1
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Gilbert G, Renaud Y, Teste C, Anglaret N, Bertrand R, Hoehn S, Jurkowski TP, Schuettengruber B, Cavalli G, Waltzer L, Vandel L. Drosophila TET acts with PRC1 to activate gene expression independently of its catalytic activity. SCIENCE ADVANCES 2024; 10:eadn5861. [PMID: 38701218 PMCID: PMC11068012 DOI: 10.1126/sciadv.adn5861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/03/2024] [Indexed: 05/05/2024]
Abstract
Enzymes of the ten-eleven translocation (TET) family play a key role in the regulation of gene expression by oxidizing 5-methylcytosine (5mC), a prominent epigenetic mark in many species. Yet, TET proteins also have less characterized noncanonical modes of action, notably in Drosophila, whose genome is devoid of 5mC. Here, we show that Drosophila TET activates the expression of genes required for larval central nervous system (CNS) development mainly in a catalytic-independent manner. Genome-wide profiling shows that TET is recruited to enhancer and promoter regions bound by Polycomb group complex (PcG) proteins. We found that TET interacts and colocalizes on chromatin preferentially with Polycomb repressor complex 1 (PRC1) rather than PRC2. Furthermore, PRC1 but not PRC2 is required for the activation of TET target genes. Last, our results suggest that TET and PRC1 binding to activated genes is interdependent. These data highlight the importance of TET noncatalytic function and the role of PRC1 for gene activation in the Drosophila larval CNS.
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Affiliation(s)
- Guerric Gilbert
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Yoan Renaud
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Camille Teste
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Nadège Anglaret
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Romane Bertrand
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Sven Hoehn
- Cardiff University, School of Biosciences, Museum Avenue, CF10 3AX Cardiff, Wales, UK
| | - Tomasz P. Jurkowski
- Cardiff University, School of Biosciences, Museum Avenue, CF10 3AX Cardiff, Wales, UK
| | - Bernd Schuettengruber
- Institute of Human Genetics, UMR9002, CNRS and University of Montpellier, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, UMR9002, CNRS and University of Montpellier, Montpellier, France
| | - Lucas Waltzer
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
| | - Laurence Vandel
- Université Clermont Auvergne, CNRS, INSERM, iGReD, F-63000 Clermont-Ferrand, France
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2
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Parreno V, Loubiere V, Schuettengruber B, Fritsch L, Rawal CC, Erokhin M, Győrffy B, Normanno D, Di Stefano M, Moreaux J, Butova NL, Chiolo I, Chetverina D, Martinez AM, Cavalli G. Transient loss of Polycomb components induces an epigenetic cancer fate. Nature 2024; 629:688-696. [PMID: 38658752 PMCID: PMC11096130 DOI: 10.1038/s41586-024-07328-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/15/2024] [Indexed: 04/26/2024]
Abstract
Although cancer initiation and progression are generally associated with the accumulation of somatic mutations1,2, substantial epigenomic alterations underlie many aspects of tumorigenesis and cancer susceptibility3-6, suggesting that genetic mechanisms might not be the only drivers of malignant transformation7. However, whether purely non-genetic mechanisms are sufficient to initiate tumorigenesis irrespective of mutations has been unknown. Here, we show that a transient perturbation of transcriptional silencing mediated by Polycomb group proteins is sufficient to induce an irreversible switch to a cancer cell fate in Drosophila. This is linked to the irreversible derepression of genes that can drive tumorigenesis, including members of the JAK-STAT signalling pathway and zfh1, the fly homologue of the ZEB1 oncogene, whose aberrant activation is required for Polycomb perturbation-induced tumorigenesis. These data show that a reversible depletion of Polycomb proteins can induce cancer in the absence of driver mutations, suggesting that tumours can emerge through epigenetic dysregulation leading to inheritance of altered cell fates.
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Affiliation(s)
- V Parreno
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - V Loubiere
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
- Research Institute of Molecular Pathology, Vienna BioCenter, Vienna, Austria
| | - B Schuettengruber
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - L Fritsch
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - C C Rawal
- University of Southern California, Los Angeles, CA, USA
| | - M Erokhin
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - B Győrffy
- Semmelweis University Department of Bioinformatics, Budapest, Hungary
- Department of Biophysics, Medical School, University of Pécs, Pécs, Hungary
| | - D Normanno
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - M Di Stefano
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
| | - J Moreaux
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France
- Department of Biological Hematology, CHU Montpellier, Montpellier, France
- UFR Medicine, University of Montpellier, Montpellier, France
| | - N L Butova
- University of Southern California, Los Angeles, CA, USA
| | - I Chiolo
- University of Southern California, Los Angeles, CA, USA
| | - D Chetverina
- Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - A-M Martinez
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France.
| | - G Cavalli
- Institute of Human Genetics, CNRS, University of Montpellier, Montpellier, France.
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3
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Guan S, Tang J, Ma X, Miao R, Cheng B. CBX7C⋅PHC2 interaction facilitates PRC1 assembly and modulates its phase separation properties. iScience 2024; 27:109548. [PMID: 38600974 PMCID: PMC11004992 DOI: 10.1016/j.isci.2024.109548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 02/04/2024] [Accepted: 03/19/2024] [Indexed: 04/12/2024] Open
Abstract
CBX7 is a key component of PRC1 complex. Cbx7C is an uncharacterized Cbx7 splicing isoform specifically expressed in mouse embryonic stem cells (mESCs). We demonstrate that CBX7C functions as an epigenetic repressor at the classic PRC1 targets in mESCs, and its preferential interaction to PHC2 facilitates PRC1 assembly. Both Cbx7C and Phc2 are significantly upregulated during cell differentiation, and knockdown of Cbx7C abolishes the differentiation of mESCs to embryoid bodies. Interestingly, CBX7C⋅PHC2 interaction at low levels efficiently undergoes the formation of functional Polycomb bodies with high mobility, whereas the coordination of the two factors at high doses results in the formation of large, low-mobility, chromatin-free aggregates. Overall, these findings uncover the unique roles and molecular basis of the CBX7C⋅PHC2 interaction in PRC1 assembly on chromatin and Pc body formation and open a new avenue of controlling PRC1 activities via modulation of its phase separation properties.
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Affiliation(s)
- Shanli Guan
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
| | - Jiajia Tang
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
| | - Xiaojun Ma
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
| | - Ruidong Miao
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
| | - Bo Cheng
- School of Life Sciences, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
- Key Laboratory of Cell Activities and Stress Adaptations, Ministry of Education, Lanzhou University, Lanzhou 730000, Gansu, P.R. China
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4
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Longhurst AD, Wang K, Suresh HG, Ketavarapu M, Ward HN, Jones IR, Narayan V, Hundley FV, Hassan AZ, Boone C, Myers CL, Shen Y, Ramani V, Andrews BJ, Toczyski DP. The PRC2.1 Subcomplex Opposes G1 Progression through Regulation of CCND1 and CCND2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585604. [PMID: 38562687 PMCID: PMC10983909 DOI: 10.1101/2024.03.18.585604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Progression through the G1 phase of the cell cycle is the most highly regulated step in cellular division. We employed a chemogenomics approach to discover novel cellular networks that regulate cell cycle progression. This approach uncovered functional clusters of genes that altered sensitivity of cells to inhibitors of the G1/S transition. Mutation of components of the Polycomb Repressor Complex 2 rescued growth inhibition caused by the CDK4/6 inhibitor palbociclib, but not to inhibitors of S phase or mitosis. In addition to its core catalytic subunits, mutation of the PRC2.1 accessory protein MTF2, but not the PRC2.2 protein JARID2, rendered cells resistant to palbociclib treatment. We found that PRC2.1 (MTF2), but not PRC2.2 (JARID2), was critical for promoting H3K27me3 deposition at CpG islands genome-wide and in promoters. This included the CpG islands in the promoter of the CDK4/6 cyclins CCND1 and CCND2, and loss of MTF2 lead to upregulation of both CCND1 and CCND2. Our results demonstrate a role for PRC2.1, but not PRC2.2, in promoting G1 progression.
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Affiliation(s)
- Adam D Longhurst
- University of California, San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kyle Wang
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Harsha Garadi Suresh
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
| | - Mythili Ketavarapu
- Gladstone Institute for Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Henry N Ward
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota - Twin Cities Minneapolis MN USA
| | - Ian R Jones
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California
| | - Vivek Narayan
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Frances V Hundley
- University of California, San Francisco, San Francisco, CA 94158, USA
- Tetrad Graduate Program, University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, MA 02115, USA
| | - Arshia Zernab Hassan
- Department of Computer Science and Engineering, University of Minnesota - Twin Cities Minneapolis MN USA
| | - Charles Boone
- Department of Molecular Genetics, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - Chad L Myers
- Bioinformatics and Computational Biology Graduate Program, University of Minnesota - Twin Cities Minneapolis MN USA
- Department of Cell Biology, Blavatnik Institute of Harvard Medical School, Boston, MA 02115, USA
| | - Yin Shen
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
| | - Vijay Ramani
- Gladstone Institute for Data Science and Biotechnology, J. David Gladstone Institutes, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Brenda J Andrews
- The Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada
| | - David P Toczyski
- University of California, San Francisco, San Francisco, CA 94158, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
- Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA
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5
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Murphy SE, Boettiger AN. Polycomb repression of Hox genes involves spatial feedback but not domain compaction or phase transition. Nat Genet 2024; 56:493-504. [PMID: 38361032 DOI: 10.1038/s41588-024-01661-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 01/10/2024] [Indexed: 02/17/2024]
Abstract
Polycomb group proteins have a critical role in silencing transcription during development. It is commonly proposed that Polycomb-dependent changes in genome folding, which compact chromatin, contribute directly to repression by blocking the binding of activating complexes. Recently, it has also been argued that liquid-liquid demixing of Polycomb proteins facilitates this compaction and repression by phase-separating target genes into a membraneless compartment. To test these models, we used Optical Reconstruction of Chromatin Architecture to trace the Hoxa gene cluster, a canonical Polycomb target, in thousands of single cells. Across multiple cell types, we find that Polycomb-bound chromatin frequently explores decompact states and partial mixing with neighboring chromatin, while remaining uniformly repressed, challenging the repression-by-compaction or phase-separation models. Using polymer simulations, we show that these observed flexible ensembles can be explained by 'spatial feedback'-transient contacts that contribute to the propagation of the epigenetic state (epigenetic memory), without inducing a globular organization.
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Affiliation(s)
- Sedona Eve Murphy
- Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
- Department of Cell Biology, Yale University, New Haven, CT, USA
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6
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Kim JJ, Steinson ER, Lau MS, de Rooij DG, Page DC, Kingston RE. Cell type-specific role of CBX2 and its disordered region in spermatogenesis. Genes Dev 2023; 37:640-660. [PMID: 37553262 PMCID: PMC10499018 DOI: 10.1101/gad.350393.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 07/28/2023] [Indexed: 08/10/2023]
Abstract
Polycomb group (PcG) proteins maintain the repressed state of lineage-inappropriate genes and are therefore essential for embryonic development and adult tissue homeostasis. One critical function of PcG complexes is modulating chromatin structure. Canonical Polycomb repressive complex 1 (cPRC1), particularly its component CBX2, can compact chromatin and phase-separate in vitro. These activities are hypothesized to be critical for forming a repressed physical environment in cells. While much has been learned by studying these PcG activities in cell culture models, it is largely unexplored how cPRC1 regulates adult stem cells and their subsequent differentiation in living animals. Here, we show in vivo evidence of a critical nonenzymatic repressive function of cPRC1 component CBX2 in the male germline. CBX2 is up-regulated as spermatogonial stem cells differentiate and is required to repress genes that were active in stem cells. CBX2 forms condensates (similar to previously described Polycomb bodies) that colocalize with target genes bound by CBX2 in differentiating spermatogonia. Single-cell analyses of mosaic Cbx2 mutant testes show that CBX2 is specifically required to produce differentiating A1 spermatogonia. Furthermore, the region of CBX2 responsible for compaction and phase separation is needed for the long-term maintenance of male germ cells in the animal. These results emphasize that the regulation of chromatin structure by CBX2 at a specific stage of spermatogenesis is critical, which distinguishes this from a mechanism that is reliant on histone modification.
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Affiliation(s)
- Jongmin J Kim
- Department of Molecular Biology, MGH Research Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Emma R Steinson
- Department of Molecular Biology, MGH Research Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, USA
| | - Mei Sheng Lau
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology, and Research (A*STAR), Proteos, Singapore 138673, Republic of Singapore
| | - Dirk G de Rooij
- Reproductive Biology Group, Division of Developmental Biology, Department of Biology, Faculty of Science, Utrecht University, Utrecht 3584 CH, the Netherlands
| | - David C Page
- Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute, Cambridge, Massachusetts 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Robert E Kingston
- Department of Molecular Biology, MGH Research Institute, Massachusetts General Hospital, Boston, Massachusetts 02114, USA;
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
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7
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Salzler HR, Vandadi V, McMichael BD, Brown JC, Boerma SA, Leatham-Jensen MP, Adams KM, Meers MP, Simon JM, Duronio RJ, McKay DJ, Matera AG. Distinct roles for canonical and variant histone H3 lysine-36 in Polycomb silencing. SCIENCE ADVANCES 2023; 9:eadf2451. [PMID: 36857457 PMCID: PMC9977188 DOI: 10.1126/sciadv.adf2451] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/31/2023] [Indexed: 05/26/2023]
Abstract
Polycomb complexes regulate cell type-specific gene expression programs through heritable silencing of target genes. Trimethylation of histone H3 lysine 27 (H3K27me3) is essential for this process. Perturbation of H3K36 is thought to interfere with H3K27me3. We show that mutants of Drosophila replication-dependent (H3.2K36R) or replication-independent (H3.3K36R) histone H3 genes generally maintain Polycomb silencing and reach later stages of development. In contrast, combined (H3.3K36RH3.2K36R) mutants display widespread Hox gene misexpression and fail to develop past the first larval stage. Chromatin profiling revealed that the H3.2K36R mutation disrupts H3K27me3 levels broadly throughout silenced domains, whereas these regions are mostly unaffected in H3.3K36R animals. Analysis of H3.3 distributions showed that this histone is enriched at presumptive Polycomb response elements located outside of silenced domains but relatively depleted from those inside. We conclude that H3.2 and H3.3 K36 residues collaborate to repress Hox genes using different mechanisms.
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Affiliation(s)
- Harmony R. Salzler
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Vasudha Vandadi
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Benjamin D. McMichael
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - John C. Brown
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Sally A. Boerma
- Department of Biology, Carleton College, Northfield, MN, USA
| | - Mary P. Leatham-Jensen
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Kirsten M. Adams
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Michael P. Meers
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Jeremy M. Simon
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Robert J. Duronio
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Daniel J. McKay
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - A. Gregory Matera
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
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8
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Mechanisms of Interaction between Enhancers and Promoters in Three Drosophila Model Systems. Int J Mol Sci 2023; 24:ijms24032855. [PMID: 36769179 PMCID: PMC9917889 DOI: 10.3390/ijms24032855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/26/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
In higher eukaryotes, the regulation of developmental gene expression is determined by enhancers, which are often located at a large distance from the promoters they regulate. Therefore, the architecture of chromosomes and the mechanisms that determine the functional interaction between enhancers and promoters are of decisive importance in the development of organisms. Mammals and the model animal Drosophila have homologous key architectural proteins and similar mechanisms in the organization of chromosome architecture. This review describes the current progress in understanding the mechanisms of the formation and regulation of long-range interactions between enhancers and promoters at three well-studied key regulatory loci in Drosophila.
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9
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Raval M, Mishra S, Tiwari AK. Epigenetic regulons in Alzheimer's disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 198:185-247. [DOI: 10.1016/bs.pmbts.2023.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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10
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Griffin KN, Walters BW, Li H, Wang H, Biancon G, Tebaldi T, Kaya CB, Kanyo J, Lam TT, Cox AL, Halene S, Chung JJ, Lesch BJ. Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction. Genome Res 2022; 32:gr.276578.122. [PMID: 36109149 PMCID: PMC9528986 DOI: 10.1101/gr.276578.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 07/21/2022] [Indexed: 11/25/2022]
Abstract
Argonaute 2 (AGO2) is a ubiquitously expressed protein critical for regulation of mRNA translation and vital to animal development. AGO2 protein is found in both cytoplasmic and nuclear compartments, and although its cytoplasmic role is well studied, the biological relevance of nuclear AGO2 is unclear. Here, we address this problem in vivo using spermatogenic cells as a model. We find that AGO2 transiently binds both chromatin and nucleus-specific mRNA transcripts of hundreds of genes required for sperm production during male meiosis in mice, and that germline conditional knockout (cKO) of Ago2 causes depletion of the encoded proteins. Correspondingly, Ago2 cKO males show abnormal sperm head morphology and reduced sperm count, along with reduced postnatal viability of offspring. Together, our data reveal an unexpected nuclear role for AGO2 in enhancing expression of developmentally important genes during mammalian male reproduction.
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Affiliation(s)
- Kimberly N Griffin
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | | | - Haixin Li
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Huafeng Wang
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Giulia Biancon
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Toma Tebaldi
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
| | - Carolyn B Kaya
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Jean Kanyo
- Keck MS & Proteomics Resource, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - TuKiet T Lam
- Keck MS & Proteomics Resource, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, USA
| | - Andy L Cox
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Stem Cell Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Center for RNA Science and Medicine, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Pathology, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Jean-Ju Chung
- Department of Cellular and Molecular Physiology, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut 06510, USA
| | - Bluma J Lesch
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Yale Comprehensive Cancer Center, Yale University School of Medicine, New Haven, Connecticut 06510, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale University School of Medicine, New Haven, Connecticut 06510, USA
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11
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Brown K, Andrianakos H, Ingersoll S, Ren X. Single-molecule imaging of epigenetic complexes in living cells: insights from studies on Polycomb group proteins. Nucleic Acids Res 2021; 49:6621-6637. [PMID: 34009336 PMCID: PMC8266577 DOI: 10.1093/nar/gkab304] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 12/30/2022] Open
Abstract
Chromatin-associated factors must locate, bind to, and assemble on specific chromatin regions to execute chromatin-templated functions. These dynamic processes are essential for understanding how chromatin achieves regulation, but direct quantification in living mammalian cells remains challenging. Over the last few years, live-cell single-molecule tracking (SMT) has emerged as a new way to observe trajectories of individual chromatin-associated factors in living mammalian cells, providing new perspectives on chromatin-templated activities. Here, we discuss the relative merits of live-cell SMT techniques currently in use. We provide new insights into how Polycomb group (PcG) proteins, master regulators of development and cell differentiation, decipher genetic and epigenetic information to achieve binding stability and highlight that Polycomb condensates facilitate target-search efficiency. We provide perspectives on liquid-liquid phase separation in organizing Polycomb targets. We suggest that epigenetic complexes integrate genetic and epigenetic information for target binding and localization and achieve target-search efficiency through nuclear organization.
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Affiliation(s)
- Kyle Brown
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | | | - Steven Ingersoll
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
| | - Xiaojun Ren
- Department of Chemistry, University of Colorado Denver, Denver, CO 80217-3364, USA
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12
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Moretti C, Stévant I, Ghavi-Helm Y. 3D genome organisation in Drosophila. Brief Funct Genomics 2021; 19:92-100. [PMID: 31796947 DOI: 10.1093/bfgp/elz029] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/02/2019] [Accepted: 09/20/2019] [Indexed: 12/17/2022] Open
Abstract
Ever since Thomas Hunt Morgan's discovery of the chromosomal basis of inheritance by using Drosophila melanogaster as a model organism, the fruit fly has remained an essential model system in studies of genome biology, including chromatin organisation. Very much as in vertebrates, in Drosophila, the genome is organised in territories, compartments and topologically associating domains (TADs). However, these domains might be formed through a slightly different mechanism than in vertebrates due to the presence of a large and potentially redundant set of insulator proteins and the minor role of dCTCF in TAD boundary formation. Here, we review the different levels of chromatin organisation in Drosophila and discuss mechanisms and factors that might be involved in TAD formation. The dynamics of TADs and enhancer-promoter interactions in the context of transcription are covered in the light of currently conflicting results. Finally, we illustrate the value of polymer modelling approaches to infer the principles governing the three-dimensional organisation of the Drosophila genome.
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Affiliation(s)
- Charlotte Moretti
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d'Italie F-69364 Lyon, France
| | - Isabelle Stévant
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d'Italie F-69364 Lyon, France
| | - Yad Ghavi-Helm
- Institut de Génomique Fonctionnelle de Lyon, Univ Lyon, CNRS UMR 5242, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 46 allée d'Italie F-69364 Lyon, France
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13
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Morrison O, Thakur J. Molecular Complexes at Euchromatin, Heterochromatin and Centromeric Chromatin. Int J Mol Sci 2021; 22:6922. [PMID: 34203193 PMCID: PMC8268097 DOI: 10.3390/ijms22136922] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 01/19/2023] Open
Abstract
Chromatin consists of a complex of DNA and histone proteins as its core components and plays an important role in both packaging DNA and regulating DNA metabolic pathways such as DNA replication, transcription, recombination, and chromosome segregation. Proper functioning of chromatin further involves a network of interactions among molecular complexes that modify chromatin structure and organization to affect the accessibility of DNA to transcription factors leading to the activation or repression of the transcription of target DNA loci. Based on its structure and compaction state, chromatin is categorized into euchromatin, heterochromatin, and centromeric chromatin. In this review, we discuss distinct chromatin factors and molecular complexes that constitute euchromatin-open chromatin structure associated with active transcription; heterochromatin-less accessible chromatin associated with silencing; centromeric chromatin-the site of spindle binding in chromosome segregation.
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Affiliation(s)
| | - Jitendra Thakur
- Department of Biology, Emory University, 1510 Clifton Rd #2006, Atlanta, GA 30322, USA;
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14
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Kemp JP, Yang XC, Dominski Z, Marzluff WF, Duronio RJ. Superresolution light microscopy of the Drosophila histone locus body reveals a core-shell organization associated with expression of replication-dependent histone genes. Mol Biol Cell 2021; 32:942-955. [PMID: 33788585 PMCID: PMC8108526 DOI: 10.1091/mbc.e20-10-0645] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The histone locus body (HLB) is an evolutionarily conserved nuclear body that regulates the transcription and processing of replication-dependent (RD) histone mRNAs, which are the only eukaryotic mRNAs lacking a poly-A tail. Many nuclear bodies contain distinct domains, but how internal organization is related to nuclear body function is not fully understood. Here, we demonstrate using structured illumination microscopy that Drosophila HLBs have a “core–shell” organization in which the internal core contains transcriptionally active RD histone genes. The N-terminus of Mxc, which contains a domain required for Mxc oligomerization, HLB assembly, and RD histone gene expression, is enriched in the HLB core. In contrast, the C-terminus of Mxc is enriched in the HLB outer shell as is FLASH, a component of the active U7 snRNP that cotranscriptionally cleaves RD histone pre-mRNA. Consistent with these results, we show biochemically that FLASH binds directly to the Mxc C-terminal region. In the rapid S-M nuclear cycles of syncytial blastoderm Drosophila embryos, the HLB disassembles at mitosis and reassembles the core–shell arrangement as histone gene transcription is activated immediately after mitosis. Thus, the core–shell organization is coupled to zygotic histone gene transcription, revealing a link between HLB internal organization and RD histone gene expression.
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Affiliation(s)
- James P Kemp
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Xiao-Cui Yang
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Zbigniew Dominski
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - William F Marzluff
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Robert J Duronio
- Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599.,Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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15
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Xu J, Zhao X, Mao F, Basrur V, Ueberheide B, Chait BT, Allis CD, Taverna SD, Gao S, Wang W, Liu Y. A Polycomb repressive complex is required for RNAi-mediated heterochromatin formation and dynamic distribution of nuclear bodies. Nucleic Acids Res 2021; 49:5407-5425. [PMID: 33412588 PMCID: PMC8191774 DOI: 10.1093/nar/gkaa1262] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 12/02/2020] [Accepted: 01/04/2021] [Indexed: 01/17/2023] Open
Abstract
Polycomb group (PcG) proteins are widely utilized for transcriptional repression in eukaryotes. Here, we characterize, in the protist Tetrahymena thermophila, the EZL1 (E(z)-like 1) complex, with components conserved in metazoan Polycomb Repressive Complexes 1 and 2 (PRC1 and PRC2). The EZL1 complex is required for histone H3 K27 and K9 methylation, heterochromatin formation, transposable element control, and programmed genome rearrangement. The EZL1 complex interacts with EMA1, a helicase required for RNA interference (RNAi). This interaction is implicated in co-transcriptional recruitment of the EZL1 complex. Binding of H3K27 and H3K9 methylation by PDD1-another PcG protein interacting with the EZL1 complex-reinforces its chromatin association. The EZL1 complex is an integral part of Polycomb bodies, which exhibit dynamic distribution in Tetrahymena development: Their dispersion is driven by chromatin association, while their coalescence by PDD1, likely via phase separation. Our results provide a molecular mechanism connecting RNAi and Polycomb repression, which coordinately regulate nuclear bodies and reorganize the genome.
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Affiliation(s)
| | | | - Fengbiao Mao
- Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Venkatesha Basrur
- Proteomics Resource Facility, Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Beatrix Ueberheide
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, the Rockefeller University, New York, NY 10065, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, the Rockefeller University, New York, NY 10065, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, the Rockefeller University, New York, NY 10065, USA
| | - Sean D Taverna
- Department of Pharmacology and Molecular Sciences and the Center for Epigenetics, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shan Gao
- Correspondence may also be addressed to Shan Gao.
| | - Wei Wang
- Correspondence may also be addressed to Wei Wang.
| | - Yifan Liu
- To whom correspondence should be addressed. Tel: +1 323 865 3852;
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16
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D'Ambrosio J, Morvezen R, Brard-Fudulea S, Bestin A, Acin Perez A, Guéméné D, Poncet C, Haffray P, Dupont-Nivet M, Phocas F. Genetic architecture and genomic selection of female reproduction traits in rainbow trout. BMC Genomics 2020; 21:558. [PMID: 32795250 PMCID: PMC7430828 DOI: 10.1186/s12864-020-06955-7] [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: 04/04/2020] [Accepted: 07/27/2020] [Indexed: 12/19/2022] Open
Abstract
Background Rainbow trout is a significant fish farming species under temperate climates. Female reproduction traits play an important role in the economy of breeding companies with the sale of fertilized eggs. The objectives of this study are threefold: to estimate the genetic parameters of female reproduction traits, to determine the genetic architecture of these traits by the identification of quantitative trait loci (QTL), and to assess the expected efficiency of a pedigree-based selection (BLUP) or genomic selection for these traits. Results A pedigreed population of 1343 trout were genotyped for 57,000 SNP markers and phenotyped for seven traits at 2 years of age: spawning date, female body weight before and after spawning, the spawn weight and the egg number of the spawn, the egg average weight and average diameter. Genetic parameters were estimated in multi-trait linear animal models. Heritability estimates were moderate, varying from 0.27 to 0.44. The female body weight was not genetically correlated to any of the reproduction traits. Spawn weight showed strong and favourable genetic correlation with the number of eggs in the spawn and individual egg size traits, but the egg number was uncorrelated to the egg size traits. The genome-wide association studies showed that all traits were very polygenic since less than 10% of the genetic variance was explained by the cumulative effects of the QTLs: for any trait, only 2 to 4 QTLs were detected that explained in-between 1 and 3% of the genetic variance. Genomic selection based on a reference population of only one thousand individuals related to candidates would improve the efficiency of BLUP selection from 16 to 37% depending on traits. Conclusions Our genetic parameter estimates made unlikely the hypothesis that selection for growth could induce any indirect improvement for female reproduction traits. It is thus important to consider direct selection for spawn weight for improving egg production traits in rainbow trout breeding programs. Due to the low proportion of genetic variance explained by the few QTLs detected for each reproduction traits, marker assisted selection cannot be effective. However genomic selection would allow significant gains of accuracy compared to pedigree-based selection.
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Affiliation(s)
- J D'Ambrosio
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.,SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes cedex, France
| | - R Morvezen
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes cedex, France
| | - S Brard-Fudulea
- SYSAAF, Section Avicole, Centre INRAE Val de Loire, 37380, Nouzilly, France
| | - A Bestin
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes cedex, France
| | - A Acin Perez
- Viviers de Sarrance, Pisciculture Labedan, 64490, Sarrance, France
| | - D Guéméné
- SYSAAF, Section Avicole, Centre INRAE Val de Loire, 37380, Nouzilly, France
| | - C Poncet
- Université Clermont-Auvergne, INRAE, GDEC, 63039, Clermont-Ferrand, France
| | - P Haffray
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes cedex, France
| | - M Dupont-Nivet
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - F Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
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17
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Zaytseva O, Mitchell NC, Guo L, Marshall OJ, Parsons LM, Hannan RD, Levens DL, Quinn LM. Transcriptional repression of Myc underlies the tumour suppressor function of AGO1 in Drosophila. Development 2020; 147:147/11/dev190231. [PMID: 32527935 PMCID: PMC7295588 DOI: 10.1242/dev.190231] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 04/27/2020] [Indexed: 12/29/2022]
Abstract
Here, we report novel tumour suppressor activity for the Drosophila Argonaute family RNA-binding protein AGO1, a component of the miRNA-dependent RNA-induced silencing complex (RISC). The mechanism for growth inhibition does not, however, involve canonical roles as part of the RISC; rather, AGO1 controls cell and tissue growth by functioning as a direct transcriptional repressor of the master regulator of growth, Myc. AGO1 depletion in wing imaginal discs drives a significant increase in ribosome biogenesis, nucleolar expansion and cell growth in a manner dependent on Myc abundance. Moreover, increased Myc promoter activity and elevated Myc mRNA in AGO1-depleted animals requires RNA polymerase II transcription. Further support for transcriptional AGO1 functions is provided by physical interaction with the RNA polymerase II transcriptional machinery (chromatin remodelling factors and Mediator Complex), punctate nuclear localisation in euchromatic regions and overlap with Polycomb Group transcriptional silencing loci. Moreover, significant AGO1 enrichment is observed on the Myc promoter and AGO1 interacts with the Myc transcriptional activator Psi. Together, our data show that Drosophila AGO1 functions outside of the RISC to repress Myc transcription and inhibit developmental cell and tissue growth. This article has an associated ‘The people behind the papers’ interview. Highlighted Article: In the Drosophila wing, the Argonaute family protein AGO1 acts independently of the miRNA-silencing pathway to restrict tissue growth by directly repressing transcription of the master growth regulator Myc.
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Affiliation(s)
- Olga Zaytseva
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - Naomi C Mitchell
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - Linna Guo
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | | | | | - Ross D Hannan
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
| | - David L Levens
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Leonie M Quinn
- Department of Cancer Biology and Therapeutics, The John Curtin School of Medical Research, The Australian National University, Canberra, ACT 2600, Australia
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18
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Polycomb Assemblies Multitask to Regulate Transcription. EPIGENOMES 2019; 3:epigenomes3020012. [PMID: 34968234 PMCID: PMC8594731 DOI: 10.3390/epigenomes3020012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/14/2019] [Accepted: 06/16/2019] [Indexed: 02/06/2023] Open
Abstract
The Polycomb system is made of an evolutionary ancient group of proteins, present throughout plants and animals. Known initially from developmental studies with the fly Drosophila melanogaster, they were associated with stable sustainment of gene repression and maintenance of cell identity. Acting as multiprotein assemblies with an ability to modify chromatin, through chemical additions to histones and organization of topological domains, they have been involved subsequently in control of developmental transitions and in cell homeostasis. Recent work has unveiled an association of Polycomb components with transcriptionally active loci and the promotion of gene expression, in clear contrast with conventional recognition as repressors. Focusing on mammalian models, I review here advances concerning roles in transcriptional control. Among new findings highlighted is the regulation of their catalytic properties, recruiting to targets, and activities in chromatin organization and compartmentalization. The need for a more integrated approach to the study of the Polycomb system, given its fundamental complexity and its adaptation to cell context, is discussed.
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19
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Weng W, Li H, Goel A. Piwi-interacting RNAs (piRNAs) and cancer: Emerging biological concepts and potential clinical implications. Biochim Biophys Acta Rev Cancer 2018; 1871:160-169. [PMID: 30599187 DOI: 10.1016/j.bbcan.2018.12.005] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 11/09/2018] [Accepted: 12/24/2018] [Indexed: 12/12/2022]
Abstract
Piwi-interacting RNAs (piRNAs) are a very recently discovered class of small non-coding RNAs (ncRNAs), with approximately 20,000 piRNA genes already identified within the human genome. These short RNAs were originally described as key functional regulators for the germline maintenance and transposon silencing. However, due to our limited knowledge regarding their function, piRNAs were for a long time assumed to be the "dark matter" of ncRNAs in our genome. However, recent evidence has now changed our viewpoint of their biological and clinical significance in various diseases, as newly emerging data reveals that aberrant expression of piRNAs is a unique and distinct feature in many diseases, including multiple human cancers. Furthermore, their altered expression in cancer patients has been significantly associated with clinical outcomes, highlighting their important biological functional role in disease progression. Functionally, piRNAs maintain genomic integrity by silencing transposable elements, and are capable of regulating the expression of specific downstream target genes in a post-transcriptional manner. Moreover, accumulating evidences demonstrates that analogous to other small ncRNAs (e.g. miRNAs) piRNAs have both oncogenic and tumor suppressive roles in cancer development. In this article, we discuss emerging insights into roles of piRNAs in a variety of cancers, reveal new findings underpinning various mechanisms of piRNAs-mediated gene regulation, and highlight their potential clinical significance in the management of cancer patients.
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Affiliation(s)
- Wenhao Weng
- Department of Clinical Laboratory, Yangpu Hospital, Tongji University School of Medicine, Shanghai 200090, China; Center for Translational Medicine, Yangpu Hospital, Tongji University School of Medicine, Shanghai 200090, China
| | - Hanhua Li
- Department of Clinical Laboratory, Yangpu Hospital, Tongji University School of Medicine, Shanghai 200090, China
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute and Charles A Sammons Cancer Center, Baylor Research Institute and Sammons Cancer Center, Baylor University Medical Center, Dallas, TX 75246-2017, USA.
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20
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Lebedeva LA, Yakovlev KV, Kozlov EN, Schedl P, Deshpande G, Shidlovskii YV. Transcriptional quiescence in primordial germ cells. Crit Rev Biochem Mol Biol 2018; 53:579-595. [PMID: 30280955 DOI: 10.1080/10409238.2018.1506733] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
In most animal species, newly formed primordial germ cells (PGCs) acquire the special characteristics that distinguish them from the surrounding somatic cells. Proper fate specification of the PGCs is coupled with transcriptional quiescence, whether they are segregated by determinative or inductive mechanisms. Inappropriate differentiation of PGCs into somatic cells is thought to be prevented due to repression of RNA polymerase (Pol) II-dependent transcription. In the case of a determinative mode of PGC formation (Drosophila, Caenorhabditis elegans, etc.), there is a broad downregulation of Pol II activity. By contrast, PGCs display only gene-specific repression in organisms that rely on inductive signaling-based mechanism (e.g., mice). In addition to the global block of Pol II activity in PGCs, gene expression can be suppressed in other ways, such as chromatin remodeling and Piwi-mediated RNAi. Here, we discuss the mechanisms responsible for the transcriptionally silent state of PGCs in common experimental animals, such as Drosophila, C. elegans, Danio rerio, Xenopus, and mouse. While a PGC-specific downregulation of transcription is a common feature among these organisms, the diverse nature of underlying mechanisms suggests that this functional trait likely evolved independently on several instances. We discuss the possible biological relevance of these silencing mechanisms vis-a-vis fate determination of PGCs.
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Affiliation(s)
- Lyubov A Lebedeva
- a Institute of Gene Biology , Russian Academy of Sciences , Moscow , Russia
| | - Konstantin V Yakovlev
- a Institute of Gene Biology , Russian Academy of Sciences , Moscow , Russia.,b Laboratory of Cytotechnology, National Scientific Center of Marine Biology, Far Eastern Branch , Russian Academy of Sciences , Vladivostok , Russia
| | - Eugene N Kozlov
- a Institute of Gene Biology , Russian Academy of Sciences , Moscow , Russia
| | - Paul Schedl
- a Institute of Gene Biology , Russian Academy of Sciences , Moscow , Russia.,c Department of Molecular Biology , Princeton University , Princeton , USA
| | - Girish Deshpande
- c Department of Molecular Biology , Princeton University , Princeton , USA
| | - Yulii V Shidlovskii
- a Institute of Gene Biology , Russian Academy of Sciences , Moscow , Russia.,d Department of Biology and General Genetics, I.M. Sechenov First Moscow State Medical University , Moscow , Russia
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21
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Cheutin T, Cavalli G. Loss of PRC1 induces higher-order opening of Hox loci independently of transcription during Drosophila embryogenesis. Nat Commun 2018; 9:3898. [PMID: 30254245 PMCID: PMC6156336 DOI: 10.1038/s41467-018-05945-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Accepted: 07/30/2018] [Indexed: 12/14/2022] Open
Abstract
Polycomb-group proteins are conserved chromatin factors that maintain the silencing of key developmental genes, notably the Hox gene clusters, outside of their expression domains. Depletion of Polycomb repressive complex 1 (PRC1) proteins typically results in chromatin unfolding, as well as ectopic transcription. To disentangle these two phenomena, here we analyze the temporal function of two PRC1 proteins, Polyhomeotic (Ph) and Polycomb (Pc), on Hox gene clusters during Drosophila embryogenesis. We show that the absence of Ph or Pc affects the higher-order chromatin folding of Hox clusters prior to ectopic Hox gene transcription, demonstrating that PRC1 primary function during early embryogenesis is to compact its target chromatin. Moreover, the differential effects of Ph and Pc on Hox cluster folding match the differences in ectopic Hox gene expression observed in these two mutants. Our data suggest that PRC1 maintains gene silencing by folding chromatin domains and impose architectural layer to gene regulation. Loss of Polycomb repressive complex 1 (PRC1) proteins usually results in both chromatin unfolding and ectopic transcription. Here, the authors analyze the temporal function of two PRC1 proteins during Drosophila embryogenesis and provide evidence that PRC1 maintains gene silencing by folding chromatin domains.
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Affiliation(s)
- Thierry Cheutin
- Institute of Human Genetics, CNRS and the University of Montpellier, Montpellier, France.
| | - Giacomo Cavalli
- Institute of Human Genetics, CNRS and the University of Montpellier, Montpellier, France.
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22
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Masuko K, Furuhashi H, Komaba K, Numao E, Nakajima R, Fuse N, Kurata S. Nuclear Lamin is required for Winged Eye-mediated transdetermination of Drosophila imaginal disc. Genes Cells 2018; 23:724-731. [PMID: 29968323 DOI: 10.1111/gtc.12608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 05/31/2018] [Accepted: 06/03/2018] [Indexed: 11/29/2022]
Abstract
Drosophila imaginal discs often change their cell fate under stress conditions, and this phenomenon, called transdetermination (TD), has long been a useful model for studying cell fate plasticity during regeneration. We previously identified a chromatin-associated protein, Winged Eye (Wge), which induces eye-to-wing TD upon its over-expression in eye imaginal discs. However, the molecular mechanism of Wge-mediated TD remains obscure. Here, we analyzed Wge-interacting proteins and found that several heterochromatin-related proteins, including a nuclear lamina protein, Lamin (Lam), were associated with Wge protein in cultured cells. Knockdown experiments revealed that Lam is indeed required for Wge-mediated eye-to-wing TD. Moreover, Wge over-expression altered the spatial organization of genomic DNA inside the cell nuclei. Accordingly, we suggest that Wge interacts with Lam to link some genomic regions with the nuclear periphery and regulates chromatin dynamics in imaginal disc TD.
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Affiliation(s)
- Keita Masuko
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Hirofumi Furuhashi
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Kanae Komaba
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Eriko Numao
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Rumi Nakajima
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Naoyuki Fuse
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | - Shoichiro Kurata
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
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23
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Shah FR, Bhat YA, Wani AH. Subnuclear distribution of proteins: Links with genome architecture. Nucleus 2018; 9:42-55. [PMID: 28910577 PMCID: PMC5973252 DOI: 10.1080/19491034.2017.1361578] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/25/2017] [Accepted: 07/26/2017] [Indexed: 02/08/2023] Open
Abstract
Metazoan genomes have a hierarchal 3-dimensional (3D) organization scaling from nucleosomes, loops, topologically associating domains (TADs), compartments, to chromosome territories. The 3D organization of genome has been linked with development, differentiation and disease. However, the principles governing the 3D chromatin architecture are just beginning to get unraveled. The nucleus has very high concentration of proteins and these proteins are either diffusely distributed throughout the nucleus, or aggregated in the form of foci/bodies/clusters/speckles or in combination of both. Several evidences suggest that the distribution of proteins within the nuclear space is linked to the organization and function of genome. Here, we describe advances made in understanding the relationship between subnuclear distribution of proteins and genome architecture.
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Affiliation(s)
- Fouziya R. Shah
- Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Younus A. Bhat
- Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
| | - Ajazul H. Wani
- Biotechnology, School of Biological Sciences, University of Kashmir, Srinagar, India
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Schuettengruber B, Bourbon HM, Di Croce L, Cavalli G. Genome Regulation by Polycomb and Trithorax: 70 Years and Counting. Cell 2017; 171:34-57. [DOI: 10.1016/j.cell.2017.08.002] [Citation(s) in RCA: 611] [Impact Index Per Article: 87.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/17/2017] [Accepted: 08/01/2017] [Indexed: 01/05/2023]
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Dutta P, Li WX. The SERTAD protein Taranis plays a role in Polycomb-mediated gene repression. PLoS One 2017; 12:e0180026. [PMID: 28665982 PMCID: PMC5493352 DOI: 10.1371/journal.pone.0180026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 06/08/2017] [Indexed: 11/19/2022] Open
Abstract
The Polycomb group (PcG) proteins have been implicated in epigenetic transcriptional repression in development, stem cell maintenance and in cancer. The chromodomain protein Polycomb (Pc) is a key member of the PcG. Pc binds to the histone mark, trimethylated histone 3 lysine 27 (H3K27me3), to initiate transcriptional repression. How PcG proteins are recruited to target loci is not fully understood. Here we show that the Drosophila SERTA domain protein Taranis (Tara) is involved in transcriptional regulation of Pc target genes. Embryos lacking Tara exhibit a partial homeotic transformation of cuticular the segments, a phenotype associated with the loss of Pc function. Moreover, Drosophila embryos homozygous for a tara hypomorphic allele also misexpress engrailed, a Pc-regulated gene, and this phenotype is associated with the loss of Pc binding to the cis response element in the engrailed enhancer. In relation to that, Pc recruitment is reduced on the salivary gland polytene chromosomes and specifically at the engrailed locus. These results suggest that Tara might be required for positioning Pc to a subset of its target genes.
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Affiliation(s)
- Pranabananda Dutta
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York, United States of America
- * E-mail:
| | - Willis X. Li
- Department of Medicine, University of California San Diego, La Jolla, California, United States of America
- Department of Biomedical Genetics, University of Rochester Medical Center, Rochester, New York, United States of America
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Three-Dimensional Genome Organization and Function in Drosophila. Genetics 2017; 205:5-24. [PMID: 28049701 PMCID: PMC5223523 DOI: 10.1534/genetics.115.185132] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 10/15/2016] [Indexed: 12/18/2022] Open
Abstract
Understanding how the metazoan genome is used during development and cell differentiation is one of the major challenges in the postgenomic era. Early studies in Drosophila suggested that three-dimensional (3D) chromosome organization plays important regulatory roles in this process and recent technological advances started to reveal connections at the molecular level. Here we will consider general features of the architectural organization of the Drosophila genome, providing historical perspective and insights from recent work. We will compare the linear and spatial segmentation of the fly genome and focus on the two key regulators of genome architecture: insulator components and Polycomb group proteins. With its unique set of genetic tools and a compact, well annotated genome, Drosophila is poised to remain a model system of choice for rapid progress in understanding principles of genome organization and to serve as a proving ground for development of 3D genome-engineering techniques.
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Harrington AW, McKain MR, Michalski D, Bauer KM, Daugherty JM, Steiniger M. Drosophila melanogaster retrotransposon and inverted repeat-derived endogenous siRNAs are differentially processed in distinct cellular locations. BMC Genomics 2017; 18:304. [PMID: 28415970 PMCID: PMC5392987 DOI: 10.1186/s12864-017-3692-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 04/07/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Endogenous small interfering (esi)RNAs repress mRNA levels and retrotransposon mobility in Drosophila somatic cells by poorly understood mechanisms. 21 nucleotide esiRNAs are primarily generated from retrotransposons and two inverted repeat (hairpin) loci in Drosophila culture cells in a Dicer2 dependent manner. Additionally, proteins involved in 3' end processing, such as Symplekin, CPSF73 and CPSR100, have been recently implicated in the esiRNA pathway. RESULTS Here we present evidence of overlap between two essential RNA metabolic pathways: esiRNA biogenesis and mRNA 3' end processing. We have identified a nucleus-specific interaction between the essential esiRNA cleavage enzyme Dicer2 (Dcr2) and Symplekin, a component of the core cleavage complex (CCC) required for 3' end processing of all eukaryotic mRNAs. This interaction is mediated by the N-terminal 271 amino acids of Symplekin; CCC factors CPSF73 and CPSF100 do not contact Dcr2. While Dcr2 binds the CCC, Dcr2 knockdown does not affect mRNA 3' end formation. RNAi-depletion of CCC components Symplekin and CPSF73 causes perturbations in esiRNA abundance that correlate with fluctuations in retrotransposon and hairpin esiRNA precursor levels. We also discovered that esiRNAs generated from retrotransposons and hairpins have distinct physical characteristics including a higher predominance of 22 nucleotide hairpin-derived esiRNAs and differences in 3' and 5' base preference. Additionally, retrotransposon precursors and derived esiRNAs are highly enriched in the nucleus while hairpins and hairpin derived esiRNAs are predominantly cytoplasmic similar to canonical mRNAs. RNAi-depletion of either CPSF73 or Symplekin results in nuclear retention of both hairpin and retrotransposon precursors suggesting that polyadenylation indirectly affects cellular localization of Dcr2 substrates. CONCLUSIONS Together, these observations support a novel mechanism in which differences in localization of esiRNA precursors impacts esiRNA biogenesis. Hairpin-derived esiRNAs are generated in the cytoplasm independent of Dcr2-Symplekin interactions, while retrotransposons are processed in the nucleus.
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Affiliation(s)
| | - Michael R McKain
- Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO, 63132, USA
| | - Daniel Michalski
- Department of Biology, University of Missouri, St. Louis, MO, 63121, USA
| | - Kaylyn M Bauer
- Department of Biology, University of Missouri, St. Louis, MO, 63121, USA
| | - Joshua M Daugherty
- Department of Biology, University of Missouri, St. Louis, MO, 63121, USA
| | - Mindy Steiniger
- Department of Biology, University of Missouri, St. Louis, MO, 63121, USA.
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March E, Farrona S. Plant Deubiquitinases and Their Role in the Control of Gene Expression Through Modification of Histones. FRONTIERS IN PLANT SCIENCE 2017; 8:2274. [PMID: 29387079 PMCID: PMC5776116 DOI: 10.3389/fpls.2017.02274] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 12/29/2017] [Indexed: 05/11/2023]
Abstract
Selective degradation of proteins in the cell occurs through ubiquitination, which consists of post-translational deposition of ubiquitin on proteins to target them for degradation by proteases. However, ubiquitination does not only impact on protein stability, but promotes changes in their functions. Whereas the deposition of ubiquitin has been amply studied and discussed, the antagonistic activity, deubiquitination, is just emerging and the full model and players involved in this mechanism are far from being completely understood. Nevertheless, it is the dynamic balance between ubiquitination and deubiquitination that is essential for the development and homeostasis of organisms. In this review, we present a detailed analysis of the members of the deubiquitinase (DUB) superfamily in plants and its division in different clades. We describe current knowledge in the molecular and functional characterisation of DUB proteins, focusing primarily on Arabidopsis thaliana. In addition, the striking function of the duality between ubiquitination and deubiquitination in the control of gene expression through the modification of chromatin is discussed and, using the available information of the activities of the DUB superfamily in yeast and animals as scaffold, we propose possible scenarios for the role of these proteins in plants.
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Buxa MK, Slotman JA, van Royen ME, Paul MW, Houtsmuller AB, Renkawitz R. Insulator speckles associated with long-distance chromatin contacts. Biol Open 2016; 5:1266-74. [PMID: 27464669 PMCID: PMC5051650 DOI: 10.1242/bio.019455] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Nuclear foci of chromatin binding factors are, in many cases, discussed as sites of long-range chromatin interaction in the three-dimensional nuclear space. Insulator binding proteins have been shown to aggregate into insulator bodies, which are large structures not involved in insulation; however, the more diffusely distributed insulator speckles have not been analysed in this respect. Furthermore, insulator binding proteins have been shown to drive binding sites for Polycomb group proteins into Polycomb bodies. Here we find that insulator speckles, marked by the insulator binding protein dCTCF, and Polycomb bodies show differential association with the insulator protein CP190. They differ in number and three-dimensional location with only 26% of the Polycomb bodies overlapping with CP190. By using fluorescence in situ hybridization (FISH) probes to identify long-range interaction (kissing) of the Hox gene clusters Antennapedia complex (ANT-C) and Bithorax complex (BX-C), we found the frequency of interaction to be very low. However, these rare kissing events were associated with insulator speckles at a significantly shorter distance and an increased speckle number. This suggests that insulator speckles are associated with long-distance interaction.
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Affiliation(s)
- Melanie K Buxa
- Institute for Genetics, Justus-Liebig-University, Heinrich-Buff-Ring 58, Giessen D35392, Germany
| | - Johan A Slotman
- Department of Pathology, Josephine Nefkens Institute, Erasmus Optical Imaging Centre, Erasmus MC, Postbus 2040, Rotterdam 3000 CA, The Netherlands
| | - Martin E van Royen
- Department of Pathology, Josephine Nefkens Institute, Erasmus Optical Imaging Centre, Erasmus MC, Postbus 2040, Rotterdam 3000 CA, The Netherlands
| | - Maarten W Paul
- Department of Pathology, Josephine Nefkens Institute, Erasmus Optical Imaging Centre, Erasmus MC, Postbus 2040, Rotterdam 3000 CA, The Netherlands
| | - Adriaan B Houtsmuller
- Department of Pathology, Josephine Nefkens Institute, Erasmus Optical Imaging Centre, Erasmus MC, Postbus 2040, Rotterdam 3000 CA, The Netherlands
| | - Rainer Renkawitz
- Institute for Genetics, Justus-Liebig-University, Heinrich-Buff-Ring 58, Giessen D35392, Germany
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Azlan A, Dzaki N, Azzam G. Argonaute: The executor of small RNA function. J Genet Genomics 2016; 43:481-94. [PMID: 27569398 DOI: 10.1016/j.jgg.2016.06.002] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 05/08/2016] [Accepted: 06/17/2016] [Indexed: 01/06/2023]
Abstract
The discovery of small non-coding RNAs - microRNA (miRNA), short interfering RNA (siRNA) and PIWI-interacting RNA (piRNA) - represents one of the most exciting frontiers in biology specifically on the mechanism of gene regulation. In order to execute their functions, these small RNAs require physical interactions with their protein partners, the Argonaute (AGO) family proteins. Over the years, numerous studies have made tremendous progress on understanding the roles of AGO in gene silencing in various organisms. In this review, we summarize recent progress of AGO-mediated gene silencing and other cellular processes in which AGO proteins have been implicated with a particular focus on progress made in flies, humans and other model organisms as compliment.
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Affiliation(s)
- Azali Azlan
- School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia
| | - Najat Dzaki
- School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia
| | - Ghows Azzam
- School of Biological Sciences, Universiti Sains Malaysia, Penang 11800, Malaysia; Advance Medical and Dental Institute, Universiti Sains Malaysia, Penang 11800, Malaysia.
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32
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Han Li C, Chen Y. Small and Long Non-Coding RNAs: Novel Targets in Perspective Cancer Therapy. Curr Genomics 2016; 16:319-26. [PMID: 27047252 PMCID: PMC4763970 DOI: 10.2174/1389202916666150707155851] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/02/2015] [Accepted: 04/04/2015] [Indexed: 02/08/2023] Open
Abstract
Non-coding RNA refers to a large group of endogenous RNA molecules that have no protein coding capacity, while having specialized cellular and molecular functions. They possess wide range of functions such as the regulation of gene transcription and translation, post-transcriptional modification, epigenetic landscape establishment, protein scaffolding and cofactors recruitments. They are further divided into small non-coding RNAs with size < 200nt (e.g. miRNA, piRNA) and long non-coding RNAs with size >= 200nt (e.g. lincRNA, NAT). Increasing evidences suggest that both non-coding RNAs groups play important roles in cancer development, progression and pathology. Clinically, non-coding RNAs aberrations show high diagnostic and prognostic values. With improved understanding of the nature and roles of non-coding RNAs, it is believed that we can develop therapeutic treatment against cancer via the modulation of these RNA molecules. Advances in nucleic acid drug technology and computational simulation prompt the development of agents to intervene the malignant effects of non-coding RNAs. In this review, we will discuss the role of non-coding RNAs in cancer, and evaluate the potential of non-coding RNA-based cancer therapies.
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Affiliation(s)
- Chi Han Li
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yangchao Chen
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong;; Shenzhen Research Institute, The Chinese University of Hong Kong, Shenzhen, China;; State Key Laboratory of Digestive Disease, Institute of Digestive Disease, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
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Sahin HB, Karatas OF, Specchia V, Tommaso SD, Diebold C, Bozzetti MP, Giangrande A. Novel mutants of the aubergine gene. Fly (Austin) 2016; 10:81-90. [PMID: 27064345 DOI: 10.1080/19336934.2016.1174355] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Abstract
Aubergine is an RNA-binding protein of the Piwi clade, functioning in germline in the piRNA pathway that silences transposons and repetitive sequences. Several mutations of this gene exist, but they mostly result in truncated proteins or correspond to mutations that also affect neighboring genes. We have generated complete aubergine knock-out mutants that do not disrupt the neighboring genes. These novel mutants are characterized by PCR and sequencing. Their nature is confirmed by female sterility and by the presence of crystals in testes, common to the aubergine loss of function mutations. These mutants provide novel and more appropriate tools for the study of the piRNA pathway that controls genome stability.
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Affiliation(s)
- H Bahar Sahin
- a IGBMC, CNRS UMR 7104 - Inserm U 964 . Illkirch Cedex / FRANCE.,b Current address: Kadir Has University , Department of Bioinformatics and Genetics , Fatih , İstanbul / TURKEY
| | - Omer Faruk Karatas
- a IGBMC, CNRS UMR 7104 - Inserm U 964 . Illkirch Cedex / FRANCE.,c Current address: Department of Molecular Biology and Genetics, Erzurum Technical University , Erzurum / TURKEY
| | - Valeria Specchia
- d DiSTeBA - Department of Biological and Environmental Science and Technology - University of Salento - Lecce , Italy
| | - Silvia Di Tommaso
- d DiSTeBA - Department of Biological and Environmental Science and Technology - University of Salento - Lecce , Italy
| | - Céline Diebold
- a IGBMC, CNRS UMR 7104 - Inserm U 964 . Illkirch Cedex / FRANCE
| | - Maria Pia Bozzetti
- d DiSTeBA - Department of Biological and Environmental Science and Technology - University of Salento - Lecce , Italy
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Heterochromatin-Associated Proteins HP1a and Piwi Collaborate to Maintain the Association of Achiasmate Homologs in Drosophila Oocytes. Genetics 2016; 203:173-89. [PMID: 26984058 DOI: 10.1534/genetics.115.186460] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 03/11/2016] [Indexed: 12/21/2022] Open
Abstract
Accurate segregation of homologous chromosomes during meiosis depends on their ability to remain physically connected throughout prophase I. For homologs that achieve a crossover, sister chromatid cohesion distal to the chiasma keeps them attached until anaphase I. However, in Drosophila melanogaster wild-type oocytes, chromosome 4 never recombines, and the X chromosome fails to cross over in 6-10% of oocytes. Proper segregation of these achiasmate homologs relies on their pericentric heterochromatin-mediated association, but the mechanism(s) underlying this attachment remains poorly understood. Using an inducible RNA interference (RNAi) strategy combined with fluorescence in situ hybridization (FISH) to monitor centromere proximal association of the achiasmate FM7a/X homolog pair, we asked whether specific heterochromatin-associated proteins are required for the association and proper segregation of achiasmate homologs in Drosophila oocytes. When we knock down HP1a, H3K9 methytransferases, or the HP1a binding partner Piwi during mid-prophase, we observe significant disruption of pericentric heterochromatin-mediated association of FM7a/X homologs. Furthermore, for both HP1a and Piwi knockdown oocytes, transgenic coexpression of the corresponding wild-type protein is able to rescue RNAi-induced defects, but expression of a mutant protein with a single amino acid change that disrupts the HP1a-Piwi interaction is unable to do so. We show that Piwi is stably bound to numerous sites along the meiotic chromosomes, including centromere proximal regions. In addition, reduction of HP1a or Piwi during meiotic prophase induces a significant increase in FM7a/X segregation errors. We present a speculative model outlining how HP1a and Piwi could collaborate to keep achiasmate chromosomes associated in a homology-dependent manner.
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Piwi maintains germline stem cells and oogenesis in Drosophila through negative regulation of Polycomb group proteins. Nat Genet 2016; 48:283-91. [PMID: 26780607 PMCID: PMC4767590 DOI: 10.1038/ng.3486] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 12/14/2015] [Indexed: 12/14/2022]
Abstract
The Drosophila Piwi protein regulates both niche and intrinsic mechanisms to maintain germline stem cells, but its underlying mechanism remains unclear. Here we report that Piwi cooperates with Polycomb Group complexes PRC1 and PRC2 in niche and germline cells to regulate ovarian germline stem cells and oogenesis. Piwi physically interacts with PRC2 subunits Su(z)12 and Esc in the ovary and in vitro. Chromatin co-immunoprecipitation of Piwi, the PRC2 enzymatic subunit E(z), lysine-27-tri-methylated histone 3 (H3K27m3), and RNA polymerase II in wild-type and piwi mutant ovaries reveals that Piwi binds a conserved DNA motif at ~72 genomic sites, and inhibits PRC2 binding to many non-Piwi-binding genomic targets and H3K27 tri-methylation. Moreover, Piwi influences RNA Polymerase II activities in Drosophila ovaries likely via inhibiting PRC2. We hypothesize that Piwi negatively regulates PRC2 binding by sequestering PRC2 in the nucleoplasm, thus reducing PRC2 binding to many targets and influences transcription during oogenesis.
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36
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Wani AH, Boettiger AN, Schorderet P, Ergun A, Münger C, Sadreyev RI, Zhuang X, Kingston RE, Francis NJ. Chromatin topology is coupled to Polycomb group protein subnuclear organization. Nat Commun 2016; 7:10291. [PMID: 26759081 PMCID: PMC4735512 DOI: 10.1038/ncomms10291] [Citation(s) in RCA: 132] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 11/26/2015] [Indexed: 12/21/2022] Open
Abstract
The genomes of metazoa are organized at multiple scales. Many proteins that regulate genome architecture, including Polycomb group (PcG) proteins, form subnuclear structures. Deciphering mechanistic links between protein organization and chromatin architecture requires precise description and mechanistic perturbations of both. Using super-resolution microscopy, here we show that PcG proteins are organized into hundreds of nanoscale protein clusters. We manipulated PcG clusters by disrupting the polymerization activity of the sterile alpha motif (SAM) of the PcG protein Polyhomeotic (Ph) or by increasing Ph levels. Ph with mutant SAM disrupts clustering of endogenous PcG complexes and chromatin interactions while elevating Ph level increases cluster number and chromatin interactions. These effects can be captured by molecular simulations based on a previously described chromatin polymer model. Both perturbations also alter gene expression. Organization of PcG proteins into small, abundant clusters on chromatin through Ph SAM polymerization activity may shape genome architecture through chromatin interactions.
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Affiliation(s)
- Ajazul H. Wani
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Alistair N. Boettiger
- Howard Hughes Medical Institute, Harvard University Cambridge, Cambridge, Massachusetts 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Patrick Schorderet
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Ayla Ergun
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Christine Münger
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
| | - Ruslan I. Sadreyev
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Xiaowei Zhuang
- Howard Hughes Medical Institute, Harvard University Cambridge, Cambridge, Massachusetts 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, USA
- Department of Physics, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Robert E. Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Nicole J. Francis
- Institut de recherches cliniques de Montréal, Montréal, Québec, Canada
- Département de biochimie et medécine moléculaire, Université de Montréal, Montréal, Québec, Canada
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Abstract
Epigenomics has grown exponentially, providing a better understanding of the mechanistic aspects of new and old phenomena originally described through genetics, as well as providing unexpected insights into the way chromatin modulates the genomic information. In this overview, some of the advances are selected for discussion and comment under six topics: (1) histone modifications, (2) weak interactions, (3) interplay with external inputs, (4) the role of RNA molecules, (5) chromatin folding and architecture, and, finally, (6) a view of the essential role of chromatin transactions in regulating the access to genomic DNA.
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Affiliation(s)
- Vincenzo Pirrotta
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey 08854
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38
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Dukowic-Schulze S, Sundararajan A, Ramaraj T, Kianian S, Pawlowski WP, Mudge J, Chen C. Novel Meiotic miRNAs and Indications for a Role of PhasiRNAs in Meiosis. FRONTIERS IN PLANT SCIENCE 2016; 7:762. [PMID: 27313591 PMCID: PMC4889585 DOI: 10.3389/fpls.2016.00762] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Accepted: 05/17/2016] [Indexed: 05/03/2023]
Abstract
Small RNAs (sRNA) add additional layers to the regulation of gene expression, with siRNAs directing gene silencing at the DNA level by RdDM (RNA-directed DNA methylation), and micro RNAs (miRNAs) directing post-transcriptional regulation of specific target genes, mostly by mRNA cleavage. We used manually isolated male meiocytes from maize (Zea mays) to investigate sRNA and DNA methylation landscapes during zygotene, an early stage of meiosis during which steps of meiotic recombination and synapsis of paired homologous chromosomes take place. We discovered two novel miRNAs from meiocytes, zma-MIR11969 and zma-MIR11970, and identified putative target genes. Furthermore, we detected abundant phasiRNAs of 21 and 24 nt length. PhasiRNAs are phased small RNAs which occur in 21 or 24 nt intervals, at a few hundred loci, specifically in male reproductive tissues in grasses. So far, the function of phasiRNAs remained elusive. Data from isolated meiocytes now revealed elevated DNA methylation at phasiRNA loci, especially in the CHH context, suggesting a role for phasiRNAs in cis DNA methylation. In addition, we consider a role of these phasiRNAs in chromatin remodeling/dynamics during meiosis. However, this is not well supported yet and will need more additional data. Here, we only lay out the idea due to other relevant literature and our additional observation of a peculiar GC content pattern at phasiRNA loci. Chromatin remodeling is also indicated by the discovery that histone genes were enriched for sRNA of 22 nt length. Taken together, we gained clues that lead us to hypothesize sRNA-driven DNA methylation and possibly chromatin remodeling during male meiosis in the monocot maize which is in line with and extends previous knowledge.
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Affiliation(s)
| | | | | | - Shahryar Kianian
- Cereal Disease Laboratory, United States Department of Agriculture – Agricultural Research Service, St. PaulMN, USA
| | - Wojciech P. Pawlowski
- Section of Plant Biology, School of Integrative Plant Science, Cornell University, IthacaNY, USA
| | - Joann Mudge
- National Center for Genome Resources, Santa FeNM, USA
| | - Changbin Chen
- Department of Horticultural Science, University of Minnesota, St. PaulMN, USA
- *Correspondence: Changbin Chen,
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39
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Affiliation(s)
- Victoria H. Meller
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202; , ,
| | - Sonal S. Joshi
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202; , ,
| | - Nikita Deshpande
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202; , ,
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40
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Drosophila Homolog of FMRP Maintains Genome Integrity by Interacting with Piwi. J Genet Genomics 2015; 43:11-24. [PMID: 26842990 DOI: 10.1016/j.jgg.2015.11.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 10/30/2015] [Accepted: 11/02/2015] [Indexed: 12/12/2022]
Abstract
Fragile X syndrome (FraX), the most common form of inherited mental retardation, is caused by the absence of the evolutionally conserved fragile X mental retardation protein (FMRP). While neuronal functions of FMRP have been intensively studied for the last two decades, its role in non-neuronal cells remains poorly understood. Piwi, a key component of the Piwi-interacting RNA (piRNA) pathway, plays an essential role in germline development. In the present study, we report that similar to piwi, dfmr1, the Drosophila homolog of human FMR1, is required for transposon suppression in the germlines. Genetic analyses showed that dfmr1 and piwi act synergistically in heterochromatic silencing, and in inhibiting the differentiation of primordial germline cells and transposon expression. Northern analyses showed that roo piRNA expression levels are reduced in dfmr1 mutant ovaries, suggesting a role of dfmr1 in piRNA biogenesis. Biochemical analysis demonstrated a physical interaction between dFMRP and Piwi via their N-termini. Taken together, we propose that dFMRP cooperates with Piwi in maintaining genome integrity by regulating heterochromatic silencing in somatic cells and suppressing transposon activity via the piRNA pathway in germlines.
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Butler AA, Webb WM, Lubin FD. Regulatory RNAs and control of epigenetic mechanisms: expectations for cognition and cognitive dysfunction. Epigenomics 2015; 8:135-51. [PMID: 26366811 DOI: 10.2217/epi.15.79] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The diverse functions of noncoding RNAs (ncRNAs) can influence virtually every aspect of the transcriptional process including epigenetic regulation of genes. In the CNS, regulatory RNA networks and epigenetic mechanisms have broad relevance to gene transcription changes involved in long-term memory formation and cognition. Thus, it is becoming increasingly clear that multiple classes of ncRNAs impact neuronal development, neuroplasticity, and cognition. Currently, a large gap exists in our knowledge of how ncRNAs facilitate epigenetic processes, and how this phenomenon affects cognitive function. In this review, we discuss recent findings highlighting a provocative role for ncRNAs including lncRNAs and piRNAs in the control of epigenetic mechanisms involved in cognitive function. Furthermore, we discuss the putative roles for these ncRNAs in cognitive disorders such as schizophrenia and Alzheimer's disease.
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Affiliation(s)
- Anderson A Butler
- Department of Neurobiology, University of Alabama at Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA
| | - William M Webb
- Department of Neurobiology, University of Alabama at Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA
| | - Farah D Lubin
- Department of Neurobiology, University of Alabama at Birmingham, 1825 University Boulevard, Birmingham, AL 35294, USA
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Ghasemi M, Pawar H, Mishra RK, Brahmachari V. The functional diversity of Drosophila Ino80 in development. Mech Dev 2015; 138 Pt 2:113-121. [PMID: 26253267 DOI: 10.1016/j.mod.2015.07.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 07/28/2015] [Accepted: 07/30/2015] [Indexed: 10/23/2022]
Abstract
Ino80 is well known as a chromatin remodeling protein with the catalytic function of DNA dependent ATPase and is highly conserved across phyla. Ino80 in human and Drosophila is known to form the Ino80 complex in association with the DNA binding protein Ying-Yang 1 (YY1)/Pleiohomeotic (Pho) the Drosophila homologue. We have earlier reported that Ino80 sub-family of proteins has two functional domains, namely, the DNA dependent ATPase and the DNA binding domain. In the background of the essential role of dIno80 in development, we provide evidence of Pho independent function of dIno80 in development and analyze the dual role of dIno80 in activation as well as repression in the context of the homeotic gene Scr (sex combs reduced) in imaginal discs. This differential effect of dIno80 in different imaginal discs suggests the contextual function of dIno80 as an Enhancer of Trithorax and Polycomb (ETP). We speculate on the role of dIno80 as a chromatin remodeler on one hand and a potential recruiter of epigenetic regulatory complexes on the other.
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Affiliation(s)
- Mohsen Ghasemi
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India
| | - Hema Pawar
- Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rakesh K Mishra
- Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad 500007, India
| | - Vani Brahmachari
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi 110007, India.
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43
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One, Two, Three: Polycomb Proteins Hit All Dimensions of Gene Regulation. Genes (Basel) 2015; 6:520-42. [PMID: 26184319 PMCID: PMC4584315 DOI: 10.3390/genes6030520] [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: 05/11/2015] [Accepted: 06/30/2015] [Indexed: 12/16/2022] Open
Abstract
Polycomb group (PcG) proteins contribute to the formation and maintenance of a specific repressive chromatin state that prevents the expression of genes in a particular space and time. Polycomb repressive complexes (PRCs) consist of several PcG proteins with specific regulatory or catalytic properties. PRCs are recruited to thousands of target genes, and various recruitment factors, including DNA-binding proteins and non-coding RNAs, are involved in the targeting. PcG proteins contribute to a multitude of biological processes by altering chromatin features at different scales. PcG proteins mediate both biochemical modifications of histone tails and biophysical modifications (e.g., chromatin fiber compaction and three-dimensional (3D) chromatin conformation). Here, we review the role of PcG proteins in nuclear architecture, describing their impact on the structure of the chromatin fiber, on chromatin interactions, and on the spatial organization of the genome in nuclei. Although little is known about the role of plant PcG proteins in nuclear organization, much is known in the animal field, and we highlight similarities and differences in the roles of PcG proteins in 3D gene regulation in plants and animals.
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Mozgova I, Köhler C, Hennig L. Keeping the gate closed: functions of the polycomb repressive complex PRC2 in development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:121-32. [PMID: 25762111 DOI: 10.1111/tpj.12828] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 03/09/2015] [Accepted: 03/10/2015] [Indexed: 05/08/2023]
Abstract
Plant ontogeny relies on the correct timing and sequence of transitions between individual developmental phases. These are specified by gene expression patterns that are established by the balanced action of activators and repressors. Polycomb repressive complexes (PRCs) represent an evolutionarily conserved system of epigenetic gene repression that governs the establishment and maintenance of cell, tissue and organ identity, contributing to the correct execution of the developmental programs. PRC2 is a four-subunit histone methyltransferase complex that catalyzes trimethylation of lysine 27 on histone H3 (H3K27me3), which contributes to the change of chromatin structure and long-lasting gene repression. Here, we review the composition and molecular function of the different known PRC2 complexes in plants, and focus on the role of PRC2 in mediating the establishment of different developmental phases and transitions between them.
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Affiliation(s)
- Iva Mozgova
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007, Uppsala, Sweden
| | - Claudia Köhler
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007, Uppsala, Sweden
| | - Lars Hennig
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, SE-75007, Uppsala, Sweden
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Widespread rearrangement of 3D chromatin organization underlies polycomb-mediated stress-induced silencing. Mol Cell 2015; 58:216-31. [PMID: 25818644 DOI: 10.1016/j.molcel.2015.02.023] [Citation(s) in RCA: 219] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Revised: 01/09/2015] [Accepted: 02/19/2015] [Indexed: 12/28/2022]
Abstract
Chromosomes of metazoan organisms are partitioned in the interphase nucleus into discrete topologically associating domains (TADs). Borders between TADs are formed in regions containing active genes and clusters of architectural protein binding sites. The transcription of most genes is repressed after temperature stress in Drosophila. Here we show that temperature stress induces relocalization of architectural proteins from TAD borders to inside TADs, and this is accompanied by a dramatic rearrangement in the 3D organization of the nucleus. TAD border strength declines, allowing for an increase in long-distance inter-TAD interactions. Similar but quantitatively weaker effects are observed upon inhibition of transcription or depletion of individual architectural proteins. Heat shock-induced inter-TAD interactions result in increased contacts among enhancers and promoters of silenced genes, which recruit Pc and form Pc bodies in the nucleolus. These results suggest that the TAD organization of metazoan genomes is plastic and can be reconfigured quickly.
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Abstract
The different cell types of an organism share the same DNA, but during cell differentiation their genomes undergo diverse structural and organizational changes that affect gene expression and other cellular functions. These can range from large-scale folding of whole chromosomes or of smaller genomic regions, to the re-organization of local interactions between enhancers and promoters, mediated by the binding of transcription factors and chromatin looping. The higher-order organization of chromatin is also influenced by the specificity of the contacts that it makes with nuclear structures such as the lamina. Sophisticated methods for mapping chromatin contacts are generating genome-wide data that provide deep insights into the formation of chromatin interactions, and into their roles in the organization and function of the eukaryotic cell nucleus.
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47
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Gavrilov AA, Razin SV. Compartmentalization of the cell nucleus and spatial organization of the genome. Mol Biol 2015. [DOI: 10.1134/s0026893315010033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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48
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Chromatin-Driven Behavior of Topologically Associating Domains. J Mol Biol 2015; 427:608-25. [DOI: 10.1016/j.jmb.2014.09.013] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 09/17/2014] [Accepted: 09/23/2014] [Indexed: 12/19/2022]
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49
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Ulianov SV, Gavrilov AA, Razin SV. Nuclear Compartments, Genome Folding, and Enhancer-Promoter Communication. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 315:183-244. [DOI: 10.1016/bs.ircmb.2014.11.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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50
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Abstract
Polycomb group (PcG) proteins are conserved chromatin regulators involved in the control of key developmental programs in eukaryotes. They collectively provide the transcriptional memory unique to each cell identity by maintaining transcriptional states of developmental genes. PcG proteins form multi-protein complexes, known as Polycomb repressive complex 1 (PRC1) and Polycomb repressive complex 2 (PRC2). PRC1 and PRC2 contribute to the stable gene silencing in part through catalyzing covalent histone modifications. Components of PRC1 and PRC2 are well conserved from plants to animals. PcG-mediated gene silencing has been extensively investigated in efforts to understand molecular mechanisms underlying developmental programs in eukaryotes. Here, we describe our current knowledge on PcG-mediated gene repression which dictates developmental programs by dynamic layers of regulatory activities, with an emphasis given to the model plant Arabidopsis thaliana.
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Affiliation(s)
- Dong-Hwan Kim
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712,
USA
| | - Sibum Sung
- Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712,
USA
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