1
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Kumar M, Tripathi PK, Ayzenshtat D, Marko A, Forotan Z, Bocobza SE. Increased rates of gene-editing events using a simplified RNAi configuration designed to reduce gene silencing. PLANT CELL REPORTS 2022; 41:1987-2003. [PMID: 35849200 DOI: 10.1007/s00299-022-02903-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 06/30/2022] [Indexed: 06/15/2023]
Abstract
An optimal RNAi configuration that could restrict gene expression most efficiently was determined. This approach was also used to target PTGS and yielded higher rates of gene-editing events. Although it was characterized long ago, transgene silencing still strongly impairs transgene overexpression, and thus is a major barrier to plant crop gene-editing. The development of strategies that could prevent transgene silencing is therefore essential to the success of gene editing assays. Transgene silencing occurs via the RNA silencing process, which regulates the expression of essential genes and protects the plant from viral infections. The RNA silencing machinery thereby controls central biological processes such as growth, development, genome integrity, and stress resistance. RNA silencing is typically induced by aberrant RNA, that may lack 5' or 3' processing, or may consist in double-stranded or hairpin RNA, and involves DICER and ARGONAUTE family proteins. In this study, RNAi inducing constructs were designed in eleven different configurations and were evaluated for their capacity to induce silencing in Nicotiana spp. using transient and stable transformation assays. Using reporter genes, it was found that the overexpression of a hairpin consisting of a forward tandem inverted repeat that started with an ATG and that was not followed downstream by a transcription terminator, could downregulate gene expression most potently. Furthermore, using this method, the downregulation of the NtSGS3 gene caused a significant increase in transgene expression both in transient and stable transformation assays. This SGS3 silencing approach was also employed in gene-editing assays and caused higher rates of gene-editing events. Taken together, these findings suggested the optimal genetic configuration to cause RNA silencing and showed that this strategy may be used to restrict PTGS during gene-editing experiments.
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Affiliation(s)
- Manoj Kumar
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Beit Dagan, Israel
| | - Pankaj Kumar Tripathi
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Beit Dagan, Israel
| | - Dana Ayzenshtat
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Beit Dagan, Israel
| | - Adar Marko
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Beit Dagan, Israel
| | - Zohar Forotan
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Beit Dagan, Israel
| | - Samuel E Bocobza
- Department of Ornamental Plants and Agricultural Biotechnology, The Institute of Plant Sciences, The Volcani Center, ARO, Beit Dagan, Israel.
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2
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Wittmeier A, Bernhardt M, Robisch AL, Cassini C, Osterhoff M, Salditt T, Köster S. Combined optical fluorescence microscopy and X-ray tomography reveals substructures in cell nuclei in 3D. BIOMEDICAL OPTICS EXPRESS 2022; 13:4954-4969. [PMID: 36187264 PMCID: PMC9484410 DOI: 10.1364/boe.462493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/08/2022] [Accepted: 07/27/2022] [Indexed: 06/16/2023]
Abstract
The function of a biological cell is fundamentally defined by the structural architecture of packaged DNA in the nucleus. Elucidating information about the packaged DNA is facilitated by high-resolution imaging. Here, we combine and correlate hard X-ray propagation-based phase contrast tomography and visible light confocal microscopy in three dimensions to probe DNA in whole cell nuclei of NIH-3T3 fibroblasts. In this way, unlabeled and fluorescently labeled substructures within the cell are visualized in a complementary manner. Our approach enables the quantification of the electron density, volume and optical fluorescence intensity of nuclear material. By joining all of this information, we are able to spatially localize and physically characterize both active and inactive heterochromatin, euchromatin, pericentric heterochromatin foci and nucleoli.
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Affiliation(s)
- Andrew Wittmeier
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Marten Bernhardt
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Anna-Lena Robisch
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Chiara Cassini
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Germany
| | - Markus Osterhoff
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
| | - Tim Salditt
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Germany
| | - Sarah Köster
- Institute for X-Ray Physics, University of Göttingen, Friedrich-Hund-Platz 1, 37077 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, Germany
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3
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Staneva DP, Carloni R, Auchynnikava T, Tong P, Rappsilber J, Jeyaprakash AA, Matthews KR, Allshire RC. A systematic analysis of Trypanosoma brucei chromatin factors identifies novel protein interaction networks associated with sites of transcription initiation and termination. Genome Res 2021; 31:2138-2154. [PMID: 34407985 PMCID: PMC8559703 DOI: 10.1101/gr.275368.121] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 08/09/2021] [Indexed: 02/07/2023]
Abstract
Nucleosomes composed of histones are the fundamental units around which DNA is wrapped to form chromatin. Transcriptionally active euchromatin or repressive heterochromatin is regulated in part by the addition or removal of histone post-translational modifications (PTMs) by "writer" and "eraser" enzymes, respectively. Nucleosomal PTMs are recognized by a variety of "reader" proteins that alter gene expression accordingly. The histone tails of the evolutionarily divergent eukaryotic parasite Trypanosoma brucei have atypical sequences and PTMs distinct from those often considered universally conserved. Here we identify 65 predicted readers, writers, and erasers of histone acetylation and methylation encoded in the T. brucei genome and, by epitope tagging, systemically localize 60 of them in the parasite's bloodstream form. ChIP-seq shows that 15 candidate proteins associate with regions of RNAPII transcription initiation. Eight other proteins show a distinct distribution with specific peaks at a subset of RNAPII transcription termination regions marked by RNAPIII-transcribed tRNA and snRNA genes. Proteomic analyses identify distinct protein interaction networks comprising known chromatin regulators and novel trypanosome-specific components. Notably, several SET- and Bromo-domain protein networks suggest parallels to RNAPII promoter-associated complexes in conventional eukaryotes. Further, we identify likely components of TbSWR1 and TbNuA4 complexes whose enrichment coincides with the SWR1-C exchange substrate H2A.Z at RNAPII transcription start regions. The systematic approach used provides details of the composition and organization of the chromatin regulatory machinery in T. brucei and establishes a route to explore divergence from eukaryotic norms in an evolutionarily ancient but experimentally accessible eukaryote.
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Affiliation(s)
- Desislava P Staneva
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Institute of Immunology and Infection Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - Roberta Carloni
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Institute of Immunology and Infection Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - Tatsiana Auchynnikava
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | | | - Juri Rappsilber
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Institute of Biotechnology, Technische Universität, 13355 Berlin, Germany
| | - A Arockia Jeyaprakash
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Keith R Matthews
- Institute of Immunology and Infection Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - Robin C Allshire
- Wellcome Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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4
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Fei Y, Pyott DE, Molnar A. Temperature modulates virus-induced transcriptional gene silencing via secondary small RNAs. THE NEW PHYTOLOGIST 2021; 232:356-371. [PMID: 34185326 DOI: 10.1111/nph.17586] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/17/2021] [Indexed: 05/08/2023]
Abstract
Virus-induced gene silencing (VIGS) can be harnessed to sequence-specifically degrade host transcripts and induce heritable epigenetic modifications referred to as virus-induced post-transcriptional gene silencing (ViPTGS) and virus-induced transcriptional gene silencing (ViTGS), respectively. Both ViPTGS and ViTGS enable manipulation of endogenous gene expression without the need for transgenesis. Although VIGS has been widely used in many plant species, it is not always uniform or highly efficient. The efficiency of VIGS is affected by developmental, physiological and environmental factors. Here, we use recombinant Tobacco rattle viruses (TRV) to study the effect of temperature on ViPTGS and ViTGS using GFP as a reporter gene of silencing in N. benthamiana 16c plants. We found that unlike ViPTGS, ViTGS was impaired at high temperature. Using a novel mismatch-small interfering RNA (siRNA) tool, which precisely distinguishes virus-derived (primary) from target-generated (secondary) siRNAs, we demonstrated that the lack of secondary siRNA production/amplification was responsible for inefficient ViTGS at 29°C. Moreover, inefficient ViTGS at 29°C inhibited the transmission of epigenetic gene silencing to the subsequent generations. Our finding contributes to understanding the impact of environmental conditions on primary and secondary siRNA production and may pave the way to design/optimize ViTGS for transgene-free crop improvement.
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Affiliation(s)
- Yue Fei
- Institute of Molecular Plant Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Douglas E Pyott
- Institute of Molecular Plant Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Attila Molnar
- Institute of Molecular Plant Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF, UK
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5
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Delbarre E, Janicki SM. Modulation of H3.3 chromatin assembly by PML: A way to regulate epigenetic inheritance. Bioessays 2021; 43:e2100038. [PMID: 34423467 DOI: 10.1002/bies.202100038] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 08/04/2021] [Accepted: 08/06/2021] [Indexed: 12/15/2022]
Abstract
Although the promyelocytic leukemia (PML) protein is renowned for regulating a wide range of cellular processes and as an essential component of PML nuclear bodies (PML-NBs), the mechanisms through which it exerts its broad physiological impact are far from fully elucidated. Here, we review recent studies supporting an emerging view that PML's pleiotropic effects derive, at least partially, from its role in regulating histone H3.3 chromatin assembly, a critical epigenetic mechanism. These studies suggest that PML maintains heterochromatin organization by restraining H3.3 incorporation. Examination of PML's contribution to H3.3 chromatin assembly in the context of the cell cycle and PML-NB assembly suggests that PML represses heterochromatic H3.3 deposition during S phase and that transcription and SUMOylation regulate PML's recruitment to heterochromatin. Elucidating PML' s contributions to H3.3-mediated epigenetic regulation will provide insight into PML's expansive influence on cellular physiology and open new avenues for studying oncogenesis linked to PML malfunction.
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Affiliation(s)
- Erwan Delbarre
- Faculty of Health Sciences, OsloMet-Oslo Metropolitan University, Oslo, Norway
| | - Susan M Janicki
- Drexel University Thomas R. Kline School of Law, Philadelphia, Pennsylvania, USA
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6
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Ebrahimzadegan R, Orooji F, Ma P, Mirzaghaderi G. Differentially Amplified Repetitive Sequences Among Aegilops tauschii Subspecies and Genotypes. FRONTIERS IN PLANT SCIENCE 2021; 12:716750. [PMID: 34490015 PMCID: PMC8417419 DOI: 10.3389/fpls.2021.716750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Genomic repetitive sequences commonly show species-specific sequence type, abundance, and distribution patterns, however, their intraspecific characteristics have been poorly described. We quantified the genomic repetitive sequences and performed single nucleotide polymorphism (SNP) analysis between 29 Ae. tauschii genotypes and subspecies using publicly available raw genomic Illumina sequence reads and used fluorescence in situ hybridization (FISH) to experimentally analyze some repeats. The majority of the identified repetitive sequences had similar contents and proportions between anathera, meyeri, and strangulata subspecies. However, two Ty3/gypsy retrotransposons (CL62 and CL87) showed significantly higher abundances, and CL1, CL119, CL213, CL217 tandem repeats, and CL142 retrotransposon (Ty1/copia type) showed significantly lower abundances in subspecies strangulata compared with the subspecies anathera and meyeri. One tandem repeat and 45S ribosomal DNA (45S rDNA) abundances showed a high variation between genotypes but their abundances were not subspecies specific. Phylogenetic analysis using the repeat abundances of the aforementioned clusters placed the strangulata subsp. in a distinct clade but could not discriminate anathera and meyeri. A near complete differentiation of anathera and strangulata subspecies was observed using SNP analysis; however, var. meyeri showed higher genetic diversity. FISH using major tandem repeats couldn't detect differences between subspecies, although (GAA)10 signal patterns generated two different karyotype groups. Taken together, the different classes of repetitive DNA sequences have differentially accumulated between strangulata and the other two subspecies of Ae. tauschii that is generally in agreement with spike morphology, implying that factors affecting repeatome evolution are variable even among highly closely related lineages.
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Affiliation(s)
- Rahman Ebrahimzadegan
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Fatemeh Orooji
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
| | - Pengtao Ma
- College of Life Sciences, Yantai University, Yantai, China
| | - Ghader Mirzaghaderi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Kurdistan, Sanandaj, Iran
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7
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Belyayev A, Jandová M, Josefiová J, Kalendar R, Mahelka V, Mandák B, Krak K. The major satellite DNA families of the diploid Chenopodium album aggregate species: Arguments for and against the "library hypothesis". PLoS One 2020; 15:e0241206. [PMID: 33108401 PMCID: PMC7591062 DOI: 10.1371/journal.pone.0241206] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 10/10/2020] [Indexed: 01/20/2023] Open
Abstract
Satellite DNA (satDNA) is one of the major fractions of the eukaryotic nuclear genome. Highly variable satDNA is involved in various genome functions, and a clear link between satellites and phenotypes exists in a wide range of organisms. However, little is known about the origin and temporal dynamics of satDNA. The “library hypothesis” indicates that the rapid evolutionary changes experienced by satDNAs are mostly quantitative. Although this hypothesis has received some confirmation, a number of its aspects are still controversial. A recently developed next-generation sequencing (NGS) method allows the determination of the satDNA landscape and could shed light on unresolved issues. Here, we explore low-coverage NGS data to infer satDNA evolution in the phylogenetic context of the diploid species of the Chenopodium album aggregate. The application of the Illumina read assembly algorithm in combination with Oxford Nanopore sequencing and fluorescent in situ hybridization allowed the estimation of eight satDNA families within the studied group, six of which were newly described. The obtained set of satDNA families of different origins can be divided into several categories, namely group-specific, lineage-specific and species-specific. In the process of evolution, satDNA families can be transmitted vertically and can be eliminated over time. Moreover, transposable element-derived satDNA families may appear repeatedly in the satellitome, creating an illusion of family conservation. Thus, the obtained data refute the “library hypothesis”, rather than confirming it, and in our opinion, it is more appropriate to speak about “the library of the mechanisms of origin”.
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Affiliation(s)
- Alexander Belyayev
- The Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
- * E-mail:
| | - Michaela Jandová
- The Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Jiřina Josefiová
- The Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Ruslan Kalendar
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
| | - Václav Mahelka
- The Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
| | - Bohumil Mandák
- The Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Praha, Suchdol, Czech Republic
| | - Karol Krak
- The Czech Academy of Sciences, Institute of Botany, Průhonice, Czech Republic
- Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Praha, Suchdol, Czech Republic
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8
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Belyayev A, Josefiová J, Jandová M, Mahelka V, Krak K, Mandák B. Transposons and satellite DNA: on the origin of the major satellite DNA family in the Chenopodium genome. Mob DNA 2020; 11:20. [PMID: 32607133 PMCID: PMC7320549 DOI: 10.1186/s13100-020-00219-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 06/19/2020] [Indexed: 11/10/2022] Open
Abstract
Extensive and complex links exist between transposable elements (TEs) and satellite DNA (satDNA), which are the two largest fractions of eukaryotic genome. These relationships have a crucial effect on genome structure, function and evolution. Here, we report a novel case of mutual relationships between TEs and satDNA. In the genomes of Chenopodium s. str. species, the deletion derivatives of tnp2 conserved domain of the newly discovered CACTA-like TE Jozin are involved in generating monomers of the most abundant satDNA family of the Chenopodium satellitome. The analysis of the relative positions of satDNA and different TEs utilizing assembled Illumina reads revealed several associations between satDNA arrays and the transposases of putative CACTA-like elements when an ~ 40 bp fragment of tnp2 served as the start monomer of the satDNA array. The high degree of identity of the consensus satDNA monomers of the investigated species and the tnp2 fragment (from 82.1 to 94.9%) provides evidence of the genesis of CficCl-61-40 satDNA family monomers from analogous regions of their respective parental elements. The results were confirmed via molecular genetic methods and Oxford Nanopore sequencing. The discovered phenomenon leads to the continuous replenishment of species genomes with new identical satDNA monomers, which in turn may increase species satellitomes similarity.
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Affiliation(s)
- Alexander Belyayev
- Czech Academy of Sciences, Institute of Botany, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Jiřina Josefiová
- Czech Academy of Sciences, Institute of Botany, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Michaela Jandová
- Czech Academy of Sciences, Institute of Botany, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Václav Mahelka
- Czech Academy of Sciences, Institute of Botany, Zámek 1, CZ-252 43 Průhonice, Czech Republic
| | - Karol Krak
- Czech Academy of Sciences, Institute of Botany, Zámek 1, CZ-252 43 Průhonice, Czech Republic.,Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha, Suchdol Czech Republic
| | - Bohumil Mandák
- Czech Academy of Sciences, Institute of Botany, Zámek 1, CZ-252 43 Průhonice, Czech Republic.,Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 00 Praha, Suchdol Czech Republic
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9
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Bhattacharjee S, Roche B, Martienssen RA. RNA-induced initiation of transcriptional silencing (RITS) complex structure and function. RNA Biol 2019; 16:1133-1146. [PMID: 31213126 DOI: 10.1080/15476286.2019.1621624] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Heterochromatic regions of the genome are epigenetically regulated to maintain a heritable '"silent state"'. In fission yeast and other organisms, epigenetic silencing is guided by nascent transcripts, which are targeted by the RNA interference pathway. The key effector complex of the RNA interference pathway consists of small interfering RNA molecules (siRNAs) associated with Argonaute, assembled into the RNA-induced transcriptional silencing (RITS) complex. This review focuses on our current understanding of how RITS promotes heterochromatin formation, and in particular on the role of Argonaute-containing complexes in many other functions such as quelling, release of RNA polymerases, cellular quiescence and genome defense.
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Affiliation(s)
- Sonali Bhattacharjee
- a Cold Spring Harbor Laboratory, Howard Hughes Medical Institute , Cold Spring Harbor , NY , USA
| | - Benjamin Roche
- a Cold Spring Harbor Laboratory, Howard Hughes Medical Institute , Cold Spring Harbor , NY , USA
| | - Robert A Martienssen
- a Cold Spring Harbor Laboratory, Howard Hughes Medical Institute , Cold Spring Harbor , NY , USA
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10
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Samoluk SS, Chalup LMI, Chavarro C, Robledo G, Bertioli DJ, Jackson SA, Seijo G. Heterochromatin evolution in Arachis investigated through genome-wide analysis of repetitive DNA. PLANTA 2019; 249:1405-1415. [PMID: 30680457 DOI: 10.1007/s00425-019-03096-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/18/2019] [Indexed: 05/21/2023]
Abstract
The most conspicuous difference among chromosomes and genomes in Arachis species, the patterns of heterochromatin, was mainly modeled by differential amplification of different members of one superfamily of satellite DNAs. Divergence in repetitive DNA is a primary driving force for genome and chromosome evolution. Section Arachis is karyotypically diverse and has six different genomes. Arachis glandulifera (D genome) has the most asymmetric karyotype and the highest reproductive isolation compared to the well-known A and B genome species. These features make A. glandulifera an interesting model species for studying the main repetitive components that accompanied the genome and chromosome diversification in the section. Here, we performed a genome-wide analysis of repetitive sequences in A. glandulifera and investigated the chromosome distribution of the identified satellite DNA sequences (satDNAs). LTR retroelements, mainly the Ty3-gypsy families "Fidel/Feral" and "Pipoka/Pipa", were the most represented. Comparative analyses with the A and B genomes showed that many of the previously described transposable elements (TEs) were differently represented in the D genome, and that this variation accompanied changes in DNA content. In addition, four major satDNAs were characterized. Agla_CL8sat was the major component of pericentromeric heterochromatin, while Agla_CL39sat, Agla_CL69sat, and Agla_CL122sat were found in heterochromatic and/or euchromatic regions. Even though Agla_CL8sat belong to a different family than that of the major satDNA (ATR-2) found in the heterochromatin of the A, K, and F genomes, both satDNAs are members of the same superfamily. This finding suggests that closely related satDNAs of an ancestral library were differentially amplified leading to the major changes in the heterochromatin patterns that accompanied the karyotype and genome differentiation in Arachis.
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Affiliation(s)
- Sergio S Samoluk
- Facultad de Ciencias Agrarias, Instituto de Botánica del Nordeste (UNNE-CONICET), Corrientes, Argentina.
| | - Laura M I Chalup
- Facultad de Ciencias Agrarias, Instituto de Botánica del Nordeste (UNNE-CONICET), Corrientes, Argentina
| | - Carolina Chavarro
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Germán Robledo
- Facultad de Ciencias Agrarias, Instituto de Botánica del Nordeste (UNNE-CONICET), Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
| | - David J Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Guillermo Seijo
- Facultad de Ciencias Agrarias, Instituto de Botánica del Nordeste (UNNE-CONICET), Corrientes, Argentina
- Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
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11
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Natural History of a Satellite DNA Family: From the Ancestral Genome Component to Species-Specific Sequences, Concerted and Non-Concerted Evolution. Int J Mol Sci 2019; 20:ijms20051201. [PMID: 30857296 PMCID: PMC6429384 DOI: 10.3390/ijms20051201] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/04/2019] [Accepted: 03/06/2019] [Indexed: 12/20/2022] Open
Abstract
Satellite DNA (satDNA) is the most variable fraction of the eukaryotic genome. Related species share a common ancestral satDNA library and changing of any library component in a particular lineage results in interspecific differences. Although the general developmental trend is clear, our knowledge of the origin and dynamics of satDNAs is still fragmentary. Here, we explore whole genome shotgun Illumina reads using the RepeatExplorer (RE) pipeline to infer satDNA family life stories in the genomes of Chenopodium species. The seven diploids studied represent separate lineages and provide an example of a species complex typical for angiosperms. Application of the RE pipeline allowed by similarity searches a determination of the satDNA family with a basic monomer of ~40 bp and to trace its transformation from the reconstructed ancestral to the species-specific sequences. As a result, three types of satDNA family evolutionary development were distinguished: (i) concerted evolution with mutation and recombination events; (ii) concerted evolution with a trend toward increased complexity and length of the satellite monomer; and (iii) non-concerted evolution, with low levels of homogenization and multidirectional trends. The third type is an example of entire repeatome transformation, thus producing a novel set of satDNA families, and genomes showing non-concerted evolution are proposed as a significant source for genomic diversity.
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12
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Parsa JY, Boudoukha S, Burke J, Homer C, Madhani HD. Polymerase pausing induced by sequence-specific RNA-binding protein drives heterochromatin assembly. Genes Dev 2018; 32:953-964. [PMID: 29967291 PMCID: PMC6075038 DOI: 10.1101/gad.310136.117] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 05/18/2018] [Indexed: 01/09/2023]
Abstract
In this study, Parsa et al. investigated the mechanisms underlying RNAi-independent heterochromatin assembly by the CTD–RRM protein Seb1 in S. pombe. They show that Seb1 promotes long-lived RNAPII pauses at pericentromeric repeat regions and that their presence correlates with the heterochromatin-triggering activities of the corresponding dg and dh DNA fragments, providing new insight into Seb1-mediated polymerase stalling as a signal necessary for heterochromatin nucleation. In Schizosaccharomyces pombe, transcripts derived from the pericentromeric dg and dh repeats promote heterochromatin formation via RNAi as well as an RNAi-independent mechanism involving the RNA polymerase II (RNAPII)-associated RNA-binding protein Seb1 and RNA processing activities. We show that Seb1 promotes long-lived RNAPII pauses at pericentromeric repeat regions and that their presence correlates with the heterochromatin-triggering activities of the corresponding dg and dh DNA fragments. Globally increasing RNAPII stalling by other means induces the formation of novel large ectopic heterochromatin domains. Such ectopic heterochromatin occurs even in cells lacking RNAi. These results uncover Seb1-mediated polymerase stalling as a signal necessary for heterochromatin nucleation.
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Affiliation(s)
- Jahan-Yar Parsa
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
| | - Selim Boudoukha
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
| | - Jordan Burke
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
| | - Christina Homer
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California at San Francisco, San Francisco, California 94158, USA.,Chan-Zuckerberg Biohub, San Francisco, California 94158, USA
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13
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McCullers TJ, Steiniger M. Transposable elements in Drosophila. Mob Genet Elements 2017; 7:1-18. [PMID: 28580197 PMCID: PMC5443660 DOI: 10.1080/2159256x.2017.1318201] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 04/07/2017] [Accepted: 04/07/2017] [Indexed: 11/09/2022] Open
Abstract
Transposable elements (TEs) are mobile genetic elements that can mobilize within host genomes. As TEs comprise more than 40% of the human genome and are linked to numerous diseases, understanding their mechanisms of mobilization and regulation is important. Drosophila melanogaster is an ideal model organism for the study of eukaryotic TEs as its genome contains a diverse array of active TEs. TEs universally impact host genome size via transposition and deletion events, but may also adopt unique functional roles in host organisms. There are 2 main classes of TEs: DNA transposons and retrotransposons. These classes are further divided into subgroups of TEs with unique structural and functional characteristics, demonstrating the significant variability among these elements. Despite this variability, D. melanogaster and other eukaryotic organisms utilize conserved mechanisms to regulate TEs. This review focuses on the transposition mechanisms and regulatory pathways of TEs, and their functional roles in D. melanogaster.
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Affiliation(s)
| | - Mindy Steiniger
- Department of Biology, University of Missouri, St. Louis, MO, USA
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14
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Almouzni G, Cedar H. Maintenance of Epigenetic Information. Cold Spring Harb Perspect Biol 2016; 8:8/5/a019372. [PMID: 27141050 DOI: 10.1101/cshperspect.a019372] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The genome is subject to a diverse array of epigenetic modifications from DNA methylation to histone posttranslational changes. Many of these marks are somatically stable through cell division. This article focuses on our knowledge of the mechanisms governing the inheritance of epigenetic marks, particularly, repressive ones, when the DNA and chromatin template are duplicated in S phase. This involves the action of histone chaperones, nucleosome-remodeling enzymes, histone and DNA methylation binding proteins, and chromatin-modifying enzymes. Last, the timing of DNA replication is discussed, including the question of whether this constitutes an epigenetic mark that facilitates the propagation of epigenetic marks.
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Affiliation(s)
- Geneviève Almouzni
- Department of Nuclear Dynamics and Genome Plasticity, Institut Curie, Section de recherche, 75231 Paris Cedex 05, France
| | - Howard Cedar
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Ein Kerem, Jerusalem, Israel 91120
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15
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Craddock EM, Gall JG, Jonas M. Hawaiian Drosophila genomes: size variation and evolutionary expansions. Genetica 2016; 144:107-24. [PMID: 26790663 DOI: 10.1007/s10709-016-9882-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 01/09/2016] [Indexed: 01/24/2023]
Abstract
This paper reports genome sizes of one Hawaiian Scaptomyza and 16 endemic Hawaiian Drosophila species that include five members of the antopocerus species group, one member of the modified mouthpart group, and ten members of the picture wing clade. Genome size expansions have occurred independently multiple times among Hawaiian Drosophila lineages, and have resulted in an over 2.3-fold range of genome sizes among species, with the largest observed in Drosophila cyrtoloma (1C = 0.41 pg). We find evidence that these repeated genome size expansions were likely driven by the addition of significant amounts of heterochromatin and satellite DNA. For example, our data reveal that the addition of seven heterochromatic chromosome arms to the ancestral haploid karyotype, and a remarkable proportion of ~70 % satellite DNA, account for the greatly expanded size of the D. cyrtoloma genome. Moreover, the genomes of 13/17 Hawaiian picture wing species are composed of substantial proportions (22-70 %) of detectable satellites (all but one of which are AT-rich). Our results suggest that in this tightly knit group of recently evolved species, genomes have expanded, in large part, via evolutionary amplifications of satellite DNA sequences in centric and pericentric domains (especially of the X and dot chromosomes), which have resulted in longer acrocentric chromosomes or metacentrics with an added heterochromatic chromosome arm. We discuss possible evolutionary mechanisms that may have shaped these patterns, including rapid fixation of novel expanded genomes during founder-effect speciation.
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Affiliation(s)
- Elysse M Craddock
- Natural Sciences Building, Purchase College, State University of New York, 735 Anderson Hill Road, Purchase, NY, 10577, USA.
| | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Mark Jonas
- Natural Sciences Building, Purchase College, State University of New York, 735 Anderson Hill Road, Purchase, NY, 10577, USA
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16
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Stunnenberg R, Kulasegaran-Shylini R, Keller C, Kirschmann MA, Gelman L, Bühler M. H3K9 methylation extends across natural boundaries of heterochromatin in the absence of an HP1 protein. EMBO J 2015; 34:2789-803. [PMID: 26438724 PMCID: PMC4682641 DOI: 10.15252/embj.201591320] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 09/03/2015] [Indexed: 12/13/2022] Open
Abstract
Proteins of the conserved HP1 family are elementary components of heterochromatin and are generally assumed to play a central role in the creation of a rigid, densely packed heterochromatic network that is inaccessible to the transcription machinery. Here, we demonstrate that the fission yeast HP1 protein Swi6 exists as a single highly dynamic population that rapidly exchanges in cis and in trans between different heterochromatic regions. Binding to methylated H3K9 or to heterochromatic RNA decelerates Swi6 mobility. We further show that Swi6 is largely dispensable to the maintenance of heterochromatin domains. In the absence of Swi6, H3K9 methylation levels are maintained by a mechanism that depends on polymeric self‐association properties of Tas3, a subunit of the RNA‐induced transcriptional silencing complex. Our results disclose a surprising role for Swi6 dimerization in demarcating constitutive heterochromatin from neighboring euchromatin. Thus, rather than promoting maintenance and spreading of heterochromatin, Swi6 appears to limit these processes and appropriately confine heterochromatin.
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Affiliation(s)
- Rieka Stunnenberg
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland University of Basel, Basel, Switzerland
| | | | - Claudia Keller
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland University of Basel, Basel, Switzerland
| | | | - Laurent Gelman
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Marc Bühler
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland University of Basel, Basel, Switzerland
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17
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Akiyama T, Xin L, Oda M, Sharov AA, Amano M, Piao Y, Cadet JS, Dudekula DB, Qian Y, Wang W, Ko SBH, Ko MSH. Transient bursts of Zscan4 expression are accompanied by the rapid derepression of heterochromatin in mouse embryonic stem cells. DNA Res 2015; 22:307-18. [PMID: 26324425 PMCID: PMC4596397 DOI: 10.1093/dnares/dsv013] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 06/24/2015] [Indexed: 01/06/2023] Open
Abstract
Mouse embryonic stem cells (mESCs) have a remarkable capacity to maintain normal genome stability and karyotype in culture. We previously showed that infrequent bursts of Zscan4 expression (Z4 events) are important for the maintenance of telomere length and genome stability in mESCs. However, the molecular details of Z4 events remain unclear. Here we show that Z4 events involve unexpected transcriptional derepression in heterochromatin regions that usually remain silent. During a Z4 event, we see rapid derepression and rerepression of heterochromatin leading to a burst of transcription that coincides with transient histone hyperacetylation and DNA demethylation, clustering of pericentromeric heterochromatin around the nucleolus, and accumulation of activating and repressive chromatin remodelling complexes. This heterochromatin-based transcriptional activity suggests that mESCs may maintain their extraordinary genome stability at least in part by transiently resetting their heterochromatin.
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Affiliation(s)
- Tomohiko Akiyama
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160, Japan Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Li Xin
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Mayumi Oda
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160, Japan
| | - Alexei A Sharov
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Misa Amano
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Yulan Piao
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - J Scotty Cadet
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Dawood B Dudekula
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Yong Qian
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Weidong Wang
- Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Shigeru B H Ko
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160, Japan
| | - Minoru S H Ko
- Department of Systems Medicine, Keio University School of Medicine, Tokyo 160, Japan Laboratory of Genetics, National Institute on Aging, NIH, Baltimore, MD 21224, USA
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18
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A Single RNaseIII Domain Protein from Entamoeba histolytica Has dsRNA Cleavage Activity and Can Help Mediate RNAi Gene Silencing in a Heterologous System. PLoS One 2015; 10:e0133740. [PMID: 26230096 PMCID: PMC4521922 DOI: 10.1371/journal.pone.0133740] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Accepted: 06/30/2015] [Indexed: 11/25/2022] Open
Abstract
Dicer enzymes process double-stranded RNA (dsRNA) into small RNAs that target gene silencing through the RNA interference (RNAi) pathway. Dicer enzymes are complex, multi-domain RNaseIII proteins, however structural minimalism of this protein has recently emerged in parasitic and fungal systems. The most minimal Dicer, Saccharomyces castellii Dicer1, has a single RNaseIII domain and two double stranded RNA binding domains. In the protozoan parasite Entamoeba histolytica 27nt small RNAs are abundant and mediate silencing, yet no canonical Dicer enzyme has been identified. Although EhRNaseIII does not exhibit robust dsRNA cleavage in vitro, it can process dsRNA in the RNAi-negative background of Saccharomyces cerevisiae, and in conjunction with S. castellii Argonaute1 can partially reconstitute the RNAi pathway. Thus, although EhRNaseIII lacks the domain architecture of canonical or minimal Dicer enzymes, it has dsRNA processing activity that contributes to gene silencing via RNAi. Our data advance the understanding of small RNA biogenesis in Entamoeba as well as broaden the spectrum of non-canonical Dicer enzymes that contribute to the RNAi pathway.
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19
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Peschansky VJ, Wahlestedt C. Non-coding RNAs as direct and indirect modulators of epigenetic regulation. Epigenetics 2015; 9:3-12. [PMID: 24739571 DOI: 10.4161/epi.27473] [Citation(s) in RCA: 341] [Impact Index Per Article: 37.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Epigenetic regulation of gene expression is an increasingly well-understood concept that explains much of the contribution of an organism's environment and experience to its biology. However, discussion persists as to which mechanisms can be classified as epigenetic. Ongoing research continues to uncover novel pathways, including the important role of non-protein coding RNA transcripts in epigenetic gene regulation. We know that the majority of human and other mammalian transcripts are not translated but that many of these are nonetheless functional. These non-coding RNAs (ncRNAs) can be short (<200 nt) or long (<200 nt) and are further classified by genomic origin and mechanism of action. We discuss examples of ncRNAs that interact with histone modifying complexes or DNA methyltransferases to regulate gene expression, others that are targets of these epigenetic mechanisms, and propose a model in which such transcripts feed back into an epigenetic regulatory network.
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Affiliation(s)
- Veronica J Peschansky
- Center for Therapeutic Innovation & Department of Psychiatry and Behavioral Sciences; University of Miami; Miller School of Medicine; Miami, FL USA
| | - Claes Wahlestedt
- Center for Therapeutic Innovation & Department of Psychiatry and Behavioral Sciences; University of Miami; Miller School of Medicine; Miami, FL USA
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20
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Gandhi SG, Bag I, Sengupta S, Pal-Bhadra M, Bhadra U. Drosophila oncogene Gas41 is an RNA interference modulator that intersects heterochromatin and the small interfering RNA pathway. FEBS J 2014; 282:153-73. [PMID: 25323651 DOI: 10.1111/febs.13115] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 10/09/2014] [Accepted: 10/15/2014] [Indexed: 12/27/2022]
Abstract
Glioma amplified sequence41 (Gas41) is a highly conserved putative transcription factor that is frequently abundant in human gliomas. Gas41 shows oncogenic activity by promoting cell growth and viability. In the present study, we show that Gas41 is required for proper functioning of RNA interference (RNAi) machinery in the nuclei, although three basic structural domains of RNAi components PAZ, PIWI and dsRNA with respect to binding are absent in the structural sequences. Variations of structural domains are highly conserved among prokaryotes and eukaryotes. Gas41 interacts with cytological RNase III enzyme Dicer1 both biochemically and genetically. However, Drosophila Gas41 functions as chromatin remodeler and interacts with different heterochromatin markers and repeat-induced transgene silencing by modulating position effect variegation. We also show that transcriptional inactive Gas41 mutant interferes with the functional assembly of heterochromatin-associated proteins, dimethylated lysine 9 of histone H3 and heterochromatic protein 1 in developing embryos. A reduction of heterochromatic markers is accompanied by the mini-w promoter sequence in Gas41 mutants. These findings suggest that Drosophila Gas41 guides the repeat associated gene silencing and the Dicer1 interaction, thereby depicting a new role for Gas41. Gas41 is a critical RNAi component. In Drosophila, Gas41 plays a dual role. On the one hand, it appears to participate with Dicer 1 in the RNAi pathway and, alternatively, it also participates in repeat-induced gene silencing by accumulating heterochromatin proteins at the mini-w array promoters. Therefore, it represents an intriguing and apparently paradoxical new finding in RNA technology with respect to the process of heterochromatin gene silencing.
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Affiliation(s)
- Sumit G Gandhi
- Functional Genomics and Gene Silencing Group, Centre for Cellular and Molecular Biology-CSIR, Hyderabad, India
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21
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Ghosh S, Kakumani PK, Kumar A, Malhotra P, Mukherjee SK, Bhatnagar RK. Genome wide screening of RNAi factors of Sf21 cells reveal several novel pathway associated proteins. BMC Genomics 2014; 15:775. [PMID: 25199785 PMCID: PMC4247154 DOI: 10.1186/1471-2164-15-775] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 08/29/2014] [Indexed: 12/18/2022] Open
Abstract
Background RNA interference (RNAi) leads to sequence specific knock-down of gene expression and has emerged as an important tool to analyse gene functions, pathway analysis and gene therapy. Although RNAi is a conserved cellular process involving common elements and factors, species-specific differences have been observed among different eukaryotes. Identification of components for RNAi pathway is pursued intensively and successful genome-wide screens have been performed for components of RNAi pathways in various organisms. Functional comparative genomics analysis offers evolutionary insight that forms basis of discoveries of novel RNAi-factors within related organisms. Keeping in view the academic and commercial utility of insect derived cell-line from Spodoptera frugiperda, we pursued the identification and functional analysis of components of RNAi-machinery of Sf21 cell-line using genome-wide application. Results The genome and transcriptome of Sf21 was assembled and annotated. In silico application of comparative genome analysis among insects allowed us to identify several RNAi factors in Sf21 line. The candidate RNAi factors from assembled genome were validated by knockdown analysis of candidate factors using the siRNA screens on the Sf21-gfp reporter cell-line. Forty two (42) potential factors were identified using the cell based assay. These include core RNAi elements including Dicer-2, Argonaute-1, Drosha, Aubergine and auxiliary modules like chromatin factors, RNA helicases, RNA processing module, signalling allied proteins and others. Phylogenetic analyses and domain architecture revealed that Spodoptera frugiperda homologs retained identity with Lepidoptera (Bombyx mori) or Coleoptera (Tribolium castaneum) sustaining an evolutionary conserved scaffold in post-transcriptional gene silencing paradigm within insects. Conclusion The database of RNAi-factors generated by whole genome association survey offers comprehensive outlook about conservation as well as specific differences of the proteins of RNAi machinery. Understanding the interior involved in different phases of gene silencing also offers impending tool for RNAi-based applications. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-775) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Pawan Malhotra
- Insect Resistance Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India.
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22
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RNAi pathway genes are resistant to small RNA mediated gene silencing in the protozoan parasite Entamoeba histolytica. PLoS One 2014; 9:e106477. [PMID: 25198343 PMCID: PMC4157801 DOI: 10.1371/journal.pone.0106477] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 08/08/2014] [Indexed: 01/19/2023] Open
Abstract
The RNA interference pathway in the protist Entamoeba histolytica plays important roles in permanent gene silencing as well as in the regulation of virulence determinants. Recently, a novel RNA interference (RNAi)-based silencing technique was developed in this parasite that uses a gene endogenously silenced by small RNAs as a “trigger” to induce silencing of other genes that are fused to it. Fusion to a trigger gene induces the production of gene-specific antisense small RNAs, resulting in robust and permanent silencing of the cognate gene. This approach has silenced multiple genes including those involved in virulence and transcriptional regulation. We now demonstrate that all tested genes of the amebic RNAi pathway are unable to be silenced using the trigger approach, including Argonaute genes (Ago2-1, Ago2-2, and Ago2-3), RNaseIII, and RNA-dependent RNA polymerase (RdRP). In all situations (except for RdRP), fusion to a trigger successfully induces production of gene-specific antisense small RNAs to the cognate gene. These small RNAs are capable of silencing a target gene in trans, indicating that they are functional; despite this, however, they cannot silence the RNAi pathway genes. Interestingly, when a trigger is fused to RdRP, small RNA induction to RdRP does not occur, a unique phenotype hinting that either RdRP is highly resistant to being a target of small RNAs or that small RNA generation may be controlled by RdRP. The inability of the small RNA pathway to silence RNAi genes in E. histolytica, despite the generation of functional small RNAs to these loci suggest that epigenetic factors may protect certain genomic loci and thus determine susceptibility to small RNA mediated silencing.
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23
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Ariel F, Jegu T, Latrasse D, Romero-Barrios N, Christ A, Benhamed M, Crespi M. Noncoding transcription by alternative RNA polymerases dynamically regulates an auxin-driven chromatin loop. Mol Cell 2014; 55:383-96. [PMID: 25018019 DOI: 10.1016/j.molcel.2014.06.011] [Citation(s) in RCA: 249] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 04/29/2014] [Accepted: 06/04/2014] [Indexed: 11/19/2022]
Abstract
The eukaryotic epigenome is shaped by the genome topology in three-dimensional space. Dynamic reversible variations in this epigenome structure directly influence the transcriptional responses to developmental cues. Here, we show that the Arabidopsis long intergenic noncoding RNA (lincRNA) APOLO is transcribed by RNA polymerases II and V in response to auxin, a phytohormone controlling numerous facets of plant development. This dual APOLO transcription regulates the formation of a chromatin loop encompassing the promoter of its neighboring gene PID, a key regulator of polar auxin transport. Altering APOLO expression affects chromatin loop formation, whereas RNA-dependent DNA methylation, active DNA demethylation, and Polycomb complexes control loop dynamics. This dynamic chromatin topology determines PID expression patterns. Hence, the dual transcription of a lincRNA influences local chromatin topology and directs dynamic auxin-controlled developmental outputs on neighboring genes. This mechanism likely underscores the adaptive success of plants in diverse environments and may be widespread in eukaryotes.
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Affiliation(s)
- Federico Ariel
- CNRS, Institut des Sciences du Végétal, Saclay Plant Sciences, 91198 Gif-sur-Yvette and Université Paris Diderot-Paris 7, 75013 Paris, France
| | - Teddy Jegu
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, SPS Saclay Plant Sciences, 91405 Orsay, France
| | - David Latrasse
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, SPS Saclay Plant Sciences, 91405 Orsay, France
| | - Natali Romero-Barrios
- CNRS, Institut des Sciences du Végétal, Saclay Plant Sciences, 91198 Gif-sur-Yvette and Université Paris Diderot-Paris 7, 75013 Paris, France
| | - Aurélie Christ
- CNRS, Institut des Sciences du Végétal, Saclay Plant Sciences, 91198 Gif-sur-Yvette and Université Paris Diderot-Paris 7, 75013 Paris, France
| | - Moussa Benhamed
- Institut de Biologie des Plantes, UMR8618 Université Paris-Sud XI, SPS Saclay Plant Sciences, 91405 Orsay, France; Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.
| | - Martin Crespi
- CNRS, Institut des Sciences du Végétal, Saclay Plant Sciences, 91198 Gif-sur-Yvette and Université Paris Diderot-Paris 7, 75013 Paris, France.
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Sentmanat M, Wang SH, Elgin SCR. Targeting heterochromatin formation to transposable elements in Drosophila: potential roles of the piRNA system. BIOCHEMISTRY (MOSCOW) 2014; 78:562-71. [PMID: 23980883 DOI: 10.1134/s0006297913060023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Successful heterochromatin formation is critical for genome stability in eukaryotes, both to maintain structures needed for mitosis and meiosis and to silence potentially harmful transposable elements. Conversely, inappropriate heterochromatin assembly can lead to inappropriate silencing and other deleterious effects. Hence targeting heterochromatin assembly to appropriate regions of the genome is of utmost importance. Here we focus on heterochromatin assembly in Drosophila melanogaster, the model organism in which variegation, or cell-to-cell variable gene expression resulting from heterochromatin formation, was first described. In particular, we review the potential role of transposable elements as genetic determinants of the chromatin state and examine how small RNA pathways may participate in the process of targeted heterochromatin formation.
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Affiliation(s)
- M Sentmanat
- Department of Biology, Washington University, St. Louis, MO 63130-4899, USA
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25
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Abstract
The former perception of the spermatozoon as a delivery device of the male genome has been expanded to include a new understanding of the cell's complex role in fertilization. Once the spermatozoon reaches the oocyte, it triggers egg activation and orchestrates the stages of pre- and post-fertilization in a preprogrammed pattern while tapping the oocyte's resources in an effort to generate a new life.
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Affiliation(s)
- Queenie V Neri
- The Ronald O. Perelman and Claudia Cohen Center for Reproductive Medicine, Weill Cornell Medical College, 1305 York Avenue, Suite 720, New York, NY, 10021, USA
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26
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Le Masson I, Jauvion V, Bouteiller N, Rivard M, Elmayan T, Vaucheret H. Mutations in the Arabidopsis H3K4me2/3 demethylase JMJ14 suppress posttranscriptional gene silencing by decreasing transgene transcription. THE PLANT CELL 2012; 24:3603-12. [PMID: 23001035 PMCID: PMC3480290 DOI: 10.1105/tpc.112.103119] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 07/23/2012] [Accepted: 08/29/2012] [Indexed: 05/23/2023]
Abstract
Posttranscriptional gene silencing (PTGS) mediated by sense transgenes (S-PTGS) results in RNA degradation and DNA methylation of the transcribed region. Through a forward genetic screen, a mutant defective in the Histone3 Lysine4 di/trimethyl (H3K4me2/3) demethylase Jumonji-C (JmjC) domain-containing protein14 (JMJ14) was identified. This mutant reactivates various transgenes silenced by S-PTGS and shows reduced Histone3 Lysine9 Lysine14 acetylation (H3K9K14Ac) levels, reduced polymerase II occupancy, reduced transgene transcription, and increased DNA methylation in the promoter region, consistent with the hypothesis that high levels of transcription are required to trigger S-PTGS. The jmj14 mutation also reduces the expression of transgenes that do not trigger S-PTGS. Moreover, expression of transgenes that undergo S-PTGS in a wild-type background is reduced in jmj14 sgs3 double mutants compared with PTGS-deficient sgs3 mutants, indicating that JMJ14 is required for high levels of transcription in a PTGS-independent manner. Whereas endogenous loci regulated by JMJ14 exhibit increased H3K4me2 and H3K4me3 levels in the jmj14 mutant, transgene loci exhibit unchanged H3K4me2 and decreased H3K4me3 levels. Because jmj14 mutations impair PTGS of transgenes expressed under various plant or viral promoters, we hypothesize that JMJ14 demethylation activity is prevented by antagonistic epigenetic marks specifically imposed at transgene loci. Removing JMJ14 likely allows other H3K4 demethylases encoded by the Arabidopsis thaliana genome to act on transgenes and reduce transcription levels, thus preventing the triggering of S-PTGS.
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Ectopic assembly of heterochromatin in Drosophila melanogaster triggered by transposable elements. Proc Natl Acad Sci U S A 2012; 109:14104-9. [PMID: 22891327 DOI: 10.1073/pnas.1207036109] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
A persistent question in biology is how cis-acting sequence elements influence trans-acting factors and the local chromatin environment to modulate gene expression. We reported previously that the DNA transposon 1360 can enhance silencing of a reporter in a heterochromatic domain of Drosophila melanogaster. We have now generated a collection of variegating phiC31 landing-pad insertion lines containing 1360 and a heat-shock protein 70 (hsp70)-driven white reporter to explore the mechanism of 1360-sensitive silencing. Many 1360-sensitive sites were identified, some in apparently euchromatic domains, although all are close to heterochromatic masses. One such site (line 1198; insertion near the base of chromosome arm 2L) has been investigated in detail. ChIP analysis shows 1360-dependent Heterochromatin Protein 1a (HP1a) accumulation at this otherwise euchromatic site. The phiC31 landing pad system allows different 1360 constructs to be swapped with the full-length element at the same genomic site to identify the sequences that mediate 1360-sensitive silencing. Short deletions over sites with homology to PIWI-interacting RNAs (piRNAs) are sufficient to compromise 1360-sensitive silencing. Similar results were obtained on replacing 1360 with Invader4 (a retrotransposon), suggesting that this phenomenon likely applies to a broader set of transposable elements. Our results suggest a model in which piRNA sequence elements behave as cis-acting targets for heterochromatin assembly, likely in the early embryo, where piRNA pathway components are abundant, with the heterochromatic state subsequently propagated by chromatin modifiers present in somatic tissue.
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Franks PJ, Leitch IJ, Ruszala EM, Hetherington AM, Beerling DJ. Physiological framework for adaptation of stomata to CO2 from glacial to future concentrations. Philos Trans R Soc Lond B Biol Sci 2012; 367:537-46. [PMID: 22232765 DOI: 10.1098/rstb.2011.0270] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
In response to short-term fluctuations in atmospheric CO(2) concentration, c(a), plants adjust leaf diffusive conductance to CO(2), g(c), via feedback regulation of stomatal aperture as part of a mechanism for optimizing CO(2) uptake with respect to water loss. The operational range of this elaborate control mechanism is determined by the maximum diffusive conductance to CO(2), g(c(max)), which is set by the size (S) and density (number per unit area, D) of stomata on the leaf surface. Here, we show that, in response to long-term exposure to elevated or subambient c(a), plants alter g(c(max)) in the direction of the short-term feedback response of g(c) to c(a) via adjustment of S and D. This adaptive feedback response to c(a), consistent with long-term optimization of leaf gas exchange, was observed in four species spanning a diverse taxonomic range (the lycophyte Selaginella uncinata, the fern Osmunda regalis and the angiosperms Commelina communis and Vicia faba). Furthermore, using direct observation as well as flow cytometry, we observed correlated increases in S, guard cell nucleus size and average apparent 1C DNA amount in epidermal cell nuclei with increasing c(a), suggesting that stomatal and leaf adaptation to c(a) is linked to genome scaling.
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Affiliation(s)
- Peter J Franks
- Faculty of Agriculture, Food and Natural Resources, University of Sydney, Sydney New South Wales 2006, Australia.
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Heterochromatin protein 1 homologue Swi6 acts in concert with Ers1 to regulate RNAi-directed heterochromatin assembly. Proc Natl Acad Sci U S A 2012; 109:6159-64. [PMID: 22474355 DOI: 10.1073/pnas.1116972109] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In fission yeast, the RNAi pathway is required for centromeric heterochromatin assembly. siRNAs derived from centromeric transcripts are incorporated into the RNA-induced transcriptional silencing (RITS) complex and direct it to nascent homologous transcripts. The RNA-induced transcriptional silencing-bound nascent transcripts further recruit the RNA-directed RNA polymerase complex (RDRC) to promote dsRNA synthesis and siRNA production. Heterochromatin coated with Swi6/Heterochromain Protein 1 is then formed following recruitment of chromatin modification machinery. Swi6 is also required for the upstream production of siRNA, although the mechanism for this has remained obscure. Here, we demonstrate that Swi6 recruits RDRC to heterochromatin through Ers1, an RNAi factor intermediate. An ers1(+) mutant allele (ers1-C62) was identified in a genetic screen for mutants that alleviate centromeric silencing, and this phenotype was suppressed by overexpression of either the Hrr1 RDRC subunit or Clr4 histone H3-K9 methyltransferase. Ers1 physically interacts with Hrr1, and loss of Ers1 impairs RDRC centromeric localization. Although Ers1 failed to bind Clr4, a direct interaction with Swi6 was detected, and centromeric localization of Swi6 was enhanced by Clr4 overexpression in ers1-C62 cells. Consistent with this, deletion of swi6(+) reduced centromeric localization of Ers1 and RDRC. Moreover, tethering of Ers1 or Hrr1 to centromeric heterochromatin partially bypassed Swi6 function. These findings demonstrate an alternative mechanism for RDRC recruitment and explain the essential role of Swi6/Heterochromain Protein 1 in RNAi-directed heterochromatin assembly.
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Abstract
Artificially modified chromosome vectors are non-integrating gene delivery platforms that can shuttle very large DNA fragments in various recipient cells: theoretically, no size limit exists for the chromosome segments that an engineered minichromosome can accommodate. Therefore, genetically manipulated chromosomes might be potentially ideal vector systems, especially when the complexity of higher eukaryotic genes is concerned. This review focuses on those chromosome vectors generated using spontaneously occurring small markers as starting material. The definition and manipulation of the centromere domain is one of the main obstacles in chromosome engineering: naturally occurring minichromosomes, due to their inherent small size, were helpful in defining some aspects of centromere function. In addition, several distinctive features of small marker chromosomes, like their appearance as supernumerary elements in otherwise normal karyotypes, have been successfully exploited to use them as gene delivery vectors. The key technologies employed for minichromosome engineering are: size reduction, gene targeting, and vector delivery in various recipient cells. In spite of the significant advances that have been recently achieved in all these fields, several unsolved problems limit the potential of artificially modified chromosomes. Still, these vector systems have been exploited in a number of applications where the investigation of the controlled expression of large DNA segments is needed. A typical example is the analysis of genes whose expression strictly depends on the chromosomal environment in which they are positioned, where engineered chromosomes can be envisaged as epigenetically regulated expression systems. A novel and exciting advance concerns the use of engineered minichromosomes to study the organization and dynamics of local chromatin structures.
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Choi ES, Strålfors A, Castillo AG, Durand-Dubief M, Ekwall K, Allshire RC. Identification of noncoding transcripts from within CENP-A chromatin at fission yeast centromeres. J Biol Chem 2011; 286:23600-7. [PMID: 21531710 PMCID: PMC3123123 DOI: 10.1074/jbc.m111.228510] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The histone H3 variant CENP-A is the most favored candidate for an epigenetic mark that specifies the centromere. In fission yeast, adjacent heterochromatin can direct CENP-ACnp1 chromatin establishment, but the underlying features governing where CENP-ACnp1 chromatin assembles are unknown. We show that, in addition to centromeric regions, a low level of CENP-ACnp1 associates with gene promoters where histone H3 is depleted by the activity of the Hrp1Chd1 chromatin-remodeling factor. Moreover, we demonstrate that noncoding RNAs are transcribed by RNA polymerase II (RNAPII) from CENP-ACnp1 chromatin at centromeres. These analyses reveal a similarity between centromeres and a subset of RNAPII genes and suggest a role for remodeling at RNAPII promoters within centromeres that influences the replacement of histone H3 with CENP-ACnp1.
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Affiliation(s)
- Eun Shik Choi
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, United Kingdom
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Chromatin states in pluripotent, differentiated, and reprogrammed cells. Curr Opin Genet Dev 2011; 21:140-6. [DOI: 10.1016/j.gde.2011.01.015] [Citation(s) in RCA: 134] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Accepted: 01/18/2011] [Indexed: 01/22/2023]
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Kamminga LM, Ketting RF. RNAi genes pave their own way. Genes Dev 2011; 25:529-33. [PMID: 21406552 DOI: 10.1101/gad.2038611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Heterochromatin formation in fission yeast and the role of RNAi in this process have been intensively studied. So far, however, nothing is known about the regulation of expression of RNAi components during these events. Gullerova and colleagues (pp. 556-568) reveal an autoregulatory loop that regulates the expression of RNAi genes and centromeric heterochromatin formation during the cell cycle. Gene orientation plays a surprising role in this process.
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Affiliation(s)
- Leonie M Kamminga
- Hubrecht Institute-KNAW, University Medical Centre Utrecht, 3584 CT Utrecht, The Netherlands.
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Abstract
RNAi plays a central role in the regulation of eukaryotic genes. In Schizosaccharomyces pombe fission yeast, RNAi involves the formation of siRNA from dsRNA that acts to establish and maintain heterochromatin over centromeres, telomeres, and mating loci. We showed previously that transient heterochromatin also forms over S. pombe convergent genes (CGs). Remarkably, most RNAi genes are themselves convergent. We demonstrate here that transient heterochromatin formed by the RNAi pathway over RNAi CGs leads to their autoregulation in G1-S. Furthermore, the switching of RNAi gene orientation from convergent to tandem causes loss of their G1-S down-regulation. Surprisingly, yeast mutants with tandemized dcr1, ago1, or clr4 genes display aberrant centromeric heterochromatin, which results in abnormal cell morphology. Our results emphasize the significance of gene orientation for correct RNAi gene expression, and suggest a role for cell cycle-dependent formation of RNAi CG heterochromatin in cellular integrity.
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Anderson HE, Kagansky A, Wardle J, Rappsilber J, Allshire RC, Whitehall SK. Silencing mediated by the Schizosaccharomyces pombe HIRA complex is dependent upon the Hpc2-like protein, Hip4. PLoS One 2010; 5:e13488. [PMID: 20976105 PMCID: PMC2956695 DOI: 10.1371/journal.pone.0013488] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 09/27/2010] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND HIRA (or Hir) proteins are conserved histone chaperones that function in multi-subunit complexes to mediate replication-independent nucleosome assembly. We have previously demonstrated that the Schizosaccharomyces pombe HIRA proteins, Hip1 and Slm9, form a complex with a TPR repeat protein called Hip3. Here we have identified a new subunit of this complex. METHODOLOGY/PRINCIPAL FINDINGS To identify proteins that interact with the HIRA complex, rapid affinity purifications of Slm9 were performed. Multiple components of the chaperonin containing TCP-1 complex (CCT) and the 19S subunit of the proteasome reproducibly co-purified with Slm9, suggesting that HIRA interacts with these complexes. Slm9 was also found to interact with a previously uncharacterised protein (SPBC947.08c), that we called Hip4. Hip4 contains a HRD domain which is a characteristic of the budding yeast and human HIRA/Hir-binding proteins, Hpc2 and UBN1. Co-precipitation experiments revealed that Hip4 is stably associated with all of the other components of the HIRA complex and deletion of hip4(+) resulted in the characteristic phenotypes of cells lacking HIRA function, such as temperature sensitivity, an elongated cell morphology and hypersensitivity to the spindle poison, thiabendazole. Moreover, loss of Hip4 function alleviated the heterochromatic silencing of reporter genes located in the mating type locus and centromeres and was associated with increased levels of non-coding transcripts derived from centromeric repeat sequences. Hip4 was also found to be required for the distinct form of silencing that controls the expression of Tf2 LTR retrotransposons. CONCLUSIONS/SIGNIFICANCE Overall, these results indicate that Hip4 is an integral component of the HIRA complex that is required for transcriptional silencing at multiple loci.
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Affiliation(s)
- Holly E. Anderson
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle, United Kingdom
| | - Alexander Kagansky
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Josephine Wardle
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle, United Kingdom
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Robin C. Allshire
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, University of Edinburgh, Edinburgh, Scotland, United Kingdom
| | - Simon K. Whitehall
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle, United Kingdom
- * E-mail:
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Ten years of genetics and genomics: what have we achieved and where are we heading? Nat Rev Genet 2010; 11:723-33. [PMID: 20820184 DOI: 10.1038/nrg2878] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
To celebrate the first 10 years of Nature Reviews Genetics, we asked eight leading researchers for their views on the key developments in genetics and genomics in the past decade and the prospects for the future. Their responses highlight the incredible changes that the field has seen, from the explosion of genomic data and the many possibilities it has opened up to the ability to reprogramme adult cells to pluripotency. The way ahead looks similarly exciting as we address questions such as how cells function as systems and how complex interactions among genetics, epigenetics and the environment combine to shape phenotypes.
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Stable transmission of reversible modifications: maintenance of epigenetic information through the cell cycle. Cell Mol Life Sci 2010; 68:27-44. [PMID: 20799050 PMCID: PMC3015210 DOI: 10.1007/s00018-010-0505-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2010] [Revised: 07/19/2010] [Accepted: 08/09/2010] [Indexed: 12/30/2022]
Abstract
Even though every cell in a multicellular organism contains the same genes, the differing spatiotemporal expression of these genes determines the eventual phenotype of a cell. This means that each cell type contains a specific epigenetic program that needs to be replicated through cell divisions, along with the genome, in order to maintain cell identity. The stable inheritance of these programs throughout the cell cycle relies on several epigenetic mechanisms. In this review, DNA methylation and histone methylation by specific histone lysine methyltransferases (KMT) and the Polycomb/Trithorax proteins are considered as the primary mediators of epigenetic inheritance. In addition, non-coding RNAs and nuclear organization are implicated in the stable transfer of epigenetic information. Although most epigenetic modifications are reversible in nature, they can be stably maintained by self-recruitment of modifying protein complexes or maintenance of these complexes or structures through the cell cycle.
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Tamaru H. Confining euchromatin/heterochromatin territory: jumonji crosses the line. Genes Dev 2010; 24:1465-78. [PMID: 20634313 DOI: 10.1101/gad.1941010] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Heterochromatin is typically highly condensed, gene-poor, and transcriptionally silent, whereas euchromatin is less condensed, gene-rich, and more accessible to transcription. Besides acting as a graveyard for selfish mobile DNA repeats, heterochromatin contributes to important biological functions, such as chromosome segregation during cell division. Multiple features of heterochromatin-including the presence or absence of specific histone modifications, DNA methylation, and small RNAs-have been implicated in distinguishing heterochromatin from euchromatin in various organisms. Cells malfunction if the genome fails to restrict repressive chromatin marks within heterochromatin domains. How euchromatin and heterochromatin territories are confined remains poorly understood. Recent studies from the fission yeast Schizosaccharomyces pombe, the flowering plant Arabidopsis thaliana, and the filamentous fungus Neurospora crassa have revealed a new role for Jumonji C (JmjC) domain-containing proteins in protecting euchromatin from heterochromatin marks.
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Affiliation(s)
- Hisashi Tamaru
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna, Austria.
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Jauvion V, Elmayan T, Vaucheret H. The conserved RNA trafficking proteins HPR1 and TEX1 are involved in the production of endogenous and exogenous small interfering RNA in Arabidopsis. THE PLANT CELL 2010; 22:2697-709. [PMID: 20798330 PMCID: PMC2947180 DOI: 10.1105/tpc.110.076638] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2010] [Revised: 07/27/2010] [Accepted: 08/05/2010] [Indexed: 05/18/2023]
Abstract
We previously identified Arabidopsis thaliana mutants defective in sense transgene posttranscriptional gene silencing (S-PTGS) that defined six loci; here, we describe mutants that define nine additional loci, including HYPER RECOMBINATION1 (HPR1), SILENCING DEFECTIVE3 (SDE3), and SDE5. Our analyses extend previous findings by showing that the requirement for the putative RNA helicase SDE3 is inversely proportional to the strength of the PTGS inducer and that the putative RNA trafficking protein SDE5 is an essential component of the trans-acting small interfering RNA (tasiRNA) pathway and is required for S-PTGS but not inverted repeat transgene-mediated PTGS (IR-PTGS). Our screen also identified HPR1 as a PTGS actor. We show that hpr1 mutations negatively impact S-PTGS, IR-PTGS, and tasiRNA pathways, resulting in increased accumulation of siRNA precursors and decreased accumulation of mature siRNA. In animals, HPR1/THO1 is a member of the conserved RNA trafficking THO/TREX complex, which also includes TEX1/THO3. We show that tex1 mutants, like hpr1 mutants, impact TAS precursor and mature tasiRNA levels, suggesting that a THO/TREX complex exists in plants and that this complex is important for the integrity of the tasiRNA pathway. We propose that both HPR1 and TEX1 participate in the trafficking of siRNA precursors to the ARGONAUTE catalytic center.
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40
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Charon C, Moreno AB, Bardou F, Crespi M. Non-protein-coding RNAs and their interacting RNA-binding proteins in the plant cell nucleus. MOLECULAR PLANT 2010; 3:729-739. [PMID: 20603381 DOI: 10.1093/mp/ssq037] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The complex responses of eukaryotic cells to external factors are governed by several transcriptional and post-transcriptional processes. Several of them occur in the nucleus and have been linked to the action of non-protein-coding RNAs (or npcRNAs), both long and small npcRNAs, that recently emerged as major regulators of gene expression. Regulatory npcRNAs acting in the nucleus include silencing-related RNAs, intergenic npcRNAs, natural antisense RNAs, and other aberrant RNAs resulting from the interplay between global transcription and RNA processing activities (such as Dicers and RNA-dependent polymerases). Generally, the resulting npcRNAs exert their regulatory effects through interactions with RNA-binding proteins (or RBPs) within ribonucleoprotein particles (or RNPs). A large group of RBPs are implicated in the silencing machinery through small interfering RNAs (siRNAs) and their localization suggests that several act in the nucleus to trigger epigenetic and chromatin changes at a whole-genome scale. Other nuclear RBPs interact with npcRNAs and change their localization. In the fission yeast, the RNA-binding Mei2p protein, playing pivotal roles in meiosis, interact with a meiotic npcRNA involved in its nuclear re-localization. Related processes have been identified in plants and the ENOD40 npcRNA was shown to re-localize a nuclear-speckle RBP from the nucleus to the cytoplasm in Medicago truncatula. Plant RBPs have been also implicated in RNA-mediated chromatin silencing in the FLC locus through interaction with specific antisense transcripts. In this review, we discuss the interactions between RBPs and npcRNAs in the context of nuclear-related processes and their implication in plant development and stress responses. We propose that these interactions may add a regulatory layer that modulates the interactions between the nuclear genome and the environment and, consequently, control plant developmental plasticity.
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Affiliation(s)
- Celine Charon
- University Paris-Sud, Institut de Biologie des Plantes, UMR8618, Orsay Cedex, F-91405, France
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Liu Q, Wang J, Miki D, Xia R, Yu W, He J, Zheng Z, Zhu JK, Gong Z. DNA replication factor C1 mediates genomic stability and transcriptional gene silencing in Arabidopsis. THE PLANT CELL 2010; 22:2336-52. [PMID: 20639449 PMCID: PMC2929113 DOI: 10.1105/tpc.110.076349] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Revised: 06/18/2010] [Accepted: 06/28/2010] [Indexed: 05/18/2023]
Abstract
Genetic screening identified a suppressor of ros1-1, a mutant of REPRESSOR OF SILENCING1 (ROS1; encoding a DNA demethylation protein). The suppressor is a mutation in the gene encoding the largest subunit of replication factor C (RFC1). This mutation of RFC1 reactivates the unlinked 35S-NPTII transgene, which is silenced in ros1 and also increases expression of the pericentromeric Athila retrotransposons named transcriptional silent information in a DNA methylation-independent manner. rfc1 is more sensitive than the wild type to the DNA-damaging agent methylmethane sulphonate and to the DNA inter- and intra- cross-linking agent cisplatin. The rfc1 mutant constitutively expresses the G2/M-specific cyclin CycB1;1 and other DNA repair-related genes. Treatment with DNA-damaging agents mimics the rfc1 mutation in releasing the silenced 35S-NPTII, suggesting that spontaneously induced genomic instability caused by the rfc1 mutation might partially contribute to the released transcriptional gene silencing (TGS). The frequency of somatic homologous recombination is significantly increased in the rfc1 mutant. Interestingly, ros1 mutants show increased telomere length, but rfc1 mutants show decreased telomere length and reduced expression of telomerase. Our results suggest that RFC1 helps mediate genomic stability and TGS in Arabidopsis thaliana.
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Affiliation(s)
- Qian Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Junguo Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Daisuke Miki
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521
- Center for Plant Stress Genomics and Technology, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Ran Xia
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Wenxiang Yu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Junna He
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhimin Zheng
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521
- Center for Plant Stress Genomics and Technology, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Jian-Kang Zhu
- Institute for Integrative Genome Biology and Department of Botany and Plant Sciences, University of California, Riverside, California 92521
- Center for Plant Stress Genomics and Technology, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
- China Agricultural University–University of California, Riverside Center for Biological Sciences and Biotechnology, Beijing 100193, China
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
- China Agricultural University–University of California, Riverside Center for Biological Sciences and Biotechnology, Beijing 100193, China
- National Center for Plant Gene Research, Beijing 100193, China
- Address correspondence to
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Abstract
Mobile small RNA in plants provides cell-to-cell communication that affects gene expression during development.
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Affiliation(s)
- Rob Martienssen
- Cold Spring Harbor Laboratory, Cold Spring Harbor NY 11724, USA
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43
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Abstract
DNA methylation is an epigenetic mark that has key roles in the control of genome activity in plants and mammals. It is critical for the stable silencing of repeat elements and is also involved in the epigenetic regulation of some genes. Despite similarities in the controlling functions of DNA methylation, its dynamics and deposition patterns differ in several respects between plants and mammals. One of the most striking differences is that plants tend to propagate pre-existing DNA methylation states across generations, whereas mammals re-establish them genome wide at every generation. Here, we review our current understanding of DNA methylation in the flowering plant Arabidopsis. We discuss in particular the role of RNAi in the incremental methylation and silencing of repeat elements over successive generations. We argue that paramutation, an epigenetic phenomenon first described in maize, is an extreme manifestation of this RNAi-dependent pathway.
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Moshkovich N, Lei EP. HP1 recruitment in the absence of argonaute proteins in Drosophila. PLoS Genet 2010; 6:e1000880. [PMID: 20300658 PMCID: PMC2837403 DOI: 10.1371/journal.pgen.1000880] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Accepted: 02/10/2010] [Indexed: 01/21/2023] Open
Abstract
Highly repetitive and transposable element rich regions of the genome must be stabilized by the presence of heterochromatin. A direct role for RNA interference in the establishment of heterochromatin has been demonstrated in fission yeast. In metazoans, which possess multiple RNA-silencing pathways that are both functionally distinct and spatially restricted, whether RNA silencing contributes directly to heterochromatin formation is not clear. Previous studies in Drosophila melanogaster have suggested the involvement of both the AGO2-dependent endogenous small interfering RNA (endo-siRNA) as well as Piwi-interacting RNA (piRNA) silencing pathways. In order to determine if these Argonaute genes are required for heterochromatin formation, we utilized transcriptional reporters and chromatin immunoprecipitation of the critical factor Heterochromatin Protein 1 (HP1) to monitor the heterochromatic state of piRNA clusters, which generate both endo-siRNAs and the bulk of piRNAs. Surprisingly, we find that mutation of AGO2 or piwi increases silencing at piRNA clusters corresponding to an increase of HP1 association. Furthermore, loss of piRNA production from a single piRNA cluster results in genome-wide redistribution of HP1 and reduction of silencing at a distant heterochromatic site, suggesting indirect effects on HP1 recruitment. Taken together, these results indicate that heterochromatin forms independently of endo-siRNA and piRNA pathways.
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Affiliation(s)
- Nellie Moshkovich
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- The Graduate Program in Molecular and Cell Biology, University of Maryland, College Park, Maryland, United States of America
| | - Elissa P. Lei
- Laboratory of Cellular and Developmental Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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45
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Kvikstad EM, Makova KD. The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important. Genome Res 2010; 20:600-13. [PMID: 20219940 DOI: 10.1101/gr.099044.109] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The densities of transposable elements (TEs) in the human genome display substantial variation both within individual chromosomes and among chromosome types (autosomes and the two sex chromosomes). Finding an explanation for this variability has been challenging, especially in light of genome landscapes unique to the sex chromosomes. Here, using a multiple regression framework, we investigate primate Alu and L1 densities shaped by regional genome features and location on a particular chromosome type. As a result of our analysis, first, we build statistical models explaining up to 79% and 44% of variation in Alu and L1 element density, respectively. Second, we analyze sex chromosome versus autosome TE densities corrected for regional genomic effects. We discover that sex-chromosome bias in Alu and L1 distributions not only persists after accounting for these effects, but even presents differences in patterns, confirming preferential Alu integration in the male germline, yet likely integration of L1s in both male and female germlines or in early embryogenesis. Additionally, our models reveal that local base composition (measured by GC content and density of L1 target sites) and natural selection (inferred via density of most conserved elements) are significant to predicting densities of L1s. Interestingly, measurements of local double-stranded breaks (a 13-mer associated with genome instability) strongly correlate with densities of Alu elements; little evidence was found for the role of recombination-driven deletion in driving TE distributions over evolutionary time. Thus, Alu and L1 densities have been influenced by the combination of distinct local genome landscapes and the unique evolutionary dynamics of sex chromosomes.
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Affiliation(s)
- Erika M Kvikstad
- Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, Pennsylvania 16802, USA.
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Bayne EH, White SA, Kagansky A, Bijos DA, Sanchez-Pulido L, Hoe KL, Kim DU, Park HO, Ponting CP, Rappsilber J, Allshire RC. Stc1: a critical link between RNAi and chromatin modification required for heterochromatin integrity. Cell 2010; 140:666-77. [PMID: 20211136 PMCID: PMC2875855 DOI: 10.1016/j.cell.2010.01.038] [Citation(s) in RCA: 170] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 11/23/2009] [Accepted: 01/21/2010] [Indexed: 12/22/2022]
Abstract
In fission yeast, RNAi directs heterochromatin formation at centromeres, telomeres, and the mating type locus. Noncoding RNAs transcribed from repeat elements generate siRNAs that are incorporated into the Argonaute-containing RITS complex and direct it to nascent homologous transcripts. This leads to recruitment of the CLRC complex, including the histone methyltransferase Clr4, promoting H3K9 methylation and heterochromatin formation. A key question is what mediates the recruitment of Clr4/CLRC to transcript-bound RITS. We have identified a LIM domain protein, Stc1, that is required for centromeric heterochromatin integrity. Our analyses show that Stc1 is specifically required to establish H3K9 methylation via RNAi, and interacts both with the RNAi effector Ago1, and with the chromatin-modifying CLRC complex. Moreover, tethering Stc1 to a euchromatic locus is sufficient to induce silencing and heterochromatin formation independently of RNAi. We conclude that Stc1 associates with RITS on centromeric transcripts and recruits CLRC, thereby coupling RNAi to chromatin modification.
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Affiliation(s)
- Elizabeth H. Bayne
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, UK
| | - Sharon A. White
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, UK
| | - Alexander Kagansky
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, UK
| | - Dominika A. Bijos
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, UK
| | - Luis Sanchez-Pulido
- MRC Functional Genomics Unit, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Kwang-Lae Hoe
- Integrative Omics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea
| | - Dong-Uk Kim
- Integrative Omics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea
| | - Han-Oh Park
- Bioneer Corporation, Daejeon 306-220, Republic of Korea
| | - Chris P. Ponting
- MRC Functional Genomics Unit, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Juri Rappsilber
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, UK
| | - Robin C. Allshire
- Wellcome Trust Centre for Cell Biology and Institute of Cell Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh EH9 3JR, Scotland, UK
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[Regulation of fertility by the small RNA pathway that defends the genome against transposons]. YI CHUAN = HEREDITAS 2010; 32:11-6. [PMID: 20085880 DOI: 10.3724/sp.j.1005.2010.00011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Small RNAs can silence transposons at transcriptional or post-transcriptional level. Newly identified small RNAs (e.g., piRNAs and endo-siRNAs) can repress the activity of transposons. Drosophila piRNAs, mouse piRNAs, mouse endo-siRNAs, and their related proteins are expressed primarily within the germline. This suggests that the small RNA pathway plays an important role in transposon silencing of the germline. Recent studies revealed the connection between small RNAs, transposon silencing, and the regulation of fertility, but the mechanism has not been clarified in detail. In this review, the advances in the control of genomic transposon activity and the regulation of fertility by the small RNA pathway were summarized and discussed.
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48
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Weber B, Wenke T, Frömmel U, Schmidt T, Heitkam T. The Ty1-copia families SALIRE and Cotzilla populating the Beta vulgaris genome show remarkable differences in abundance, chromosomal distribution, and age. Chromosome Res 2009; 18:247-63. [DOI: 10.1007/s10577-009-9104-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Accepted: 11/25/2009] [Indexed: 01/22/2023]
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49
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The endogenous siRNA pathway is involved in heterochromatin formation in Drosophila. Proc Natl Acad Sci U S A 2009; 106:21258-63. [PMID: 19948966 DOI: 10.1073/pnas.0809208105] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
A new class of small RNAs (endo-siRNAs) produced from endogenous double-stranded RNA (dsRNA) precursors was recently shown to mediate transposable element (TE) silencing in the Drosophila soma. These endo-siRNAs might play a role in heterochromatin formation, as has been shown in S. pombe for siRNAs derived from repetitive sequences in chromosome pericentromeres. To address this possibility, we used the viral suppressors of RNA silencing B2 and P19. These proteins normally counteract the RNAi host defense by blocking the biogenesis or activity of virus-derived siRNAs. We hypothesized that both proteins would similarly block endo-siRNA processing or function, thereby revealing the contribution of endo-siRNA to heterochromatin formation. Accordingly, P19 as well as a nuclear form of P19 expressed in Drosophila somatic cells were found to sequester TE-derived siRNAs whereas B2 predominantly bound their longer precursors. Strikingly, B2 or the nuclear form of P19, but not P19, suppressed silencing of heterochromatin gene markers in adult flies, and altered histone H3-K9 methylation as well as chromosomal distribution of histone methyl transferase Su(var)3-9 and Heterochromatin Protein 1 in larvae. Similar effects were observed in dcr2, r2d2, and ago2 mutants. Our findings provide evidence that a nuclear pool of TE-derived endo-siRNAs is involved in heterochromatin formation in somatic tissues in Drosophila.
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50
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David P, Chen NW, Pedrosa-Harand A, Thareau V, Sévignac M, Cannon SB, Debouck D, Langin T, Geffroy V. A nomadic subtelomeric disease resistance gene cluster in common bean. PLANT PHYSIOLOGY 2009; 151:1048-65. [PMID: 19776165 PMCID: PMC2773105 DOI: 10.1104/pp.109.142109] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Accepted: 09/17/2009] [Indexed: 05/18/2023]
Abstract
The B4 resistance (R) gene cluster is one of the largest clusters known in common bean (Phaseolus vulgaris [Pv]). It is located in a peculiar genomic environment in the subtelomeric region of the short arm of chromosome 4, adjacent to two heterochromatic blocks (knobs). We sequenced 650 kb spanning this locus and annotated 97 genes, 26 of which correspond to Coiled-Coil-Nucleotide-Binding-Site-Leucine-Rich-Repeat (CNL). Conserved microsynteny was observed between the Pv B4 locus and corresponding regions of Medicago truncatula and Lotus japonicus in chromosomes Mt6 and Lj2, respectively. The notable exception was the CNL sequences, which were completely absent in these regions. The origin of the Pv B4-CNL sequences was investigated through phylogenetic analysis, which reveals that, in the Pv genome, paralogous CNL genes are shared among nonhomologous chromosomes (4 and 11). Together, our results suggest that Pv B4-CNL was derived from CNL sequences from another cluster, the Co-2 cluster, through an ectopic recombination event. Integration of the soybean (Glycine max) genome data enables us to date more precisely this event and also to infer that a single CNL moved from the Co-2 to the B4 cluster. Moreover, we identified a new 528-bp satellite repeat, referred to as khipu, specific to the Phaseolus genus, present both between B4-CNL sequences and in the two knobs identified at the B4 R gene cluster. The khipu repeat is present on most chromosomal termini, indicating the existence of frequent ectopic recombination events in Pv subtelomeric regions. Our results highlight the importance of ectopic recombination in R gene evolution.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Valérie Geffroy
- Institut de Biotechnologie des Plantes, UMR-CNRS 8618, Université Paris-Sud, 91405 Orsay cedex, France (P.D., N.W.G.C., V.T., M.S., T.L., V.G.); Unité Mixte de Recherche de Génétique Végétale, Institut National de la Recherche Agronomique, 91190 Gif-sur-Yvette, France (V.G.); Laboratório de Citogenética Vegetal, Departamento de Botânica-Centro de Ciências Biológicas, Universidade Federal de Pernambuco, Recife-Pernambuco 50670–420, Brazil (A.P.-H.); United States Department of Agriculture-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa 50011 (S.B.C.); and Genetic Resources Unit, Centro Internacional de Agricultura Tropical, AA 6713 Cali, Colombia (D.D.)
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