unexpectedly active during DNA replication to repair replication-born DNA lesions and to safeguard replication fork integrity. However, erroneous NHEJ events are deleterious to genome stability. RNAs are novel regulators of NHEJ activity through their ability to modulate the assembly of repair complexes in trans. At DNA damage sites, RNAs and DNA-embedded ribonucleotides modulate repair efficiency and fidelity. We discuss here how RNAs and associated proteins, including RNA binding proteins, may regulate NHEJ to sustain genome stability during DNA replication.
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Affiliation(s)
- Charlotte Audoynaud
- Institut Curie, Université PSL, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Equipes Labélisées Ligue Nationale Contre Le Cancer, 91400 Orsay, France
| | - Stéphan Vagner
- Institut Curie, Université PSL, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Equipes Labélisées Ligue Nationale Contre Le Cancer, 91400 Orsay, France
| | - Sarah Lambert
- Institut Curie, Université PSL, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Université Paris-Saclay, CNRS UMR3348, INSERM U1278, 91400 Orsay, France; Equipes Labélisées Ligue Nationale Contre Le Cancer, 91400 Orsay, France.
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4
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Lee SR, Pollard DA, Galati DF, Kelly ML, Miller B, Mong C, Morris MN, Roberts-Nygren K, Kapler GM, Zinkgraf M, Dang HQ, Branham E, Sasser J, Tessier E, Yoshiyama C, Matsumoto M, Turman G. Disruption of a ∼23-24 nucleotide small RNA pathway elevates DNA damage responses in Tetrahymena thermophila. Mol Biol Cell 2021; 32:1335-1346. [PMID: 34010017 PMCID: PMC8694037 DOI: 10.1091/mbc.e20-10-0631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Endogenous RNA interference (RNAi) pathways regulate a wide range of cellular processes in diverse eukaryotes, yet in the ciliated eukaryote, Tetrahymena thermophila, the cellular purpose of RNAi pathways that generate ∼23–24 nucleotide (nt) small (s)RNAs has remained unknown. Here, we investigated the phenotypic and gene expression impacts on vegetatively growing cells when genes involved in ∼23–24 nt sRNA biogenesis are disrupted. We observed slower proliferation and increased expression of genes involved in DNA metabolism and chromosome organization and maintenance in sRNA biogenesis mutants RSP1Δ, RDN2Δ, and RDF2Δ. In addition, RSP1Δ and RDN2Δ cells frequently exhibited enlarged chromatin extrusion bodies, which are nonnuclear, DNA-containing structures that may be akin to mammalian micronuclei. Expression of homologous recombination factor Rad51 was specifically elevated in RSP1Δ and RDN2Δ strains, with Rad51 and double-stranded DNA break marker γ-H2A.X localized to discrete macronuclear foci. In addition, an increase in Rad51 and γ-H2A.X foci was also found in knockouts of TWI8, a macronucleus-localized PIWI protein. Together, our findings suggest that an evolutionarily conserved role for RNAi pathways in maintaining genome integrity may be extended even to the early branching eukaryotic lineage that gave rise to Tetrahymena thermophila.
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Affiliation(s)
- Suzanne R Lee
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Daniel A Pollard
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Domenico F Galati
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Megan L Kelly
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Brian Miller
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Christina Mong
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Megan N Morris
- Biology Department, Western Washington University, Bellingham, WA 98225
| | | | - Geoffrey M Kapler
- Molecular and Cellular Medicine, Texas A&M University, College Station, TX 77843
| | - Matthew Zinkgraf
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Hung Q Dang
- Molecular and Cellular Medicine, Texas A&M University, College Station, TX 77843
| | - Erica Branham
- Molecular and Cellular Medicine, Texas A&M University, College Station, TX 77843
| | - Jason Sasser
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Erin Tessier
- Biology Department, Western Washington University, Bellingham, WA 98225
| | | | - Maya Matsumoto
- Biology Department, Western Washington University, Bellingham, WA 98225
| | - Gaea Turman
- Biology Department, Western Washington University, Bellingham, WA 98225
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5
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Copy number-dependent DNA methylation of the Pyricularia oryzae MAGGY retrotransposon is triggered by DNA damage. Commun Biol 2021; 4:351. [PMID: 33742058 PMCID: PMC7979813 DOI: 10.1038/s42003-021-01836-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 02/11/2021] [Indexed: 11/08/2022] Open
Abstract
Transposable elements are common targets for transcriptional and post-transcriptional gene silencing in eukaryotic genomes. However, the molecular mechanisms responsible for sensing such repeated sequences in the genome remain largely unknown. Here, we show that machinery of homologous recombination (HR) and RNA silencing play cooperative roles in copy number-dependent de novo DNA methylation of the retrotransposon MAGGY in the fungus Pyricularia oryzae. Genetic and physical interaction studies revealed that RecA domain-containing proteins, including P. oryzae homologs of Rad51, Rad55, and Rad57, together with an uncharacterized protein, Ddnm1, form complex(es) and mediate either the overall level or the copy number-dependence of de novo MAGGY DNA methylation, likely in conjunction with DNA repair. Interestingly, P. oryzae mutants of specific RNA silencing components (MoDCL1 and MoAGO2) were impaired in copy number-dependence of MAGGY methylation. Co-immunoprecipitation of MoAGO2 and HR components suggested a physical interaction between the HR and RNA silencing machinery in the process.
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6
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Regulation of DNA break repair by RNA. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 163:23-33. [PMID: 33385412 DOI: 10.1016/j.pbiomolbio.2020.12.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 11/25/2020] [Accepted: 12/17/2020] [Indexed: 12/19/2022]
Abstract
Genomic stability is critical for cell survival and its effective repair when damaged is a vital process for preserving genetic information. Failure to correctly repair the genome can lead to the accumulation of mutations that ultimately drives carcinogenesis. Life has evolved sophisticated surveillance, repair pathways, and mechanisms to recognize and mend genomic lesions to preserve its integrity. Many of these pathways involve a cascade of protein effectors that act to identify the type of damage, such as double-strand (ds) DNA breaks, propagate the damage signal, and recruit an array of other protein factors to resolve the damage without loss of genetic information. It is now becoming increasingly clear that there are a number of RNA processing factors, such as the transcriptional machinery, and microRNA biogenesis components, as well as RNA itself, that facilitate the repair of DNA damage. Here, some of the recent work unravelling the role of RNA in the DNA Damage Response (DDR), in particular the dsDNA break repair pathway, will be reviewed.
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7
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Honda S, Eusebio-Cope A, Miyashita S, Yokoyama A, Aulia A, Shahi S, Kondo H, Suzuki N. Establishment of Neurospora crassa as a model organism for fungal virology. Nat Commun 2020; 11:5627. [PMID: 33159072 PMCID: PMC7648066 DOI: 10.1038/s41467-020-19355-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 10/08/2020] [Indexed: 01/07/2023] Open
Abstract
The filamentous fungus Neurospora crassa is used as a model organism for genetics, developmental biology and molecular biology. Remarkably, it is not known to host or to be susceptible to infection with any viruses. Here, we identify diverse RNA viruses in N. crassa and other Neurospora species, and show that N. crassa supports the replication of these viruses as well as some viruses from other fungi. Several encapsidated double-stranded RNA viruses and capsid-less positive-sense single-stranded RNA viruses can be experimentally introduced into N. crassa protoplasts or spheroplasts. This allowed us to examine viral replication and RNAi-mediated antiviral responses in this organism. We show that viral infection upregulates the transcription of RNAi components, and that Dicer proteins (DCL-1, DCL-2) and an Argonaute (QDE-2) participate in suppression of viral replication. Our study thus establishes N. crassa as a model system for the study of host-virus interactions. The fungus Neurospora crassa is a model organism for the study of various biological processes, but it is not known to be infected by any viruses. Here, Honda et al. identify RNA viruses that infect N. crassa and examine viral replication and RNAi-mediated antiviral responses, thus establishing this fungus as a model for the study of host-virus interactions.
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Affiliation(s)
- Shinji Honda
- Faculty of Medical Sciences, University of Fukui, Fukui, 910-1193, Japan
| | - Ana Eusebio-Cope
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Shuhei Miyashita
- Graduate School of Agricultural Science, Tohoku University, 468-1, Aramaki-Aza- Aoba, Sendai, 980-0845, Japan
| | - Ayumi Yokoyama
- Faculty of Medical Sciences, University of Fukui, Fukui, 910-1193, Japan
| | - Annisa Aulia
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Sabitree Shahi
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Hideki Kondo
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan
| | - Nobuhiro Suzuki
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, 710-0046, Japan.
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8
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The critical impacts of small RNA biogenesis proteins on aging, longevity and age-related diseases. Ageing Res Rev 2020; 62:101087. [PMID: 32497728 DOI: 10.1016/j.arr.2020.101087] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 04/01/2020] [Accepted: 05/11/2020] [Indexed: 12/13/2022]
Abstract
Small RNAs and enzymes that provide their biogenesis and functioning are involved in the organism development and coordination of biological processes, including metabolism, maintaining genome integrity, immune and stress responses. In this review, we focused on the role of small RNA biogenesis proteins in determining the aging and longevity of animals and human. A number of studies have revealed that changes in expression profiles of key enzymes, in particular proteins of the Drosha, Dicer and Argonaute families, are associated with the aging process, as well as with some age-related diseases and progeroid syndromes. Down-regulation of small RNA biogenesis proteins leads to global alterations in the expression of regulatory RNAs, disruption of key molecular, cellular and systemic processes, which leads to a lifespan shortening. In contrast, overexpression of Dicer prolongs lifespan and improves cellular defense. Additionally, the role of small RNA biogenesis proteins in the pathogenesis of age-related diseases, including cancer, inflammaging, neurodegeneration, cardiovascular, metabolic and immune disorders, has been conclusively evidenced. Recent advances in biomedicine allow using these proteins as diagnostic and prognostic biomarkers and therapeutic targets.
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9
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Gutbrod MJ, Martienssen RA. Conserved chromosomal functions of RNA interference. Nat Rev Genet 2020; 21:311-331. [PMID: 32051563 DOI: 10.1038/s41576-019-0203-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/26/2019] [Indexed: 12/21/2022]
Abstract
RNA interference (RNAi), a cellular process through which small RNAs target and regulate complementary RNA transcripts, has well-characterized roles in post-transcriptional gene regulation and transposon repression. Recent studies have revealed additional conserved roles for RNAi proteins, such as Argonaute and Dicer, in chromosome function. By guiding chromatin modification, RNAi components promote chromosome segregation during both mitosis and meiosis and regulate chromosomal and genomic dosage response. Small RNAs and the RNAi machinery also participate in the resolution of DNA damage. Interestingly, many of these lesser-studied functions seem to be more strongly conserved across eukaryotes than are well-characterized functions such as the processing of microRNAs. These findings have implications for the evolution of RNAi since the last eukaryotic common ancestor, and they provide a more complete view of the functions of RNAi.
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Affiliation(s)
- Michael J Gutbrod
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Robert A Martienssen
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. .,Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
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10
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Bhattacharjee S, Roche B, Martienssen RA. RNA-induced initiation of transcriptional silencing (RITS) complex structure and function. RNA Biol 2019; 16:1133-1146. [PMID: 31213126 DOI: 10.1080/15476286.2019.1621624] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Heterochromatic regions of the genome are epigenetically regulated to maintain a heritable '"silent state"'. In fission yeast and other organisms, epigenetic silencing is guided by nascent transcripts, which are targeted by the RNA interference pathway. The key effector complex of the RNA interference pathway consists of small interfering RNA molecules (siRNAs) associated with Argonaute, assembled into the RNA-induced transcriptional silencing (RITS) complex. This review focuses on our current understanding of how RITS promotes heterochromatin formation, and in particular on the role of Argonaute-containing complexes in many other functions such as quelling, release of RNA polymerases, cellular quiescence and genome defense.
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Affiliation(s)
- Sonali Bhattacharjee
- a Cold Spring Harbor Laboratory, Howard Hughes Medical Institute , Cold Spring Harbor , NY , USA
| | - Benjamin Roche
- a Cold Spring Harbor Laboratory, Howard Hughes Medical Institute , Cold Spring Harbor , NY , USA
| | - Robert A Martienssen
- a Cold Spring Harbor Laboratory, Howard Hughes Medical Institute , Cold Spring Harbor , NY , USA
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11
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Yang B, Xu X, Russell L, Sullenberger MT, Yanowitz JL, Maine EM. A DNA repair protein and histone methyltransferase interact to promote genome stability in the Caenorhabditis elegans germ line. PLoS Genet 2019; 15:e1007992. [PMID: 30794539 PMCID: PMC6402707 DOI: 10.1371/journal.pgen.1007992] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 03/06/2019] [Accepted: 01/28/2019] [Indexed: 12/29/2022] Open
Abstract
Histone modifications regulate gene expression and chromosomal events, yet how histone-modifying enzymes are targeted is poorly understood. Here we report that a conserved DNA repair protein, SMRC-1, associates with MET-2, the C. elegans histone methyltransferase responsible for H3K9me1 and me2 deposition. We used molecular, genetic, and biochemical methods to investigate the biological role of SMRC-1 and to explore its relationship with MET-2. SMRC-1, like its mammalian ortholog SMARCAL1, provides protection from DNA replication stress. SMRC-1 limits accumulation of DNA damage and promotes germline and embryonic viability. MET-2 and SMRC-1 localize to mitotic and meiotic germline nuclei, and SMRC-1 promotes an increase in MET-2 abundance in mitotic germline nuclei upon replication stress. In the absence of SMRC-1, germline H3K9me2 generally decreases after multiple generations at high culture temperature. Genetic data are consistent with MET-2 and SMRC-1 functioning together to limit replication stress in the germ line and in parallel to promote other germline processes. We hypothesize that loss of SMRC-1 activity causes chronic replication stress, in part because of insufficient recruitment of MET-2 to nuclei.
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Affiliation(s)
- Bing Yang
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Xia Xu
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
| | - Logan Russell
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | | | - Judith L. Yanowitz
- Department of Obstetrics, Gynecology, and Reproductive Sciences, Magee-Womens Research Institute, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Eleanor M. Maine
- Department of Biology, Syracuse University, Syracuse, New York, United States of America
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12
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Michelini F, Jalihal AP, Francia S, Meers C, Neeb ZT, Rossiello F, Gioia U, Aguado J, Jones-Weinert C, Luke B, Biamonti G, Nowacki M, Storici F, Carninci P, Walter NG, d'Adda di Fagagna F. From "Cellular" RNA to "Smart" RNA: Multiple Roles of RNA in Genome Stability and Beyond. Chem Rev 2018; 118:4365-4403. [PMID: 29600857 DOI: 10.1021/acs.chemrev.7b00487] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Coding for proteins has been considered the main function of RNA since the "central dogma" of biology was proposed. The discovery of noncoding transcripts shed light on additional roles of RNA, ranging from the support of polypeptide synthesis, to the assembly of subnuclear structures, to gene expression modulation. Cellular RNA has therefore been recognized as a central player in often unanticipated biological processes, including genomic stability. This ever-expanding list of functions inspired us to think of RNA as a "smart" phone, which has replaced the older obsolete "cellular" phone. In this review, we summarize the last two decades of advances in research on the interface between RNA biology and genome stability. We start with an account of the emergence of noncoding RNA, and then we discuss the involvement of RNA in DNA damage signaling and repair, telomere maintenance, and genomic rearrangements. We continue with the depiction of single-molecule RNA detection techniques, and we conclude by illustrating the possibilities of RNA modulation in hopes of creating or improving new therapies. The widespread biological functions of RNA have made this molecule a reoccurring theme in basic and translational research, warranting it the transcendence from classically studied "cellular" RNA to "smart" RNA.
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Affiliation(s)
- Flavia Michelini
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy
| | - Ameya P Jalihal
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Sofia Francia
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy.,Istituto di Genetica Molecolare , CNR - Consiglio Nazionale delle Ricerche , Pavia , 27100 , Italy
| | - Chance Meers
- School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Zachary T Neeb
- Institute of Cell Biology , University of Bern , Baltzerstrasse 4 , 3012 Bern , Switzerland
| | | | - Ubaldo Gioia
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy
| | - Julio Aguado
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy
| | | | - Brian Luke
- Institute of Developmental Biology and Neurobiology , Johannes Gutenberg University , 55099 Mainz , Germany.,Institute of Molecular Biology (IMB) , 55128 Mainz , Germany
| | - Giuseppe Biamonti
- Istituto di Genetica Molecolare , CNR - Consiglio Nazionale delle Ricerche , Pavia , 27100 , Italy
| | - Mariusz Nowacki
- Institute of Cell Biology , University of Bern , Baltzerstrasse 4 , 3012 Bern , Switzerland
| | - Francesca Storici
- School of Biological Sciences , Georgia Institute of Technology , Atlanta , Georgia 30332 , United States
| | - Piero Carninci
- RIKEN Center for Life Science Technologies , 1-7-22 Suehiro-cho, Tsurumi-ku , Yokohama City , Kanagawa 230-0045 , Japan
| | - Nils G Walter
- Single Molecule Analysis Group and Center for RNA Biomedicine, Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109-1055 , United States
| | - Fabrizio d'Adda di Fagagna
- IFOM - The FIRC Institute of Molecular Oncology , Milan , 20139 , Italy.,Istituto di Genetica Molecolare , CNR - Consiglio Nazionale delle Ricerche , Pavia , 27100 , Italy
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13
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D'Alessandro G, d'Adda di Fagagna F. Transcription and DNA Damage: Holding Hands or Crossing Swords? J Mol Biol 2017; 429:3215-3229. [DOI: 10.1016/j.jmb.2016.11.002] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 11/02/2016] [Accepted: 11/03/2016] [Indexed: 01/12/2023]
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14
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Abstract
In modern molecular biology, RNA has emerged as a versatile macromolecule capable of mediating an astonishing number of biological functions beyond its role as a transient messenger of genetic information. The recent discovery and functional analyses of new classes of noncoding RNAs (ncRNAs) have revealed their widespread use in many pathways, including several in the nucleus. This Review focuses on the mechanisms by which nuclear ncRNAs directly contribute to the maintenance of genome stability. We discuss how ncRNAs inhibit spurious recombination among repetitive DNA elements, repress mobilization of transposable elements (TEs), template or bridge DNA double-strand breaks (DSBs) during repair, and direct developmentally regulated genome rearrangements in some ciliates. These studies reveal an unexpected repertoire of mechanisms by which ncRNAs contribute to genome stability and even potentially fuel evolution by acting as templates for genome modification.
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15
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Abstract
RNA interference (RNAi) is a mechanism conserved in eukaryotes, including fungi, that represses gene expression by means of small noncoding RNAs (sRNAs) of about 20 to 30 nucleotides. Its discovery is one of the most important scientific breakthroughs of the past 20 years, and it has revolutionized our perception of the functioning of the cell. Initially described and characterized in Neurospora crassa, the RNAi is widespread in fungi, suggesting that it plays important functions in the fungal kingdom. Several RNAi-related mechanisms for maintenance of genome integrity, particularly protection against exogenous nucleic acids such as mobile elements, have been described in several fungi, suggesting that this is the main function of RNAi in the fungal kingdom. However, an increasing number of fungal sRNAs with regulatory functions generated by specific RNAi pathways have been identified. Several mechanistic aspects of the biogenesis of these sRNAs are known, but their function in fungal development and physiology is scarce, except for remarkable examples such as Mucor circinelloides, in which specific sRNAs clearly regulate responses to environmental and endogenous signals. Despite the retention of RNAi in most species, some fungal groups and species lack an active RNAi mechanism, suggesting that its loss may provide some selective advantage. This article summarizes the current understanding of RNAi functions in the fungal kingdom.
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16
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Torres-Martínez S, Ruiz-Vázquez RM. The RNAi Universe in Fungi: A Varied Landscape of Small RNAs and Biological Functions. Annu Rev Microbiol 2017; 71:371-391. [PMID: 28657888 DOI: 10.1146/annurev-micro-090816-093352] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA interference (RNAi) is a conserved eukaryotic mechanism that uses small RNA molecules to suppress gene expression through sequence-specific messenger RNA degradation, translational repression, or transcriptional inhibition. In filamentous fungi, the protective function of RNAi in the maintenance of genome integrity is well known. However, knowledge of the regulatory role of RNAi in fungi has had to wait until the recent identification of different endogenous small RNA classes, which are generated by distinct RNAi pathways. In addition, RNAi research on new fungal models has uncovered the role of small RNAs and RNAi pathways in the regulation of diverse biological functions. In this review, we give an up-to-date overview of the different classes of small RNAs and RNAi pathways in fungi and their roles in the defense of genome integrity and regulation of fungal physiology and development, as well as in the interaction of fungi with biotic and abiotic environments.
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17
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Liu X, Dang Y, Matsu-Ura T, He Y, He Q, Hong CI, Liu Y. DNA Replication Is Required for Circadian Clock Function by Regulating Rhythmic Nucleosome Composition. Mol Cell 2017. [PMID: 28648778 DOI: 10.1016/j.molcel.2017.05.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Although the coupling between circadian and cell cycles allows circadian clocks to gate cell division and DNA replication in many organisms, circadian clocks were thought to function independently of cell cycle. Here, we show that DNA replication is required for circadian clock function in Neurospora. Genetic and pharmacological inhibition of DNA replication abolished both overt and molecular rhythmicities by repressing frequency (frq) gene transcription. DNA replication is essential for the rhythmic changes of nucleosome composition at the frq promoter. The FACT complex, known to be involved in histone disassembly/reassembly, is required for clock function and is recruited to the frq promoter in a replication-dependent manner to promote replacement of histone H2A.Z by H2A. Finally, deletion of H2A.Z uncoupled the dependence of the circadian clock on DNA replication. Together, these results establish circadian clock and cell cycle as interdependent coupled oscillators and identify DNA replication as a critical process in the circadian mechanism.
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Affiliation(s)
- Xiao Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA
| | - Yunkun Dang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA
| | - Toru Matsu-Ura
- Department of Molecular and Cellular Physiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Yubo He
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA; Department of Biochemistry and Cell Biology, McMurtry College, Rice University, Houston, TX 77005, USA
| | - Qun He
- State Key Laboratory of Agrobiotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Christian I Hong
- Department of Molecular and Cellular Physiology, University of Cincinnati, Cincinnati, OH 45267, USA
| | - Yi Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9040, USA.
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18
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Merk K, Breinig M, Böttcher R, Krebs S, Blum H, Boutros M, Förstemann K. Splicing stimulates siRNA formation at Drosophila DNA double-strand breaks. PLoS Genet 2017. [PMID: 28628606 PMCID: PMC5495518 DOI: 10.1371/journal.pgen.1006861] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
DNA double-strand breaks trigger the production of locus-derived siRNAs in fruit flies, human cells and plants. At least in flies, their biogenesis depends on active transcription running towards the break. Since siRNAs derive from a double-stranded RNA precursor, a major question is how broken DNA ends can generate matching sense and antisense transcripts. We performed a genome-wide RNAi-screen in cultured Drosophila cells, which revealed that in addition to DNA repair factors, many spliceosome components are required for efficient siRNA generation. We validated this observation through site-specific DNA cleavage with CRISPR-cas9 followed by deep sequencing of small RNAs. DNA breaks in intron-less genes or upstream of a gene's first intron did not efficiently trigger siRNA production. When DNA double-strand breaks were induced downstream of an intron, however, this led to robust siRNA generation. Furthermore, a downstream break slowed down splicing of the upstream intron and a detailed analysis of siRNA coverage at the targeted locus revealed that unspliced pre-mRNA contributes the sense strand to the siRNA precursor. Since splicing factors are stimulating the response but unspliced transcripts are entering the siRNA biogenesis, the spliceosome is apparently stalled in a pre-catalytic state and serves as a signaling hub. We conclude that convergent transcription at DNA breaks is stimulated by a splicing dependent control process. The resulting double-stranded RNA is converted into siRNAs that instruct the degradation of cognate mRNAs. In addition to a potential role in DNA repair, the break-induced transcription may thus be a means to cull improper RNAs from the transcriptome of Drosophila melanogaster. Since the splicing factors identified in our screen also stimulated siRNA production from high copy transgenes, it is possible that this surveillance mechanism serves in genome defense beyond DNA double-strand breaks.
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Affiliation(s)
- Karin Merk
- Gene Center and Dept. of Biochemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Marco Breinig
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, Germany
| | - Romy Böttcher
- Gene Center and Dept. of Biochemistry, Ludwig-Maximilians-Universität München, München, Germany
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, München, Germany
| | - Michael Boutros
- Division Signaling and Functional Genomics, German Cancer Research Center (DKFZ) and Heidelberg University, Im Neuenheimer Feld 580, Heidelberg, Germany
| | - Klaus Förstemann
- Gene Center and Dept. of Biochemistry, Ludwig-Maximilians-Universität München, München, Germany
- * E-mail:
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19
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Villalobos-Escobedo JM, Herrera-Estrella A, Carreras-Villaseñor N. The interaction of fungi with the environment orchestrated by RNAi. Mycologia 2017; 108:556-71. [DOI: 10.3852/15-246] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 01/07/2016] [Indexed: 11/10/2022]
Affiliation(s)
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad. Cinvestav Campus Guanajuato. Km 9.6 Libramiento Norte, carretera Irapuato-León. 36821 Irapuato, Guanajuato, Mexico
| | - Nohemí Carreras-Villaseñor
- StelaGenomics México, S de RL de CV, Av. Camino Real de Guanajuato S/N, 36821 Irapuato, Guanajuato, Mexico
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20
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Roche B, Arcangioli B, Martienssen RA. RNA interference is essential for cellular quiescence. Science 2016; 354:science.aah5651. [PMID: 27738016 DOI: 10.1126/science.aah5651] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/27/2016] [Indexed: 12/19/2022]
Abstract
Quiescent cells play a predominant role in most organisms. Here we identify RNA interference (RNAi) as a major requirement for quiescence (G0 phase of the cell cycle) in Schizosaccharomyces pombe RNAi mutants lose viability at G0 entry and are unable to maintain long-term quiescence. We identified suppressors of G0 defects in cells lacking Dicer (dcr1Δ), which mapped to genes involved in chromosome segregation, RNA polymerase-associated factors, and heterochromatin formation. We propose a model in which RNAi promotes the release of RNA polymerase in cycling and quiescent cells: (i) RNA polymerase II release mediates heterochromatin formation at centromeres, allowing proper chromosome segregation during mitotic growth and G0 entry, and (ii) RNA polymerase I release prevents heterochromatin formation at ribosomal DNA during quiescence maintenance. Our model may account for the codependency of RNAi and histone H3 lysine 9 methylation throughout eukaryotic evolution.
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Affiliation(s)
- B Roche
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - B Arcangioli
- Dynamics of the Genome Unit, Department of Genomes and Genetics, Institut Pasteur, UMR3525, 25-28 rue du Docteur Roux, Paris 75015, France
| | - R A Martienssen
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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21
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Gvozdev VA, Stolyarenko AD, Klenov MS. Functions of piRNAs and the Piwi protein in Drosophila. RUSS J GENET+ 2015. [DOI: 10.1134/s1022795415040055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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22
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Abstract
Repetitive DNA loci are a major source for the production of eukaryotic small RNAs, but how these small RNAs are produced is not clear. Yang et al. show that DNA tandem repeats and double-strand breaks are necessary and, when both are present, sufficient to trigger gene silencing and siRNA production. In addition to siRNA production, the quelling pathway also maintains tandem repeats by regulating homologous recombination. RNAi is a conserved genome defense mechanism in eukaryotes that protects against deleterious effects of transposons and viral invasion. Repetitive DNA loci are a major source for the production of eukaryotic small RNAs, but how these small RNAs are produced is not clear. Quelling in Neurospora is one of the first known RNAi-related phenomena and is triggered by the presence of multiple copies of transgenes. Here we showed that DNA tandem repeats and double-strand breaks are necessary and, when both are present, sufficient to trigger gene silencing and siRNA production. Introduction of a site-specific double-strand break or DNA fragile site resulted in homologous recombination of repetitive sequences, which is required for gene silencing. In addition to siRNA production, the quelling pathway also maintains tandem repeats by regulating homologous recombination. Our study identified the mechanistic trigger for siRNA production from repetitive DNA and established a role for siRNA in maintaining genome stability.
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Affiliation(s)
- Qiuying Yang
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Qiaohong Anne Ye
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
| | - Yi Liu
- Department of Physiology, The University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA
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23
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Mikhaleva EA, Yakushev EY, Stolyarenko AD, Klenov MS, Rozovsky YM, Gvozdev VA. Piwi protein as a nucleolus visitor in Drosophila melanogaster. Mol Biol 2015. [DOI: 10.1134/s0026893315010100] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Castel SE, Ren J, Bhattacharjee S, Chang AY, Sánchez M, Valbuena A, Antequera F, Martienssen RA. Dicer promotes transcription termination at sites of replication stress to maintain genome stability. Cell 2014; 159:572-83. [PMID: 25417108 DOI: 10.1016/j.cell.2014.09.031] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 07/29/2014] [Accepted: 09/17/2014] [Indexed: 12/12/2022]
Abstract
Nuclear RNAi is an important regulator of transcription and epigenetic modification, but the underlying mechanisms remain elusive. Using a genome-wide approach in the fission yeast S. pombe, we have found that Dcr1, but not other components of the canonical RNAi pathway, promotes the release of Pol II from the 3? end of highly transcribed genes, and, surprisingly, from antisense transcription of rRNA and tRNA genes, which are normally transcribed by Pol I and Pol III. These Dcr1-terminated loci correspond to sites of replication stress and DNA damage, likely resulting from transcription-replication collisions. At the rDNA loci, release of Pol II facilitates DNA replication and prevents homologous recombination, which would otherwise lead to loss of rDNA repeats especially during meiosis. Our results reveal a novel role for Dcr1-mediated transcription termination in genome maintenance and may account for widespread regulation of genome stability by nuclear RNAi in higher eukaryotes.
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Affiliation(s)
- Stephane E Castel
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Jie Ren
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Sonali Bhattacharjee
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - An-Yun Chang
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY 11794, USA
| | - Mar Sánchez
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca, Salamanca 37007, Spain
| | - Alberto Valbuena
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca, Salamanca 37007, Spain
| | - Francisco Antequera
- Instituto de Biología Funcional y Genómica, CSIC/Universidad de Salamanca, Salamanca 37007, Spain
| | - Robert A Martienssen
- Howard Hughes Medical Institute-Gordon and Betty Moore Foundation, Watson School of Biological Sciences Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY 11794, USA.
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25
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Efficient detection of unpaired DNA requires a member of the rad54-like family of homologous recombination proteins. Genetics 2014; 198:895-904. [PMID: 25146971 DOI: 10.1534/genetics.114.168187] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Meiotic silencing by unpaired DNA (MSUD) is a process that detects unpaired regions between homologous chromosomes and silences them for the duration of sexual development. While the phenomenon of MSUD is well recognized, the process that detects unpaired DNA is poorly understood. In this report, we provide two lines of evidence linking unpaired DNA detection to a physical search for DNA homology. First, we have found that a putative SNF2-family protein (SAD-6) is required for efficient MSUD in Neurospora crassa. SAD-6 is closely related to Rad54, a protein known to facilitate key steps in the repair of double-strand breaks by homologous recombination. Second, we have successfully masked unpaired DNA by placing identical transgenes at slightly different locations on homologous chromosomes. This masking falls apart when the distance between the transgenes is increased. We propose a model where unpaired DNA detection during MSUD is achieved through a spatially constrained search for DNA homology. The identity of SAD-6 as a Rad54 paralog suggests that this process may be similar to the searching mechanism used during homologous recombination.
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26
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Abstract
RNAi is conserved and has been studied in a broad cross-section of the fungal kingdom, including Neurospora crassa, Schizosaccharomyces pombe, Cryptococcus neoformans, and Mucor circinelloides. And yet well known species, including the model yeast Saccharomyces cerevisiae and the plant pathogen Ustilago maydis, have lost RNAi, providing insights and opportunities to illuminate benefits conferred both by the presence of RNAi and its loss. Some of the earliest studies of RNAi were conducted in Neurospora, contemporaneously with the elucidation of RNAi in Caenorhabditis elegans. RNAi is a key epigenetic mechanism for maintaining genomic stability and integrity, as well as to defend against viruses, and given its ubiquity was likely present in the last eukaryotic common ancestor. In this review, we describe the diversity of RNAi mechanisms found in the fungi, highlighting recent work in Neurospora, S. pombe, and Cryptococcus. Finally, we consider frequent, independent losses of RNAi in diverse fungal lineages and both review and speculate on evolutionary forces that may drive the losses or result therefrom.
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27
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Zhang Z, Yang Q, Sun G, Chen S, He Q, Li S, Liu Y. Histone H3K56 acetylation is required for quelling-induced small RNA production through its role in homologous recombination. J Biol Chem 2014; 289:9365-71. [PMID: 24554705 DOI: 10.1074/jbc.m113.528521] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Quelling and DNA damage-induced small RNA (qiRNA) production are RNA interference (RNAi)-related phenomenon from repetitive genomic loci in Neurospora. We have recently proposed that homologous recombination from repetitive DNA loci allows the RNAi pathway to recognize repetitive DNA to produce small RNA. However, the mechanistic detail of this pathway remains largely unclear. By systematically screening the Neurospora knock-out library, we identified RTT109 as a novel component required for small RNA production. RTT109 is a histone acetyltransferase for histone H3 lysine 56 (H3K56) and H3K56 acetylation is essential for the small RNA biogenesis pathway. Furthermore, we showed that RTT109 is required for homologous recombination and H3K56Ac is enriched around double strand break, which overlaps with RAD51 binding. Taken together, our results suggest that H3K56 acetylation is required for small RNA production through its role in homologous recombination.
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Affiliation(s)
- Zhenyu Zhang
- From the Department of Physiology, The University of Texas Southwestern Medical Center at Dallas, Dallas, Texas 75390
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28
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Weiberg A, Wang M, Bellinger M, Jin H. Small RNAs: a new paradigm in plant-microbe interactions. ANNUAL REVIEW OF PHYTOPATHOLOGY 2014; 52:495-516. [PMID: 25090478 DOI: 10.1146/annurev-phyto-102313-045933] [Citation(s) in RCA: 117] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
A never-ending arms race drives coevolution between pathogens and hosts. In plants, pathogen attacks invoke multiple layers of host immune responses. Many pathogens deliver effector proteins into host cells to suppress host immunity, and many plants have evolved resistance proteins to recognize effectors and trigger robust resistance. Here, we discuss findings on noncoding small RNAs (sRNAs) from plants and pathogens, which regulate host immunity and pathogen virulence. Recent discoveries have unveiled the role of noncoding sRNAs from eukaryotic pathogens and bacteria in pathogenicity in both plant and animal hosts. The discovery of fungal sRNAs that are delivered into host cells to suppress plant immunity added sRNAs to the list of pathogen effectors. Similar to protein effector genes, many of these sRNAs are generated from transposable element (TE) regions, which are likely to contribute to rapidly evolving virulence and host adaptation. We also discuss RNA silencing that occurs between organisms.
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Affiliation(s)
- Arne Weiberg
- Department of Plant Pathology and Microbiology, University of California, Riverside, California 92521;
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29
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Dumesic PA, Madhani HD. Recognizing the enemy within: licensing RNA-guided genome defense. Trends Biochem Sci 2013; 39:25-34. [PMID: 24280023 DOI: 10.1016/j.tibs.2013.10.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 10/26/2013] [Accepted: 10/28/2013] [Indexed: 02/06/2023]
Abstract
How do cells distinguish normal genes from transposons? Although much has been learned about RNAi-related RNA silencing pathways responsible for genome defense, this fundamental question remains. The literature points to several classes of mechanisms. In some cases, double-stranded RNA (dsRNA) structures produced by transposon inverted repeats or antisense integration trigger endogenous small interfering RNA (siRNA) biogenesis. In other instances, DNA features associated with transposons--such as their unusual copy number, chromosomal arrangement, and/or chromatin environment--license RNA silencing. Finally, recent studies have identified improper transcript processing events, such as stalled pre-mRNA splicing, as signals for siRNA production. Thus, the suboptimal gene expression properties of selfish elements can enable their identification by RNA silencing pathways.
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Affiliation(s)
- Phillip A Dumesic
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA.
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30
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Nicolás FE, Ruiz-Vázquez RM. Functional diversity of RNAi-associated sRNAs in fungi. Int J Mol Sci 2013; 14:15348-60. [PMID: 23887655 PMCID: PMC3759863 DOI: 10.3390/ijms140815348] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Revised: 07/05/2013] [Accepted: 07/09/2013] [Indexed: 12/21/2022] Open
Abstract
Yeast and filamentous fungi have been essential model systems for unveiling the secrets of RNA interference (RNAi). Research on these organisms has contributed to identifying general mechanisms and conserved eukaryotic RNAi machinery that can be found from fungi to mammals. The development of deep sequencing technologies has brought on the last wave of studies on RNAi in fungi, which has been focused on the identification of new types of functional small RNAs (sRNAs). These studies have discovered an unexpected diversity of sRNA, biogenesis pathways and new functions that are the focus of this review.
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Affiliation(s)
- Francisco E. Nicolás
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia 30100, Spain; E-Mail:
- Regional Campus of International Excellence “Campus Mare Nostrum”, Murcia 30100, Spain
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +34-868-887135; Fax: +34-868-883963
| | - Rosa M. Ruiz-Vázquez
- Department of Genetics and Microbiology, Faculty of Biology, University of Murcia, Murcia 30100, Spain; E-Mail:
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