1
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Pliota P, Marvanova H, Koreshova A, Kaufman Y, Tikanova P, Krogull D, Hagmüller A, Widen SA, Handler D, Gokcezade J, Duchek P, Brennecke J, Ben-David E, Burga A. Selfish conflict underlies RNA-mediated parent-of-origin effects. Nature 2024; 628:122-129. [PMID: 38448590 PMCID: PMC10990930 DOI: 10.1038/s41586-024-07155-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 02/02/2024] [Indexed: 03/08/2024]
Abstract
Genomic imprinting-the non-equivalence of maternal and paternal genomes-is a critical process that has evolved independently in many plant and mammalian species1,2. According to kinship theory, imprinting is the inevitable consequence of conflictive selective forces acting on differentially expressed parental alleles3,4. Yet, how these epigenetic differences evolve in the first place is poorly understood3,5,6. Here we report the identification and molecular dissection of a parent-of-origin effect on gene expression that might help to clarify this fundamental question. Toxin-antidote elements (TAs) are selfish elements that spread in populations by poisoning non-carrier individuals7-9. In reciprocal crosses between two Caenorhabditis tropicalis wild isolates, we found that the slow-1/grow-1 TA is specifically inactive when paternally inherited. This parent-of-origin effect stems from transcriptional repression of the slow-1 toxin by the PIWI-interacting RNA (piRNA) host defence pathway. The repression requires PIWI Argonaute and SET-32 histone methyltransferase activities and is transgenerationally inherited via small RNAs. Remarkably, when slow-1/grow-1 is maternally inherited, slow-1 repression is halted by a translation-independent role of its maternal mRNA. That is, slow-1 transcripts loaded into eggs-but not SLOW-1 protein-are necessary and sufficient to counteract piRNA-mediated repression. Our findings show that parent-of-origin effects can evolve by co-option of the piRNA pathway and hinder the spread of selfish genes that require sex for their propagation.
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Affiliation(s)
- Pinelopi Pliota
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Hana Marvanova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Alevtina Koreshova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Yotam Kaufman
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Polina Tikanova
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Daniel Krogull
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
| | - Andreas Hagmüller
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Sonya A Widen
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Dominik Handler
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Joseph Gokcezade
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Peter Duchek
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Julius Brennecke
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Eyal Ben-David
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Hebrew University of Jerusalem, Jerusalem, Israel
- Illumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA
| | - Alejandro Burga
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
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2
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Chen S, Phillips CM. HRDE-2 drives small RNA specificity for the nuclear Argonaute protein HRDE-1. Nat Commun 2024; 15:957. [PMID: 38302462 PMCID: PMC10834429 DOI: 10.1038/s41467-024-45245-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 01/18/2024] [Indexed: 02/03/2024] Open
Abstract
RNA interference (RNAi) is a conserved gene silencing process that exists in diverse organisms to protect genome integrity and regulate gene expression. In C. elegans, the majority of RNAi pathway proteins localize to perinuclear, phase-separated germ granules, which are comprised of sub-domains referred to as P granules, Mutator foci, Z granules, and SIMR foci. However, the protein components and function of the newly discovered SIMR foci are unknown. Here we demonstrate that HRDE-2 localizes to SIMR foci and interacts with the germline nuclear Argonaute HRDE-1 in its small RNA unbound state. In the absence of HRDE-2, HRDE-1 exclusively loads CSR-class 22G-RNAs rather than WAGO-class 22G-RNAs, resulting in inappropriate H3K9me3 deposition on CSR-target genes. Thus, our study demonstrates that the recruitment of unloaded HRDE-1 to germ granules, mediated by HRDE-2, is critical to ensure that the correct small RNAs are used to guide nuclear RNA silencing in the C. elegans germline.
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Affiliation(s)
- Shihui Chen
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA
| | - Carolyn M Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089, USA.
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3
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Gajic Z, Kaur D, Ni J, Zhu Z, Zhebrun A, Gajic M, Kim M, Hong J, Priyadarshini M, Frøkjær-Jensen C, Gu S. Target-dependent suppression of siRNA production modulates the levels of endogenous siRNAs in the Caenorhabditis elegans germline. Development 2022; 149:dev200692. [PMID: 35876680 PMCID: PMC9481970 DOI: 10.1242/dev.200692] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/14/2022] [Indexed: 08/24/2023]
Abstract
Despite the prominent role of endo-siRNAs in transposon silencing, their expression is not limited to these 'nonself' DNA elements. Transcripts of protein-coding genes ('self' DNA) in some cases also produce endo-siRNAs in yeast, plants and animals. How cells distinguish these two populations of siRNAs to prevent unwanted silencing of active genes in animals is not well understood. To address this question, we inserted various self-gene or gfp fragments into an LTR retrotransposon that produces abundant siRNAs and examined the propensity of these gene fragments to produce ectopic siRNAs in the Caenorhabditis elegans germline. We found that fragments of germline genes are generally protected from production of ectopic siRNAs. This phenomenon, which we termed 'target-directed suppression of siRNA production' (or siRNA suppression), is dependent on the germline expression of target mRNA and requires germline P-granule components. We found that siRNA suppression can also occur in naturally produced endo-siRNAs. We suggest that siRNA suppression plays an important role in regulating siRNA expression and preventing self-genes from aberrant epigenetic silencing. This article has an associated 'The people behind the papers' interview.
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Affiliation(s)
- Zoran Gajic
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Diljeet Kaur
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Julie Ni
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Zhaorong Zhu
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Anna Zhebrun
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Maria Gajic
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Matthew Kim
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Julia Hong
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Monika Priyadarshini
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955–6900, Kingdom of Saudi Arabia
| | - Christian Frøkjær-Jensen
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955–6900, Kingdom of Saudi Arabia
| | - Sam Gu
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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4
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Davis MB, Jash E, Chawla B, Haines RA, Tushman LE, Troll R, Csankovszki G. Dual roles for nuclear RNAi Argonautes in Caenorhabditis elegans dosage compensation. Genetics 2022; 221:6540857. [PMID: 35234908 PMCID: PMC9071528 DOI: 10.1093/genetics/iyac033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/21/2022] [Indexed: 11/14/2022] Open
Abstract
Dosage compensation involves chromosome-wide gene regulatory mechanisms which impact higher order chromatin structure and are crucial for organismal health. Using a genetic approach, we identified Argonaute genes which promote dosage compensation in Caenorhabditis elegans. Dosage compensation in C. elegans hermaphrodites is initiated by the silencing of xol-1 and subsequent activation of the dosage compensation complex which binds to both hermaphrodite X chromosomes and reduces transcriptional output by half. A hallmark phenotype of dosage compensation mutants is decondensation of the X chromosomes. We characterized this phenotype in Argonaute mutants using X chromosome paint probes and fluorescence microscopy. We found that while nuclear Argonaute mutants hrde-1 and nrde-3, as well as mutants for the piRNA Argonaute prg-1, exhibit derepression of xol-1 transcripts, they also affect X chromosome condensation in a xol-1-independent manner. We also characterized the physiological contribution of Argonaute genes to dosage compensation using genetic assays and found that hrde-1 and nrde-3 contribute to healthy dosage compensation both upstream and downstream of xol-1.
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Affiliation(s)
- Michael B Davis
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Eshna Jash
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bahaar Chawla
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Rebecca A Haines
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lillian E Tushman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Ryan Troll
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Györgyi Csankovszki
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA,Corresponding author: Department of Molecular, Cellular, and Developmental Biology, University of Michigan, 1105 N. University Ave, Ann Arbor, MI 48109-1085, USA.
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5
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Seroussi U, Li C, Sundby AE, Lee TL, Claycomb JM, Saltzman AL. Mechanisms of epigenetic regulation by C. elegans nuclear RNA interference pathways. Semin Cell Dev Biol 2021; 127:142-154. [PMID: 34876343 DOI: 10.1016/j.semcdb.2021.11.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/17/2021] [Accepted: 11/17/2021] [Indexed: 01/06/2023]
Abstract
RNA interference (RNAi) is a highly conserved gene regulatory phenomenon whereby Argonaute/small RNA (AGO/sRNA) complexes target transcripts by antisense complementarity to modulate gene expression. While initially appreciated as a cytoplasmic process, RNAi can also occur in the nucleus where AGO/sRNA complexes are recruited to nascent transcripts. Nuclear AGO/sRNA complexes recruit co-factors that regulate transcription by inhibiting RNA Polymerase II, modifying histones, compacting chromatin and, in some organisms, methylating DNA. C. elegans has a longstanding history in unveiling the mechanisms of RNAi and has become an outstanding model to delineate the mechanisms underlying nuclear RNAi. In this review we highlight recent discoveries in the field of nuclear RNAi in C. elegans and the roles of nuclear RNAi in the regulation of gene expression, chromatin organization, genome stability, and transgenerational epigenetic inheritance.
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Affiliation(s)
- Uri Seroussi
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Chengyin Li
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Adam E Sundby
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Tammy L Lee
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
| | - Arneet L Saltzman
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON, Canada.
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6
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Zaghet N, Madsen K, Rossi F, Perez DF, Amendola PG, Demharter S, Pfisterer U, Khodosevich K, Pasini D, Salcini AE. Coordinated maintenance of H3K36/K27 methylation by histone demethylases preserves germ cell identity and immortality. Cell Rep 2021; 37:110050. [PMID: 34818537 PMCID: PMC8640224 DOI: 10.1016/j.celrep.2021.110050] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 09/18/2021] [Accepted: 11/02/2021] [Indexed: 12/01/2022] Open
Abstract
Germ cells have evolved unique mechanisms to ensure the transmission of genetically and nongenetically encoded information, whose alteration compromises germ cell immortality. Chromatin factors play fundamental roles in these mechanisms. H3K36 and H3K27 methyltransferases shape and propagate a pattern of histone methylation essential for C. elegans germ cell maintenance, but the role of respective histone demethylases remains unexplored. Here, we show that jmjd-5 regulates H3K36me2 and H3K27me3 levels, preserves germline immortality, and protects germ cell identity by controlling gene expression. The transcriptional and biological effects of jmjd-5 loss can be hindered by the removal of H3K27demethylases, indicating that H3K36/K27 demethylases act in a transcriptional framework and promote the balance between H3K36 and H3K27 methylation required for germ cell immortality. Furthermore, we find that in wild-type, but not in jmjd-5 mutants, alterations of H3K36 methylation and transcription occur at high temperature, suggesting a role for jmjd-5 in adaptation to environmental changes. jmjd-5 is required for germ cell immortality at high temperature jmjd-5 sustains the expression of germline genes and represses somatic fate Mutations in jmjd-5 result in a global increase of H3K36me2 and H3K27me3 Ablation of H3K27 demethylases counteracts the effects of jmjd-5 mutations
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Affiliation(s)
- Nico Zaghet
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Katrine Madsen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Federico Rossi
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Daniel Fernandez Perez
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy
| | - Pier Giorgio Amendola
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Samuel Demharter
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Ulrich Pfisterer
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Konstantin Khodosevich
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark
| | - Diego Pasini
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Via Adamello 16, 20139 Milan, Italy; Department of Health Sciences, University of Milan, Via A. di Rudini 8, 20142 Milan, Italy
| | - Anna Elisabetta Salcini
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes vej 5, Copenhagen DK-2200, Denmark.
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7
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Burton NO, Greer EL. Multigenerational epigenetic inheritance: Transmitting information across generations. Semin Cell Dev Biol 2021; 127:121-132. [PMID: 34426067 DOI: 10.1016/j.semcdb.2021.08.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 01/07/2023]
Abstract
Inherited epigenetic information has been observed to regulate a variety of complex organismal phenotypes across diverse taxa of life. This continually expanding body of literature suggests that epigenetic inheritance plays a significant, and potentially fundamental, role in inheritance. Despite the important role these types of effects play in biology, the molecular mediators of this non-genetic transmission of information are just now beginning to be deciphered. Here we provide an intellectual framework for interpreting these findings and how they can interact with each other. We also define the different types of mechanisms that have been found to mediate epigenetic inheritance and to regulate whether epigenetic information persists for one or many generations. The field of epigenetic inheritance is entering an exciting phase, in which we are beginning to understand the mechanisms by which non-genetic information is transmitted to, and deciphered by, subsequent generations to maintain essential environmental information without permanently altering the genetic code. A more complete understanding of how and when epigenetic inheritance occurs will advance our understanding of numerous different aspects of biology ranging from how organisms cope with changing environments to human pathologies influenced by a parent's environment.
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Affiliation(s)
- Nicholas O Burton
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK; Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA.
| | - Eric L Greer
- Division of Newborn Medicine, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; Harvard Medical School Initiative for RNA Medicine, Boston, MA 02115, USA.
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8
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Frolows N, Ashe A. Small RNAs and chromatin in the multigenerational epigenetic landscape of Caenorhabditis elegans. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200112. [PMID: 33866817 DOI: 10.1098/rstb.2020.0112] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
For decades, it was thought that the only heritable information transmitted from one individual to another was that encoded in the DNA sequence. However, it has become increasingly clear that this is not the case and that the transmission of molecules from within the cytoplasm of the gamete also plays a significant role in heritability. The roundworm, Caenorhabditis elegans, has emerged as one of the leading model organisms in which to study the mechanisms of transgenerational epigenetic inheritance (TEI). Collaborative efforts over the past few years have revealed that RNA molecules play a critical role in transmitting transgenerational responses, but precisely how they do so is as yet uncertain. In addition, the role of histone modifications in epigenetic inheritance is increasingly apparent, and RNA and histones interact in a way that we do not yet fully understand. Furthermore, both exogenous and endogenous RNA molecules, as well as other environmental triggers, are able to induce heritable epigenetic changes that affect transcription across the genome. In most cases, these epigenetic changes last only for a handful of generations, but occasionally can be maintained much longer: perhaps indefinitely. In this review, we discuss the current understanding of the role of RNA and histones in TEI, as well as making clear the gaps in our knowledge. We also speculate on the evolutionary implications of epigenetic inheritance, particularly in the context of a short-lived, clonally propagating species. This article is part of the theme issue 'How does epigenetics influence the course of evolution?'
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Affiliation(s)
- Natalya Frolows
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia.,CSIRO Health and Biosecurity, Sydney, New South Wales, 2113, Australia
| | - Alyson Ashe
- School of Life and Environmental Sciences, University of Sydney, New South Wales, 2006, Australia
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9
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How do histone modifications contribute to transgenerational epigenetic inheritance in C. elegans? Biochem Soc Trans 2021; 48:1019-1034. [PMID: 32539084 DOI: 10.1042/bst20190944] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/11/2020] [Accepted: 05/14/2020] [Indexed: 12/20/2022]
Abstract
Gene regulatory information can be inherited between generations in a phenomenon termed transgenerational epigenetic inheritance (TEI). While examples of TEI in many animals accumulate, the nematode Caenorhabditis elegans has proven particularly useful in investigating the underlying molecular mechanisms of this phenomenon. In C. elegans and other animals, the modification of histone proteins has emerged as a potential carrier and effector of transgenerational epigenetic information. In this review, we explore the contribution of histone modifications to TEI in C. elegans. We describe the role of repressive histone marks, histone methyltransferases, and associated chromatin factors in heritable gene silencing, and discuss recent developments and unanswered questions in how these factors integrate with other known TEI mechanisms. We also review the transgenerational effects of the manipulation of histone modifications on germline health and longevity.
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10
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Bergthorsson U, Sheeba CJ, Konrad A, Belicard T, Beltran T, Katju V, Sarkies P. Long-term experimental evolution reveals purifying selection on piRNA-mediated control of transposable element expression. BMC Biol 2020; 18:162. [PMID: 33158445 PMCID: PMC7646084 DOI: 10.1186/s12915-020-00897-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 10/13/2020] [Indexed: 11/29/2022] Open
Abstract
Background Transposable elements (TEs) are an almost universal constituent of eukaryotic genomes. In animals, Piwi-interacting small RNAs (piRNAs) and repressive chromatin often play crucial roles in preventing TE transcription and thus restricting TE activity. Nevertheless, TE content varies widely across eukaryotes and the dynamics of TE activity and TE silencing across evolutionary time is poorly understood. Results Here, we used experimentally evolved populations of C. elegans to study the dynamics of TE expression over 409 generations. The experimental populations were evolved at population sizes of 1, 10 and 100 individuals to manipulate the efficiency of natural selection versus genetic drift. We demonstrate increased TE expression relative to the ancestral population, with the largest increases occurring in the smallest populations. We show that the transcriptional activation of TEs within active regions of the genome is associated with failure of piRNA-mediated silencing, whilst desilenced TEs in repressed chromatin domains retain small RNAs. Additionally, we find that the sequence context of the surrounding region influences the propensity of TEs to lose silencing through failure of small RNA-mediated silencing. Conclusions Our results show that natural selection in C. elegans is responsible for maintaining low levels of TE expression, and provide new insights into the epigenomic features responsible.
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Affiliation(s)
- Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77845, USA
| | - Caroline J Sheeba
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Anke Konrad
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77845, USA.,Present Address: Intituto Gulbenkian de Ciencia, Rua da Quinta Grande, 6, 2780-156, Oeiras, Portugal
| | - Tony Belicard
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Toni Beltran
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK.,Institute of Clinical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK.,Present Address: Centre for Genomic Regulation, PRBB Building, 08003, Barcelona, Spain
| | - Vaishali Katju
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, 77845, USA.
| | - Peter Sarkies
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK. .,Institute of Clinical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK.
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11
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Rogers AK, Phillips CM. A Small-RNA-Mediated Feedback Loop Maintains Proper Levels of 22G-RNAs in C. elegans. Cell Rep 2020; 33:108279. [PMID: 33086057 PMCID: PMC7603289 DOI: 10.1016/j.celrep.2020.108279] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 08/27/2020] [Accepted: 09/24/2020] [Indexed: 02/06/2023] Open
Abstract
RNA interference (RNAi) is an essential regulatory mechanism in all animals. In Caenorhabditis elegans, several classes of small RNAs act to silence or license expression of mRNA targets. ERI-6/7 is required for the production of some endogenous small interfering RNAs (siRNAs) and acts as a negative regulator of the exogenous RNAi pathway. We find that the genomic locus encoding eri-6/7 contains two distinct regions that are targeted by endogenous siRNAs. Loss of these siRNAs disrupts eri-6/7 mRNA expression, resulting in increased production of siRNAs from other small RNA pathways because these pathways compete with eri-6/7-dependent transcripts for access to the downstream siRNA amplification machinery. Thus, the pathway acts like a small-RNA-mediated feedback loop to ensure homeostasis of gene expression by small RNA pathways. Similar feedback loops that maintain chromatin homeostasis have been identified in yeast and Drosophila melanogaster, suggesting an evolutionary conservation of feedback mechanisms in gene regulatory pathways.
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Affiliation(s)
- Alicia K Rogers
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Carolyn M Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
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12
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Schwartz-Orbach L, Zhang C, Sidoli S, Amin R, Kaur D, Zhebrun A, Ni J, Gu SG. Caenorhabditis elegans nuclear RNAi factor SET-32 deposits the transgenerational histone modification, H3K23me3. eLife 2020; 9:e54309. [PMID: 32804637 PMCID: PMC7431132 DOI: 10.7554/elife.54309] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 08/04/2020] [Indexed: 12/29/2022] Open
Abstract
Nuclear RNAi provides a highly tractable system to study RNA-mediated chromatin changes and epigenetic inheritance. Recent studies have indicated that the regulation and function of nuclear RNAi-mediated heterochromatin are highly complex. Our knowledge of histone modifications and the corresponding histonemodifying enzymes involved in the system remains limited. In this study, we show that the heterochromatin mark, H3K23me3, is induced by nuclear RNAi at both exogenous and endogenous targets in C. elegans. In addition, dsRNA-induced H3K23me3 can persist for multiple generations after the dsRNA exposure has stopped. We demonstrate that the histone methyltransferase SET-32, methylates H3K23 in vitro. Both set-32 and the germline nuclear RNAi Argonaute, hrde-1, are required for nuclear RNAi-induced H3K23me3 in vivo. Our data poise H3K23me3 as an additional chromatin modification in the nuclear RNAi pathway and provides the field with a new target for uncovering the role of heterochromatin in transgenerational epigenetic silencing.
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Affiliation(s)
- Lianna Schwartz-Orbach
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New JerseyPiscatawayUnited States
| | - Chenzhen Zhang
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New JerseyPiscatawayUnited States
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, BronxNew YorkUnited States
| | - Richa Amin
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New JerseyPiscatawayUnited States
| | - Diljeet Kaur
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New JerseyPiscatawayUnited States
| | - Anna Zhebrun
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New JerseyPiscatawayUnited States
| | - Julie Ni
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New JerseyPiscatawayUnited States
| | - Sam G Gu
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New JerseyPiscatawayUnited States
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13
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Esse R, Grishok A. Caenorhabditis elegans Deficient in DOT-1.1 Exhibit Increases in H3K9me2 at Enhancer and Certain RNAi-Regulated Regions. Cells 2020; 9:cells9081846. [PMID: 32781660 PMCID: PMC7464606 DOI: 10.3390/cells9081846] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/29/2020] [Accepted: 07/29/2020] [Indexed: 01/06/2023] Open
Abstract
The methylation of histone H3 at lysine 79 is a feature of open chromatin. It is deposited by the conserved histone methyltransferase DOT1. Recently, DOT1 localization and H3K79 methylation (H3K79me) have been correlated with enhancers in C. elegans and mammalian cells. Since earlier research implicated H3K79me in preventing heterochromatin formation both in yeast and leukemic cells, we sought to inquire whether a H3K79me deficiency would lead to higher levels of heterochromatic histone modifications, specifically H3K9me2, at developmental enhancers in C. elegans. Therefore, we used H3K9me2 ChIP-seq to compare its abundance in control and dot-1.1 loss-of-function mutant worms, as well as in rde-4; dot-1.1 and rde-1; dot-1.1 double mutants. The rde-1 and rde-4 genes are components of the RNAi pathway in C. elegans, and RNAi is known to initiate H3K9 methylation in many organisms, including C. elegans. We have previously shown that dot-1.1(-) lethality is rescued by rde-1 and rde-4 loss-of-function. Here we found that H3K9me2 was elevated in enhancer, but not promoter, regions bound by the DOT-1.1/ZFP-1 complex in dot-1.1(-) worms. We also found increased H3K9me2 at genes targeted by the ALG-3/4-dependent small RNAs and repeat regions. Our results suggest that ectopic H3K9me2 in dot-1.1(-) could, in some cases, be induced by small RNAs.
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14
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Rogers AK, Phillips CM. RNAi pathways repress reprogramming of C. elegans germ cells during heat stress. Nucleic Acids Res 2020; 48:4256-4273. [PMID: 32187370 PMCID: PMC7192617 DOI: 10.1093/nar/gkaa174] [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: 08/05/2019] [Revised: 03/02/2020] [Accepted: 03/10/2020] [Indexed: 01/08/2023] Open
Abstract
Repression of cellular reprogramming in germ cells is critical to maintaining cell fate and fertility. When germ cells mis-express somatic genes they can be directly converted into other cell types, resulting in loss of totipotency and reproductive potential. Identifying the molecular mechanisms that coordinate these cell fate decisions is an active area of investigation. Here we show that RNAi pathways play a key role in maintaining germline gene expression and totipotency after heat stress. By examining transcriptional changes that occur in mut-16 mutants, lacking a key protein in the RNAi pathway, at elevated temperature we found that genes normally expressed in the soma are mis-expressed in germ cells. Furthermore, these genes displayed increased chromatin accessibility in the germlines of mut-16 mutants at elevated temperature. These findings indicate that the RNAi pathway plays a key role in preventing aberrant expression of somatic genes in the germline during heat stress. This regulation occurs in part through the maintenance of germline chromatin, likely acting through the nuclear RNAi pathway. Identification of new pathways governing germ cell reprogramming is critical to understanding how cells maintain proper gene expression and may provide key insights into how cell identity is lost in some germ cell tumors.
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Affiliation(s)
- Alicia K Rogers
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Carolyn M Phillips
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
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15
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Caenorhabditis elegans ADAR editing and the ERI-6/7/MOV10 RNAi pathway silence endogenous viral elements and LTR retrotransposons. Proc Natl Acad Sci U S A 2020; 117:5987-5996. [PMID: 32123111 PMCID: PMC7084138 DOI: 10.1073/pnas.1919028117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Silencing of transposable elements and viruses is critical for the maintenance of genome integrity, cellular homeostasis, and organismal health. Here we describe multiple factors that control different types of transposable elements, providing insight into how they are regulated. We also identify stress response pathways that are triggered upon misregulation of these transposable elements. The conservation of these factors and pathways in human suggests that our studies in Caenorhabditis elegans can provide general insight into the regulation of and response to transposable elements and viruses. Endogenous retroviruses and long terminal repeat (LTR) retrotransposons are mobile genetic elements that are closely related to retroviruses. Desilenced endogenous retroviruses are associated with human autoimmune disorders and neurodegenerative diseases. Caenorhabditis elegans and related Caenorhabditis spp. contain LTR retrotransposons and, as described here, numerous integrated viral genes including viral envelope genes that are part of LTR retrotransposons. We found that both LTR retrotransposons and endogenous viral elements are silenced by ADARs [adenosine deaminases acting on double-stranded RNA (dsRNA)] together with the endogenous RNA interference (RNAi) factor ERI-6/7, a homolog of MOV10 helicase, a retrotransposon and retrovirus restriction factor in human. siRNAs corresponding to integrated viral genes and LTR retrotransposons, but not to DNA transposons, are dependent on the ADARs and ERI-6/7. siRNAs corresponding to palindromic repeats are independent of the ADARs and ERI-6/7, and are in fact increased in adar- and eri-6/7–defective mutants because of an antiviral RNAi response to dsRNA. Silencing of LTR retrotransposons is dependent on downstream RNAi factors and P granule components but is independent of the viral sensor DRH-1/RIG-I and the nuclear Argonaute NRDE-3. The activation of retrotransposons in the ADAR- and ERI-6/7/MOV10–defective mutant is associated with the induction of the unfolded protein response (UPR), a common response to viral infection. The overlap between genes induced upon viral infection and infection with intracellular pathogens and genes coexpressed with retrotransposons suggests that there is a common response to different types of foreign elements that includes a response to proteotoxicity presumably caused by the burden of replicating pathogens and expressed retrotransposons.
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16
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Barucci G, Cornes E, Singh M, Li B, Ugolini M, Samolygo A, Didier C, Dingli F, Loew D, Quarato P, Cecere G. Small-RNA-mediated transgenerational silencing of histone genes impairs fertility in piRNA mutants. Nat Cell Biol 2020; 22:235-245. [PMID: 32015436 PMCID: PMC7272227 DOI: 10.1038/s41556-020-0462-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 01/05/2020] [Indexed: 11/09/2022]
Abstract
PIWI-interacting RNAs (piRNAs) promote fertility in many animals. However, whether this is due to their conserved role in repressing repetitive elements (REs) remains unclear. Here, we show that the progressive loss of fertility in Caenorhabditis elegans lacking piRNAs is not caused by derepression of REs or other piRNA targets but, rather, is mediated by epigenetic silencing of all of the replicative histone genes. In the absence of piRNAs, downstream components of the piRNA pathway relocalize from germ granules and piRNA targets to histone mRNAs to synthesize antisense small RNAs (sRNAs) and induce transgenerational silencing. Removal of the downstream components of the piRNA pathway restores histone mRNA expression and fertility in piRNA mutants, and the inheritance of histone sRNAs in wild-type worms adversely affects their fertility for multiple generations. We conclude that sRNA-mediated silencing of histone genes impairs the fertility of piRNA mutants and may serve to maintain piRNAs across evolution.
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Affiliation(s)
- Giorgia Barucci
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris, France
- Sorbonne Université, Collège doctoral, Paris, France
| | - Eric Cornes
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris, France
| | - Meetali Singh
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris, France
| | - Blaise Li
- Bioinformatics and Biostatistics Hub, C3BI, Institut Pasteur, USR 3756, CNRS, Paris, France
| | - Martino Ugolini
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris, France
- Scuola Normale Superiore, Pisa, Italy
| | - Aleksei Samolygo
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris, France
- Moscow Institute of Physics and Technology, Moscow, Russia
| | - Celine Didier
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris, France
| | - Florent Dingli
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, PSL Research University, Paris, France
| | - Damarys Loew
- Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, Institut Curie, PSL Research University, Paris, France
| | - Piergiuseppe Quarato
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris, France
- Sorbonne Université, Collège doctoral, Paris, France
| | - Germano Cecere
- Mechanisms of Epigenetic Inheritance, Department of Developmental and Stem Cell Biology, Institut Pasteur, UMR 3738, CNRS, Paris, France.
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17
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Visualization and Quantification of Transposon Activity in Caenorhabditis elegans RNAi Pathway Mutants. G3-GENES GENOMES GENETICS 2019; 9:3825-3832. [PMID: 31533956 PMCID: PMC6829131 DOI: 10.1534/g3.119.400639] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
RNA silencing pathways play critical roles in maintaining quiescence of transposons in germ cells to promote genome integrity. However the precise mechanism by which different types of transposons are recognized by these pathways is not fully understood. Furthermore, the location in the germline where this transposition occurs after disruption of transposon silencing was previously unknown. Here we utilize the spatial and temporal organization of the Caenorhabditis elegans germline to demonstrate that transposition of DNA transposons in RNA silencing pathway mutants occur in all stages of adult germ cells. We further demonstrate that the double-strand breaks generated by transposons can restore homologous recombination in a mutant defective for the generation of meiosis-specific double-strand breaks. Finally, we detected clear differences in transposase expression and transposon excision between distinct branches of the RNA silencing pathway, emphasizing that there are multiple mechanisms by which transposons can be recognized and routed for small-RNA-mediated silencing.
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18
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Chromatin Compaction by Small RNAs and the Nuclear RNAi Machinery in C. elegans. Sci Rep 2019; 9:9030. [PMID: 31227740 PMCID: PMC6588724 DOI: 10.1038/s41598-019-45052-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 05/28/2019] [Indexed: 11/25/2022] Open
Abstract
DNA is organized and compacted into higher-order structures in order to fit within nuclei and to facilitate gene regulation. Mechanisms by which higher order chromatin structures are established and maintained are poorly understood. In C. elegans, nuclear-localized small RNAs engage the nuclear RNAi machinery to regulate gene expression and direct the post-translational modification of histone proteins. Here we confirm a recent report suggesting that nuclear small RNAs initiate or maintain chromatin compaction states in C. elegans germ cells. Additionally, we show that experimentally provided small RNAs are sufficient to direct chromatin compaction and that this compaction requires the small RNA-binding Argonaute NRDE-3, the pre-mRNA associated factor NRDE-2, and the HP1-like protein HPL-2. Our results show that small RNAs, acting via the nuclear RNAi machinery and an HP1-like protein, are capable of driving chromatin compaction in C. elegans.
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19
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Gushchanskaia ES, Esse R, Ma Q, Lau NC, Grishok A. Interplay between small RNA pathways shapes chromatin landscapes in C. elegans. Nucleic Acids Res 2019; 47:5603-5616. [PMID: 31216042 PMCID: PMC6582410 DOI: 10.1093/nar/gkz275] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 04/01/2019] [Accepted: 04/04/2019] [Indexed: 12/20/2022] Open
Abstract
The nematode Caenorhabditis elegans contains several types of endogenous small interfering RNAs (endo-siRNAs) produced by RNA-dependent RNA polymerase (RdRP) complexes. Both 'silencing' siRNAs bound by Worm-specific Argonautes (WAGO) and 'activating' siRNAs bound by the CSR-1 Argonaute require the DRH-3 helicase, an RdRP component. Here, we show that, in the drh-3(ne4253) mutant deficient in RdRP-produced secondary endo-siRNAs, the silencing histone mark H3K9me3 is largely depleted, whereas in the csr-1 partially rescued null mutant strain (WM193), this mark is ectopically deposited on CSR-1 target genes. Moreover, we observe ectopic H3K9me3 at enhancer elements and an increased number of small RNAs that match enhancers in both drh-3 and csr-1 mutants. Finally, we detect accumulation of H3K27me3 at highly expressed genes in the drh-3(ne4253) mutant, which correlates with their reduced transcription. Our study shows that when abundant RdRP-produced siRNAs are depleted, there is ectopic elevation of noncoding RNAs linked to sites with increased silencing chromatin marks. Moreover, our results suggest that enhancer small RNAs may guide local H3K9 methylation.
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Affiliation(s)
| | - Ruben Esse
- Boston University School of Medicine, Department of Biochemistry, Boston, MA 02118, USA
| | - Qicheng Ma
- Boston University School of Medicine, Department of Biochemistry, Boston, MA 02118, USA
| | - Nelson C Lau
- Boston University School of Medicine, Department of Biochemistry, Boston, MA 02118, USA
- Genome Science Institute, Boston University School of Medicine, Boston, MA 02118, USA
| | - Alla Grishok
- Boston University School of Medicine, Department of Biochemistry, Boston, MA 02118, USA
- Genome Science Institute, Boston University School of Medicine, Boston, MA 02118, USA
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20
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Weiser NE, Kim JK. Multigenerational Regulation of the Caenorhabditis elegans Chromatin Landscape by Germline Small RNAs. Annu Rev Genet 2019; 53:289-311. [PMID: 31150586 DOI: 10.1146/annurev-genet-112618-043505] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In animals, small noncoding RNAs that are expressed in the germline and transmitted to progeny control gene expression to promote fertility. Germline-expressed small RNAs, including endogenous small interfering RNAs (endo-siRNAs) and Piwi-interacting RNAs (piRNAs), drive the repression of deleterious transcripts such as transposons, repetitive elements, and pseudogenes. Recent studies have highlighted an important role for small RNAs in transgenerational epigenetic inheritance via regulation of heritable chromatin marks; therefore, small RNAs are thought to convey an epigenetic memory of genomic self and nonself elements. Small RNA pathways are highly conserved in metazoans and have been best described for the model organism Caenorhabditis elegans. In this review, we describe the biogenesis, regulation, and function of C. elegans endo-siRNAs and piRNAs, along with recent insights into how these distinct pathways are integrated to collectively regulate germline gene expression, transgenerational epigenetic inheritance, and ultimately, animal fertility.
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Affiliation(s)
- Natasha E Weiser
- Program in Cellular and Molecular Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - John K Kim
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA;
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21
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Kalinava N, Ni JZ, Gajic Z, Kim M, Ushakov H, Gu SG. C. elegans Heterochromatin Factor SET-32 Plays an Essential Role in Transgenerational Establishment of Nuclear RNAi-Mediated Epigenetic Silencing. Cell Rep 2018; 25:2273-2284.e3. [PMID: 30463021 PMCID: PMC6317888 DOI: 10.1016/j.celrep.2018.10.086] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 09/24/2018] [Accepted: 10/24/2018] [Indexed: 12/14/2022] Open
Abstract
The dynamic process by which nuclear RNAi engages a transcriptionally active target, before the repressive state is stably established, remains largely a mystery. Here, we found that the onset of exogenous dsRNA-induced nuclear RNAi in C. elegans is a transgenerational process, and it requires a putative histone methyltransferase (HMT), SET-32. By developing a CRISPR-based genetic approach, we found that silencing establishment at the endogenous targets of germline nuclear RNAi also requires SET-32. Although SET-32 and two H3K9 HMTs, MET-2 and SET-25, are dispensable for the maintenance of silencing, they do contribute to transcriptional repression in mutants that lack the germline nuclear Argonaute protein HRDE-1, suggesting a conditional role of heterochromatin in the maintenance phase. Our study indicates that (1) establishment and maintenance of siRNA-guided transcriptional repression are two distinct processes with different genetic requirements and (2) the rate-limiting step of the establishment phase is a transgenerational, chromatin-based process.
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Affiliation(s)
- Natallia Kalinava
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Julie Zhouli Ni
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Zoran Gajic
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Matthew Kim
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Helen Ushakov
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
| | - Sam Guoping Gu
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
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22
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Kelleher ES, Azevedo RBR, Zheng Y. The Evolution of Small-RNA-Mediated Silencing of an Invading Transposable Element. Genome Biol Evol 2018; 10:3038-3057. [PMID: 30252073 PMCID: PMC6404463 DOI: 10.1093/gbe/evy218] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/24/2018] [Indexed: 12/11/2022] Open
Abstract
Transposable elements (TEs) are genomic parasites that impose fitness costs on their
hosts by producing deleterious mutations and disrupting gametogenesis. Host genomes avoid
these costs by regulating TE activity, particularly in germline cells where new insertions
are heritable and TEs are exceptionally active. However, the capacity of different
TE-associated fitness costs to select for repression in the host, and the role of
selection in the evolution of TE regulation more generally remain controversial. In this
study, we use forward, individual-based simulations to examine the evolution of
small-RNA-mediated TE regulation, a conserved mechanism for TE repression that is employed
by both prokaryotes and eukaryotes. To design and parameterize a biologically realistic
model, we drew on an extensive survey of empirical studies of the transposition and
regulation of P-element DNA transposons in Drosophila
melanogaster. We observed that even under conservative assumptions, where
small-RNA-mediated regulation reduces transposition only, repression evolves rapidly and
adaptively after the genome is invaded by a new TE in simulated populations. We further
show that the spread of repressor alleles through simulated populations is greatly
enhanced by two additional TE-imposed fitness costs: dysgenic sterility and ectopic
recombination. Finally, we demonstrate that the adaptive mutation rate to repression is a
critical parameter that influences both the evolutionary trajectory of host repression and
the associated proliferation of TEs after invasion in simulated populations. Our findings
suggest that adaptive evolution of TE regulation may be stronger and more prevalent than
previously appreciated, and provide a framework for interpreting empirical data.
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Affiliation(s)
- Erin S Kelleher
- Department of Biology and Biochemistry, University of Houston, Houston
| | | | - Yichen Zheng
- Department of Biology and Biochemistry, University of Houston, Houston.,Biodiversitt und Klima Forschungszentrum, Senckenberg Gesellschaft fr Naturforschung, Frankfurt am Main, Germany.,Institute of Genetics, University of Cologne, 50674 Cologne, NRW, Germany
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23
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Ni JZ, Kalinava N, Mendoza SG, Gu SG. The spatial and temporal dynamics of nuclear RNAi-targeted retrotransposon transcripts in Caenorhabditis elegans. Development 2018; 145:dev167346. [PMID: 30254142 PMCID: PMC6215403 DOI: 10.1242/dev.167346] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 09/17/2018] [Indexed: 02/03/2023]
Abstract
Nuclear RNA interference provides a unique approach to the study of RNA-mediated transgenerational epigenetic inheritance. A paradox in the field is that expression of target loci is necessary for the initiation and maintenance of their silencing. How expression and repression are coordinated during animal development is poorly understood. To resolve this gap, we took imaging, deep-sequencing and genetic approaches towards delineating the developmental regulation and subcellular localization of RNA transcripts of two representative endogenous targets, the LTR retrotransposons Cer3 and Cer8. By examining wild-type worms and a collection of mutant strains, we found that the expression and silencing cycle of Cer3 and Cer8 is coupled with embryonic and germline development. Strikingly, endogenous targets exhibit a hallmark of nuclear enrichment of their RNA transcripts. In addition, germline and somatic repressions of Cer3 have different genetic requirements for three heterochromatin enzymes, MET-2, SET-25 and SET-32, in conjunction with the nuclear Argonaute protein HRDE-1. These results provide the first comprehensive cellular and developmental characterization of nuclear RNAi activities throughout the animal reproductive cycle.
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Affiliation(s)
- Julie Zhouli Ni
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Natallia Kalinava
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sofia Galindo Mendoza
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Sam Guoping Gu
- Department of Molecular Biology and Biochemistry, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
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24
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Rechavi O, Lev I. Principles of Transgenerational Small RNA Inheritance in Caenorhabditis elegans. Curr Biol 2018; 27:R720-R730. [PMID: 28743023 DOI: 10.1016/j.cub.2017.05.043] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Examples of transgenerational inheritance of environmental responses are rapidly accumulating. In Caenorhabditis elegans nematodes, such heritable information transmits across generations in the form of RNA-dependent RNA polymerase-amplified small RNAs. Regulatory small RNAs enable sequence-specific gene regulation, and unlike chromatin modifications, can move between tissues, and escape from immediate germline reprogramming. In this review, we discuss the path that small RNAs take from the soma to the germline, and elaborate on the mechanisms that maintain or erase parental small RNA responses after a specific number of generations. We focus on the intricate interactions between heritable small RNAs and histone modifications, deposited on specific loci. A trace of heritable chromatin marks, in particular trimethylation of histone H3 lysine 9, is deposited on RNAi-targeted loci. However, how these modifications regulate RNAi or small RNA inheritance was until recently unclear. Integrating the very latest literature, we suggest that changes to histone marks may instigate transgenerational gene regulation indirectly, by affecting the biogenesis of heritable small RNAs. Inheritance of small RNAs could spread adaptive ancestral responses.
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Affiliation(s)
- Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School for Neuroscience, Tel Aviv University, Tel Aviv, Israel 69978.
| | - Itamar Lev
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School for Neuroscience, Tel Aviv University, Tel Aviv, Israel 69978.
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25
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Chaudhary V, Jangra S, Yadav NR. Nanotechnology based approaches for detection and delivery of microRNA in healthcare and crop protection. J Nanobiotechnology 2018; 16:40. [PMID: 29653577 PMCID: PMC5897953 DOI: 10.1186/s12951-018-0368-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 04/07/2018] [Indexed: 12/31/2022] Open
Abstract
Nanobiotechnology has the potential to revolutionize diverse sectors including medicine, agriculture, food, textile and pharmaceuticals. Disease diagnostics, therapeutics and crop protection strategies are fast emerging using nanomaterials preferably nanobiomaterials. It has potential for development of novel nanobiomolecules which offer several advantages over conventional treatment methods. RNA nanoparticles with many unique features are promising candidates in disease treatment. The miRNAs are involved in many biochemical and developmental pathways and their regulation in plants and animals. These appear to be a powerful tool for controlling various pathological diseases in human, plants and animals, however there are challenges associated with miRNA based nanotechnology. Several advancements made in the field of miRNA therapeutics make it an attractive approach, but a lot more has to be explored in nanotechnology assisted miRNA therapy. The miRNA based technologies can be employed for detection and combating crop diseases as well. Despite these potential advantages, nanobiotechnology applications in the agricultural sector are still in its infancy and have not yet made its mark in comparison with healthcare sector. The review provides a platform to discuss nature, role and use of miRNAs in nanobiotechnology applications.
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Affiliation(s)
- Vrantika Chaudhary
- Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, Hisar, 125004 India
| | - Sumit Jangra
- Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, Hisar, 125004 India
| | - Neelam R. Yadav
- Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, Hisar, 125004 India
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26
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Akay A, Di Domenico T, Suen KM, Nabih A, Parada GE, Larance M, Medhi R, Berkyurek AC, Zhang X, Wedeles CJ, Rudolph KLM, Engelhardt J, Hemberg M, Ma P, Lamond AI, Claycomb JM, Miska EA. The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription. Dev Cell 2017; 42:241-255.e6. [PMID: 28787591 PMCID: PMC5554785 DOI: 10.1016/j.devcel.2017.07.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 05/14/2017] [Accepted: 07/05/2017] [Indexed: 02/02/2023]
Abstract
Small RNAs play a crucial role in genome defense against transposable elements and guide Argonaute proteins to nascent RNA transcripts to induce co-transcriptional gene silencing. However, the molecular basis of this process remains unknown. Here, we identify the conserved RNA helicase Aquarius/EMB-4 as a direct and essential link between small RNA pathways and the transcriptional machinery in Caenorhabditis elegans. Aquarius physically interacts with the germline Argonaute HRDE-1. Aquarius is required to initiate small-RNA-induced heritable gene silencing. HRDE-1 and Aquarius silence overlapping sets of genes and transposable elements. Surprisingly, removal of introns from a target gene abolishes the requirement for Aquarius, but not HRDE-1, for small RNA-dependent gene silencing. We conclude that Aquarius allows small RNA pathways to compete for access to nascent transcripts undergoing co-transcriptional splicing in order to detect and silence transposable elements. Thus, Aquarius and HRDE-1 act as gatekeepers coordinating gene expression and genome defense.
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Affiliation(s)
- Alper Akay
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Tomas Di Domenico
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Kin M Suen
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Amena Nabih
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Guillermo E Parada
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Mark Larance
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Ragini Medhi
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Ahmet C Berkyurek
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Xinlian Zhang
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
| | - Christopher J Wedeles
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Konrad L M Rudolph
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Jan Engelhardt
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Haertelstraße 16-18, Leipzig 04107, Germany
| | - Martin Hemberg
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK
| | - Ping Ma
- Department of Statistics, University of Georgia, Athens, GA 30602, USA
| | - Angus I Lamond
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Julie M Claycomb
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Eric A Miska
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK; Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK; Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SA, UK.
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27
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Tyc KM, Nabih A, Wu MZ, Wedeles CJ, Sobotka JA, Claycomb JM. The Conserved Intron Binding Protein EMB-4 Plays Differential Roles in Germline Small RNA Pathways of C. elegans. Dev Cell 2017; 42:256-270.e6. [DOI: 10.1016/j.devcel.2017.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Revised: 05/15/2017] [Accepted: 07/05/2017] [Indexed: 02/08/2023]
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Reexamining the P-Element Invasion of Drosophila melanogaster Through the Lens of piRNA Silencing. Genetics 2017; 203:1513-31. [PMID: 27516614 DOI: 10.1534/genetics.115.184119] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 05/25/2016] [Indexed: 11/18/2022] Open
Abstract
Transposable elements (TEs) are both important drivers of genome evolution and genetic parasites with potentially dramatic consequences for host fitness. The recent explosion of research on regulatory RNAs reveals that small RNA-mediated silencing is a conserved genetic mechanism through which hosts repress TE activity. The invasion of the Drosophila melanogaster genome by P elements, which happened on a historical timescale, represents an incomparable opportunity to understand how small RNA-mediated silencing of TEs evolves. Repression of P-element transposition emerged almost concurrently with its invasion. Recent studies suggest that this repression is implemented in part, and perhaps predominantly, by the Piwi-interacting RNA (piRNA) pathway, a small RNA-mediated silencing pathway that regulates TE activity in many metazoan germlines. In this review, I consider the P-element invasion from both a molecular and evolutionary genetic perspective, reconciling classic studies of P-element regulation with the new mechanistic framework provided by the piRNA pathway. I further explore the utility of the P-element invasion as an exemplar of the evolution of piRNA-mediated silencing. In light of the highly-conserved role for piRNAs in regulating TEs, discoveries from this system have taxonomically broad implications for the evolution of repression.
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The RNAi Inheritance Machinery of Caenorhabditis elegans. Genetics 2017; 206:1403-1416. [PMID: 28533440 DOI: 10.1534/genetics.116.198812] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 04/17/2017] [Indexed: 12/30/2022] Open
Abstract
Gene silencing mediated by dsRNA (RNAi) can persist for multiple generations in Caenorhabditis elegans (termed RNAi inheritance). Here we describe the results of a forward genetic screen in C. elegans that has identified six factors required for RNAi inheritance: GLH-1/VASA, PUP-1/CDE-1, MORC-1, SET-32, and two novel nematode-specific factors that we term here (heritable RNAi defective) HRDE-2 and HRDE-4 The new RNAi inheritance factors exhibit mortal germline (Mrt) phenotypes, which we show is likely caused by epigenetic deregulation in germ cells. We also show that HRDE-2 contributes to RNAi inheritance by facilitating the binding of small RNAs to the inheritance Argonaute (Ago) HRDE-1 Together, our results identify additional components of the RNAi inheritance machinery whose conservation provides insights into the molecular mechanism of RNAi inheritance, further our understanding of how the RNAi inheritance machinery promotes germline immortality, and show that HRDE-2 couples the inheritance Ago HRDE-1 with the small RNAs it needs to direct RNAi inheritance and germline immortality.
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McMurchy AN, Stempor P, Gaarenstroom T, Wysolmerski B, Dong Y, Aussianikava D, Appert A, Huang N, Kolasinska-Zwierz P, Sapetschnig A, Miska EA, Ahringer J. A team of heterochromatin factors collaborates with small RNA pathways to combat repetitive elements and germline stress. eLife 2017; 6:e21666. [PMID: 28294943 PMCID: PMC5395297 DOI: 10.7554/elife.21666] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 03/10/2017] [Indexed: 12/26/2022] Open
Abstract
Repetitive sequences derived from transposons make up a large fraction of eukaryotic genomes and must be silenced to protect genome integrity. Repetitive elements are often found in heterochromatin; however, the roles and interactions of heterochromatin proteins in repeat regulation are poorly understood. Here we show that a diverse set of C. elegans heterochromatin proteins act together with the piRNA and nuclear RNAi pathways to silence repetitive elements and prevent genotoxic stress in the germ line. Mutants in genes encoding HPL-2/HP1, LIN-13, LIN-61, LET-418/Mi-2, and H3K9me2 histone methyltransferase MET-2/SETDB1 also show functionally redundant sterility, increased germline apoptosis, DNA repair defects, and interactions with small RNA pathways. Remarkably, fertility of heterochromatin mutants could be partially restored by inhibiting cep-1/p53, endogenous meiotic double strand breaks, or the expression of MIRAGE1 DNA transposons. Functional redundancy among factors and pathways underlies the importance of safeguarding the genome through multiple means.
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Affiliation(s)
- Alicia N McMurchy
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Przemyslaw Stempor
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Tessa Gaarenstroom
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Brian Wysolmerski
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Yan Dong
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Darya Aussianikava
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Alex Appert
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Ni Huang
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | | | - Alexandra Sapetschnig
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Eric A Miska
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Julie Ahringer
- The Gurdon Institute and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
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31
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Jasinski D, Haque F, Binzel DW, Guo P. Advancement of the Emerging Field of RNA Nanotechnology. ACS NANO 2017; 11:1142-1164. [PMID: 28045501 PMCID: PMC5333189 DOI: 10.1021/acsnano.6b05737] [Citation(s) in RCA: 222] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/03/2017] [Indexed: 05/14/2023]
Abstract
The field of RNA nanotechnology has advanced rapidly during the past decade. A variety of programmable RNA nanoparticles with defined shape, size, and stoichiometry have been developed for diverse applications in nanobiotechnology. The rising popularity of RNA nanoparticles is due to a number of factors: (1) removing the concern of RNA degradation in vitro and in vivo by introducing chemical modification into nucleotides without significant alteration of the RNA property in folding and self-assembly; (2) confirming the concept that RNA displays very high thermodynamic stability and is suitable for in vivo trafficking and other applications; (3) obtaining the knowledge to tune the immunogenic properties of synthetic RNA constructs for in vivo applications; (4) increased understanding of the 4D structure and intermolecular interaction of RNA molecules; (5) developing methods to control shape, size, and stoichiometry of RNA nanoparticles; (6) increasing knowledge of regulation and processing functions of RNA in cells; (7) decreasing cost of RNA production by biological and chemical synthesis; and (8) proving the concept that RNA is a safe and specific therapeutic modality for cancer and other diseases with little or no accumulation in vital organs. Other applications of RNA nanotechnology, such as adapting them to construct 2D, 3D, and 4D structures for use in tissue engineering, biosensing, resistive biomemory, and potential computer logic gate modules, have stimulated the interest of the scientific community. This review aims to outline the current state of the art of RNA nanoparticles as programmable smart complexes and offers perspectives on the promising avenues of research in this fast-growing field.
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Affiliation(s)
| | | | - Daniel W Binzel
- College of Pharmacy, Division
of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine,
Department of Physiology & Cell Biology; and Dorothy M. Davis
Heart and Lung Research Institute, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Peixuan Guo
- College of Pharmacy, Division
of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine,
Department of Physiology & Cell Biology; and Dorothy M. Davis
Heart and Lung Research Institute, The Ohio
State University, Columbus, Ohio 43210, United States
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32
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Kalinava N, Ni JZ, Peterman K, Chen E, Gu SG. Decoupling the downstream effects of germline nuclear RNAi reveals that H3K9me3 is dispensable for heritable RNAi and the maintenance of endogenous siRNA-mediated transcriptional silencing in Caenorhabditis elegans. Epigenetics Chromatin 2017; 10:6. [PMID: 28228846 PMCID: PMC5311726 DOI: 10.1186/s13072-017-0114-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 02/08/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Germline nuclear RNAi in C. elegans is a transgenerational gene-silencing pathway that leads to H3K9 trimethylation (H3K9me3) and transcriptional silencing at the target genes. H3K9me3 induced by either exogenous double-stranded RNA (dsRNA) or endogenous siRNA (endo-siRNA) is highly specific to the target loci and transgenerationally heritable. Despite these features, the role of H3K9me3 in siRNA-mediated transcriptional silencing and inheritance of the silencing state at native target genes is unclear. In this study, we took combined genetic and whole-genome approaches to address this question. RESULTS Here we demonstrate that siRNA-mediated H3K9me3 requires combined activities of three H3K9 histone methyltransferases: MET-2, SET-25, and SET-32. set-32 single, met-2 set-25 double, and met-2 set-25;set-32 triple mutant adult animals all exhibit prominent reductions in H3K9me3 throughout the genome, with met-2 set-25;set-32 mutant worms losing all detectable H3K9me3 signals. Surprisingly, loss of high-magnitude H3K9me3 at the native nuclear RNAi targets has no effect on the transcriptional silencing state. In addition, the exogenous dsRNA-induced transcriptional silencing and heritable RNAi at oma-1, a well-established nuclear RNAi reporter gene, are completely resistant to the loss of H3K9me3. CONCLUSIONS Nuclear RNAi-mediated H3K9me3 in C. elegans requires multiple histone methyltransferases, including MET-2, SET-25, and SET-32. H3K9me3 is not essential for dsRNA-induced heritable RNAi or the maintenance of endo-siRNA-mediated transcriptional silencing in C. elegans. We propose that siRNA-mediated transcriptional silencing in C. elegans can be maintained by an H3K9me3-independent mechanism.
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Affiliation(s)
- Natallia Kalinava
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Julie Zhouli Ni
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Kimberly Peterman
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Esteban Chen
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Sam Guoping Gu
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA.,Nelson Labs A125, 604 Allison Road, Piscataway, NJ 08854 USA
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Lau AC, Zhu KP, Brouhard EA, Davis MB, Csankovszki G. An H4K16 histone acetyltransferase mediates decondensation of the X chromosome in C. elegans males. Epigenetics Chromatin 2016; 9:44. [PMID: 27777629 PMCID: PMC5070013 DOI: 10.1186/s13072-016-0097-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/05/2016] [Indexed: 02/08/2023] Open
Abstract
Background In C. elegans, in order to equalize gene expression between the sexes and balance X and autosomal expression, two steps are believed to be required. First, an unknown mechanism is hypothesized to upregulate the X chromosome in both sexes. This mechanism balances the X to autosomal expression in males, but creates X overexpression in hermaphrodites. Therefore, to restore the balance, hermaphrodites downregulate gene expression twofold on both X chromosomes. While many studies have focused on X chromosome downregulation, the mechanism of X upregulation is not known. Results To gain more insight into X upregulation, we studied the effects of chromatin condensation and histone acetylation on gene expression levels in male C. elegans. We have found that the H4K16 histone acetyltransferase MYS-1/Tip60 mediates dramatic decondensation of the male X chromosome as measured by FISH. However, RNA-seq analysis revealed that MYS-1 contributes only slightly to upregulation of gene expression on the X chromosome. These results suggest that the level of chromosome decondensation does not necessarily correlate with the degree of gene expression change in vivo. Furthermore, the X chromosome is more sensitive to MYS-1-mediated decondensation than the autosomes, despite similar levels of H4K16ac on all chromosomes, as measured by ChIP-seq. H4K16ac levels weakly correlate with gene expression levels on both the X and the autosomes, but highly expressed genes on the X chromosome do not contain exceptionally high levels of H4K16ac. Conclusion These results indicate that H4K16ac and chromosome decondensation influence regulation of the male X chromosome; however, they do not fully account for the high levels of gene expression observed on the X chromosomes. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0097-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Alyssa C Lau
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N. University Ave., Ann Arbor, MI 48109-1048 USA ; Genome Technologies, The Jackson Laboratory for Genomic Medicine, Farmington, CT 06032 USA
| | - Kevin P Zhu
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N. University Ave., Ann Arbor, MI 48109-1048 USA
| | - Elizabeth A Brouhard
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N. University Ave., Ann Arbor, MI 48109-1048 USA
| | - Michael B Davis
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N. University Ave., Ann Arbor, MI 48109-1048 USA
| | - Györgyi Csankovszki
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N. University Ave., Ann Arbor, MI 48109-1048 USA
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Ni JZ, Kalinava N, Chen E, Huang A, Trinh T, Gu SG. A transgenerational role of the germline nuclear RNAi pathway in repressing heat stress-induced transcriptional activation in C. elegans. Epigenetics Chromatin 2016; 9:3. [PMID: 26779286 PMCID: PMC4714518 DOI: 10.1186/s13072-016-0052-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/05/2016] [Indexed: 02/07/2023] Open
Abstract
Background Environmental stress-induced transgenerational epigenetic effects have been observed in various model organisms and human. The capacity and mechanism of such phenomena are poorly understood. In C. elegans, siRNA mediates transgenerational gene
silencing through the germline nuclear RNAi pathway. This pathway is also required to maintain the germline immortality when C. elegans is under heat stress. However, the underlying molecular mechanism is unknown. In this study, we investigated the impact of heat stress on chromatin, transcription, and siRNAs at the whole-genome level, and whether any of the heat-induced effects is transgenerationally heritable in either the wild-type or the germline nuclear RNAi mutant animals. Results We performed 12-generation temperature-shift experiments using the wild-type C. elegans and a mutant strain that lacks the germline-specific nuclear Argonaute protein HRDE-1/WAGO-9. By examining the mRNA, small RNA, RNA polymerase II, and H3K9 trimethylation profiles at the whole-genome level, we revealed an epigenetic role of HRDE-1 in repressing heat stress-induced transcriptional activation of over 280 genes. Many of these genes are in or near LTR (long-terminal repeat) retrotransposons. Strikingly, for some of these genes, the heat stress-induced transcriptional activation in the hrde-1 mutant intensifies in the late generations under the heat stress and is heritable for at least two generations after the mutant animals are shifted back to lower temperature. hrde-1 mutation also leads to siRNA expression changes of many genes. This effect on siRNA is dependent on both the temperature and generation. Conclusions Our study demonstrated that a large number of the endogenous targets of the germline nuclear RNAi pathway in C. elegans are sensitive to heat-induced transcriptional activation. This effect at certain genomic loci including LTR retrotransposons is transgenerational. Germline nuclear RNAi antagonizes this temperature effect at the transcriptional level and therefore may play a key role in heat stress response in C. elegans. Electronic supplementary material The online version of this article (doi:10.1186/s13072-016-0052-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julie Zhouli Ni
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Natallia Kalinava
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Esteban Chen
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Alex Huang
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Thi Trinh
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA
| | - Sam Guoping Gu
- Department of Molecular Biology and Biochemistry, Rutgers the State University of New Jersey, Piscataway, NJ 08854 USA ; Nelson Labs A125, 604 Allison Road, Piscataway, NJ 08854 USA
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35
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Guo Y, Yang B, Li Y, Xu X, Maine EM. Enrichment of H3K9me2 on Unsynapsed Chromatin in Caenorhabditis elegans Does Not Target de Novo Sites. G3 (BETHESDA, MD.) 2015; 5:1865-78. [PMID: 26156747 PMCID: PMC4555223 DOI: 10.1534/g3.115.019828] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 07/06/2015] [Indexed: 12/16/2022]
Abstract
Many organisms alter the chromatin state of unsynapsed chromosomes during meiotic prophase, a phenomenon hypothesized to function in maintaining germline integrity. In Caenorhabditis elegans, histone H3 lysine 9 dimethylation (H3K9me2) is detected by immunolabeling as enriched on unsynapsed meiotic chromosomes. Loss of the SET domain protein, MET-2, greatly reduces H3K9me2 abundance and results in germline mortality. Here, we used him-8 mutations to disable X chromosome synapsis and performed a combination of molecular assays to map the sites of H3K9me2 accumulation, evaluate H3K9me2 abundance in germline vs. whole animals, and evaluate the impact of H3K9me2 loss on the germline transcriptome. Our data indicate that H3K9me2 is elevated broadly across the X chromosome and at defined X chromosomal sites in him-8 adults compared with controls. H3K9me2 levels are also elevated to a lesser degree at sites on synapsed chromosomes in him-8 adults compared with controls. These results suggest that MET-2 activity is elevated in him-8 mutants generally as well as targeted preferentially to the unsynapsed X. Abundance of H3K9me2 and other histone H3 modifications is low in germline chromatin compared with whole animals, which may facilitate genome reprogramming during gametogenesis. Loss of H3K9me2 has a subtle impact on the him-8 germline transcriptome, suggesting H3K9me2 may not be a major regulator of developmental gene expression in C. elegans. We hypothesize H3K9me2 may have a structural function critical for germline immortality, and a greater abundance of these marks may be required when a chromosome does not synapse.
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Affiliation(s)
- Yiqing Guo
- Department of Biology, Syracuse University, Syracuse, New York 13244
| | - Bing Yang
- Department of Biology, Syracuse University, Syracuse, New York 13244
| | - Yini Li
- Department of Biology, Syracuse University, Syracuse, New York 13244
| | - Xia Xu
- Department of Biology, Syracuse University, Syracuse, New York 13244
| | - Eleanor M Maine
- Department of Biology, Syracuse University, Syracuse, New York 13244
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Sapetschnig A, Sarkies P, Lehrbach NJ, Miska EA. Tertiary siRNAs mediate paramutation in C. elegans. PLoS Genet 2015; 11:e1005078. [PMID: 25811365 PMCID: PMC4374809 DOI: 10.1371/journal.pgen.1005078] [Citation(s) in RCA: 87] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 02/17/2015] [Indexed: 12/17/2022] Open
Abstract
In the nematode Caenorhabditis elegans, different small RNA-dependent gene silencing mechanisms act in the germline to initiate transgenerational gene silencing. Piwi-interacting RNAs (piRNAs) can initiate transposon and gene silencing by acting upstream of endogenous short interfering RNAs (siRNAs), which engage a nuclear RNA interference (RNAi) pathway to trigger transcriptional gene silencing. Once gene silencing has been established, it can be stably maintained over multiple generations without the requirement of the initial trigger and is also referred to as RNAe or paramutation. This heritable silencing depends on the integrity of the nuclear RNAi pathway. However, the exact mechanism by which silencing is maintained across generations is not understood. Here we demonstrate that silencing of piRNA targets involves the production of two distinct classes of small RNAs with different genetic requirements. The first class, secondary siRNAs, are localized close to the direct target site for piRNAs. Nuclear import of the secondary siRNAs by the Argonaute HRDE-1 leads to the production of a distinct class of small RNAs that map throughout the transcript, which we term tertiary siRNAs. Both classes of small RNAs are necessary for full repression of the target gene and can be maintained independently of the initial piRNA trigger. Consistently, we observed a form of paramutation associated with tertiary siRNAs. Once paramutated, a tertiary siRNA generating allele confers dominant silencing in the progeny regardless of its own transmission, suggesting germline-transmitted siRNAs are sufficient for multigenerational silencing. This work uncovers a multi-step siRNA amplification pathway that promotes germline integrity via epigenetic silencing of endogenous and invading genetic elements. In addition, the same pathway can be engaged in environmentally induced heritable gene silencing and could therefore promote the inheritance of acquired traits. Transgenerational epigenetic gene silencing has been shown to be important for organisms to react directly to their environment without the need to acquire genetic mutations. The inheritance of acquired traits via the gametes can prove advantageous in fast reproducing organisms. In Caenorhabditis elegans, a free-living nematode, multigenerational epigenetic inheritance can be induced by exogenous (experimentally provided) and endogenous cues that trigger small RNA-dependent gene silencing in the germline of these animals. PIWI interacting small RNAs (piRNAs) are required for the initiation of stable silencing of invading genomic elements in the germline such as transposons. Gene silencing established by piRNAs can subsequently be maintained over multiple generations without the original trigger. In C. elegans, this stable maintenance of silencing requires an additional class of small interfering RNAs (siRNAs) that must be amplified in each generation in order to maintain multigenerational silencing. Here we show that these siRNAs fall into two distinct classes, which we call secondary and tertiary siRNAs. We find that the production of tertiary siRNAs is part of a nuclear amplification pathway associated with the stable heritable silencing of an allele, a form of paramutation. This amplification pathway therefore promotes germline integrity and possibly the inheritance of acquired physiological traits.
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Affiliation(s)
- Alexandra Sapetschnig
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Peter Sarkies
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Nicolas J. Lehrbach
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
| | - Eric A. Miska
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Biochemistry and Department of Genetics, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
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