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Sato H, Wu B, Delahaye F, Singer RH, Greally JM. Retargeting of macroH2A following mitosis to cytogenetic-scale heterochromatic domains. J Cell Biol 2019; 218:1810-1823. [PMID: 31110057 PMCID: PMC6548134 DOI: 10.1083/jcb.201811109] [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: 11/20/2018] [Revised: 03/20/2019] [Accepted: 04/19/2019] [Indexed: 12/12/2022] Open
Abstract
How macroH2A, a histone variant involved in silencing gene expression, is inherited from parent to daughter cells is unclear. Using a combination of imaging, biochemical, and genomic approaches, Sato et al. describe how newly synthesized macroH2A is incorporated predominantly in the G1 phase of human mitosis, targeting heterochromatic regions. The heritability of chromatin states through cell division is a potential contributor to the epigenetic maintenance of cellular memory of prior states. The macroH2A histone variant has properties of a regulator of epigenetic cell memory, including roles controlling gene silencing and cell differentiation. Its mechanisms of regional genomic targeting and maintenance through cell division are unknown. Here, we combined in vivo imaging with biochemical and genomic approaches to show that human macroH2A is incorporated into chromatin in the G1 phase of the cell cycle following DNA replication. The newly incorporated macroH2A retargets the same large heterochromatic domains where macroH2A was already enriched in the previous cell cycle. It remains heterotypic, targeting individual nucleosomes that do not already contain a macroH2A molecule. The pattern observed resembles that of a new deposition of centromeric histone variants during the cell cycle, indicating mechanistic similarities for macrodomain-scale regulation of epigenetic properties of the cell.
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Affiliation(s)
- Hanae Sato
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY.,Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY
| | - Bin Wu
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY.,Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY
| | - Fabien Delahaye
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY.,Department of Obstetrics and Gynecology and Women's Health, Albert Einstein College of Medicine, Bronx, NY
| | - Robert H Singer
- Department of Anatomy and Structural Biology, Albert Einstein College of Medicine, Bronx, NY .,Gruss Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY.,Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, NY.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA
| | - John M Greally
- Center for Epigenomics and Department of Genetics, Albert Einstein College of Medicine, Bronx, NY
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102
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Domsch K, Carnesecchi J, Disela V, Friedrich J, Trost N, Ermakova O, Polychronidou M, Lohmann I. The Hox transcription factor Ubx stabilizes lineage commitment by suppressing cellular plasticity in Drosophila. eLife 2019; 8:42675. [PMID: 31050646 PMCID: PMC6513553 DOI: 10.7554/elife.42675] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 04/30/2019] [Indexed: 12/22/2022] Open
Abstract
During development cells become restricted in their differentiation potential by repressing alternative cell fates, and the Polycomb complex plays a crucial role in this process. However, how alternative fate genes are lineage-specifically silenced is unclear. We studied Ultrabithorax (Ubx), a multi-lineage transcription factor of the Hox class, in two tissue lineages using sorted nuclei and interfered with Ubx in mesodermal cells. We find that depletion of Ubx leads to the de-repression of genes normally expressed in other lineages. Ubx silences expression of alternative fate genes by retaining the Polycomb Group protein Pleiohomeotic at Ubx targeted genomic regions, thereby stabilizing repressive chromatin marks in a lineage-dependent manner. Our study demonstrates that Ubx stabilizes lineage choice by suppressing the multipotency encoded in the genome via its interaction with Pho. This mechanism may explain why the Hox code is maintained throughout the lifecycle, since it could set a block to transdifferentiation in adult cells.
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Affiliation(s)
- Katrin Domsch
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg, Germany
| | | | - Vanessa Disela
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg, Germany
| | - Jana Friedrich
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg, Germany
| | - Nils Trost
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg, Germany
| | - Olga Ermakova
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg, Germany
| | | | - Ingrid Lohmann
- Centre for Organismal Studies (COS) Heidelberg, Heidelberg, Germany
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103
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Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nat Commun 2019; 10:1931. [PMID: 31036804 PMCID: PMC6488670 DOI: 10.1038/s41467-019-09628-6] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Accepted: 03/19/2019] [Indexed: 12/16/2022] Open
Abstract
Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates.
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Affiliation(s)
- Hagar F Moussa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Daniel Bsteh
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
- Department of Biochemistry and Molecular Medicine and Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, CA, 90089, USA
| | - Ramesh Yelagandula
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Carina Pribitzer
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Karin Stecher
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Katarina Bartalska
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400, Klosterneuburg, Austria
| | - Luca Michetti
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Jingkui Wang
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030, Vienna, Austria
| | - Jorge A Zepeda-Martinez
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Jacob I Stuckey
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, MA, 02142, USA
| | - Lindsey I James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Stephen V Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Oliver Bell
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria.
- Department of Biochemistry and Molecular Medicine and Norris Comprehensive Cancer Center, Keck School of Medicine of the University of Southern California, Los Angeles, CA, 90089, USA.
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104
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Laugesen A, Højfeldt JW, Helin K. Molecular Mechanisms Directing PRC2 Recruitment and H3K27 Methylation. Mol Cell 2019; 74:8-18. [PMID: 30951652 PMCID: PMC6452890 DOI: 10.1016/j.molcel.2019.03.011] [Citation(s) in RCA: 354] [Impact Index Per Article: 70.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/12/2019] [Accepted: 03/05/2019] [Indexed: 02/07/2023]
Abstract
The polycomb repressive complex 2 (PRC2) is a chromatin-associated methyltransferase catalyzing mono-, di-, and trimethylation of lysine 27 on histone H3 (H3K27). This activity is required for normal organismal development and maintenance of gene expression patterns to uphold cell identity. PRC2 function is often deregulated in disease and is a promising candidate for therapeutic targeting in cancer. In this review, we discuss the molecular mechanisms proposed to take part in modulating PRC2 recruitment and shaping H3K27 methylation patterns across the genome. This includes consideration of factors influencing PRC2 residence time on chromatin and PRC2 catalytic activity with a focus on the mechanisms giving rise to regional preferences and differential deposition of H3K27 methylation. We further discuss existing evidence for functional diversity between distinct subsets of PRC2 complexes with the aim of extracting key concepts and highlighting major open questions toward a more complete understanding of PRC2 function.
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Affiliation(s)
- Anne Laugesen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Jonas Westergaard Højfeldt
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen N, Denmark; The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark; Cell Biology Program and Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center (MSKCC), 1275 York Avenue, New York, NY 10065, USA.
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105
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Fukushima HS, Takeda H, Nakamura R. Targeted in vivo epigenome editing of H3K27me3. Epigenetics Chromatin 2019; 12:17. [PMID: 30871638 PMCID: PMC6419334 DOI: 10.1186/s13072-019-0263-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/07/2019] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Epigenetic modifications have a central role in transcriptional regulation. While several studies using next-generation sequencing have revealed genome-wide associations between epigenetic modifications and transcriptional states, a direct causal relationship at specific genomic loci has not been fully demonstrated, due to a lack of technology for targeted manipulation of epigenetic modifications. Recently, epigenome editing techniques based on the CRISPR-Cas9 system have been reported to directly manipulate specific modifications at precise genomic regions. However, the number of editable modifications as well as studies applying these techniques in vivo is still limited. RESULTS Here, we report direct modification of the epigenome in medaka (Japanese killifish, Oryzias latipes) embryos. Specifically, we developed a method to ectopically induce the repressive histone modification, H3K27me3 in a locus-specific manner, using a fusion construct of Oryzias latipes H3K27 methyltransferase Ezh2 (olEzh2) and dCas9 (dCas9-olEzh2). Co-injection of dCas9-olEzh2 mRNA with single guide RNAs (sgRNAs) into one-cell-stage embryos induced specific H3K27me3 accumulation at the targeted loci and induced downregulation of gene expression. CONCLUSION In this study, we established the in vivo epigenome editing of H3K27me3 using medaka embryos. The locus-specific manipulation of the epigenome in living organisms will lead to a previously inaccessible understanding of the role of epigenetic modifications in development and disease.
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Affiliation(s)
- Hiroto S. Fukushima
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 Japan
| | - Hiroyuki Takeda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 Japan
| | - Ryohei Nakamura
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033 Japan
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106
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Affiliation(s)
- Sandip De
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Judith A Kassis
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
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107
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Loubiere V, Martinez AM, Cavalli G. Cell Fate and Developmental Regulation Dynamics by Polycomb Proteins and 3D Genome Architecture. Bioessays 2019; 41:e1800222. [PMID: 30793782 DOI: 10.1002/bies.201800222] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 12/22/2018] [Indexed: 12/14/2022]
Abstract
Targeted transitions in chromatin states at thousands of genes are essential drivers of eukaryotic development. Therefore, understanding the in vivo dynamics of epigenetic regulators is crucial for deciphering the mechanisms underpinning cell fate decisions. This review illustrates how, in addition to its cell memory function, the Polycomb group of transcriptional regulators orchestrates temporal, cell and tissue-specific expression of master genes during development. These highly sophisticated developmental transitions are dependent on the context- and tissue-specific assembly of the different types of Polycomb Group (PcG) complexes, which regulates their targeting and/or activities on chromatin. Here, an overview is provided of how PcG complexes function at multiple scales to regulate transcription, local chromatin environment, and higher order structures that support normal differentiation and are perturbed in tumorigenesis.
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Affiliation(s)
- Vincent Loubiere
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, 34396, Montpellier, France
| | - Anne-Marie Martinez
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, 34396, Montpellier, France
| | - Giacomo Cavalli
- Institute of Human Genetics, UMR 9002, CNRS and University of Montpellier, 34396, Montpellier, France
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108
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An H3K27me3 demethylase-HSFA2 regulatory loop orchestrates transgenerational thermomemory in Arabidopsis. Cell Res 2019; 29:379-390. [PMID: 30778176 PMCID: PMC6796840 DOI: 10.1038/s41422-019-0145-8] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/22/2019] [Indexed: 01/18/2023] Open
Abstract
Global warming has profound effects on plant growth and fitness. Plants have evolved sophisticated epigenetic machinery to respond quickly to heat, and exhibit transgenerational memory of the heat-induced release of post-transcriptional gene silencing (PTGS). However, how thermomemory is transmitted to progeny and the physiological relevance are elusive. Here we show that heat-induced HEAT SHOCK TRANSCRIPTION FACTOR A2 (HSFA2) directly activates the H3K27me3 demethylase RELATIVE OF EARLY FLOWERING 6 (REF6), which in turn derepresses HSFA2. REF6 and HSFA2 establish a heritable feedback loop, and activate an E3 ubiquitin ligase, SUPPRESSOR OF GENE SILENCING 3 (SGS3)-INTERACTING PROTEIN 1 (SGIP1). SGIP1-mediated SGS3 degradation leads to inhibited biosynthesis of trans-acting siRNA (tasiRNA). The REF6-HSFA2 loop and reduced tasiRNA converge to release HEAT-INDUCED TAS1 TARGET 5 (HTT5), which drives early flowering but attenuates immunity. Thus, heat induces transmitted phenotypes via a coordinated epigenetic network involving histone demethylases, transcription factors, and tasiRNAs, ensuring reproductive success and transgenerational stress adaptation.
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109
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Wang Z, Chu T, Choate LA, Danko CG. Identification of regulatory elements from nascent transcription using dREG. Genome Res 2019; 29:293-303. [PMID: 30573452 PMCID: PMC6360809 DOI: 10.1101/gr.238279.118] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Accepted: 12/18/2018] [Indexed: 02/02/2023]
Abstract
Our genomes encode a wealth of transcription initiation regions (TIRs) that can be identified by their distinctive patterns of actively elongating RNA polymerase. We previously introduced dREG to identify TIRs using PRO-seq data. Here, we introduce an efficient new implementation of dREG that uses PRO-seq data to identify both uni- and bidirectionally transcribed TIRs with 70% improvement in accuracy, three- to fourfold higher resolution, and >100-fold increases in computational efficiency. Using a novel strategy to identify TIRs based on their statistical confidence reveals extensive overlap with orthogonal assays, yet also reveals thousands of additional weakly transcribed TIRs that were not identified by H3K27ac ChIP-seq or DNase-seq. Novel TIRs discovered by dREG were often associated with RNA polymerase III initiation, bound by pioneer transcription factors, or located in broad domains marked by repressive chromatin modifications. Our results suggest that transcription initiation can be a powerful tool for expanding the catalog of functional elements.
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Affiliation(s)
- Zhong Wang
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
| | - Tinyi Chu
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
- Graduate Field of Computational Biology, Cornell University, Ithaca, New York 14853, USA
| | - Lauren A Choate
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York 14853, USA
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110
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Khateb M, Azriel A, Levi BZ. The Third Intron of IRF8 Is a Cell-Type-Specific Chromatin Priming Element during Mouse Embryonal Stem Cell Differentiation. J Mol Biol 2019; 431:210-222. [PMID: 30502383 DOI: 10.1016/j.jmb.2018.11.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 11/07/2018] [Accepted: 11/20/2018] [Indexed: 01/09/2023]
Abstract
Interferon regulatory factor 8 (IRF8) is a nuclear transcription factor that plays a key role in the hierarchical differentiation of hematopoietic stem cells toward monocyte/dendritic cell lineages. Therefore, its expression is mainly limited to bone marrow-derived cells. The molecular mechanisms governing this cell-type-restricted expression have been described. However, the molecular mechanisms that are responsible for its silencing in non-hematopoietic cells are elusive. Recently, we demonstrated a role for IRF8 third intron in restricting its expression in non-hematopoietic cells. Furthermore, we showed that this intron alone is sufficient to promote repressed chromatin a cell-type-specific manner. Here we demonstrate the effect of the IRF8 third intron on chromatin conformation during murine embryonal stem cell differentiation. Using genome editing, we provide data showing that the third intron plays a key role in priming the chromatin state of the IRF8 locus during cell differentiation. It mediates dual regulatory effects in a cell-type-specific mode. It acts as a repressor element governing chromatin state of the IRF8 locus during embryonal stem cell differentiation to cardiomyocytes that are expression-restrictive cells. Conversely, it functions as an activator element that is essential for open chromatin structure during the differentiation of these cells to dendritic cells that are expression-permissive cells. Together, these results point to the role of IRF8 third intron as a cell-type-specific chromatin priming element during embryonal stem cell differentiation. These data add another layer to our understanding of the molecular mechanisms governing misexpression of a cell-type-specific gene such as IRF8.
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Affiliation(s)
- Mamduh Khateb
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Aviva Azriel
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | - Ben-Zion Levi
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel.
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111
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Hamada A, Torre C, Drancourt M, Ghigo E. Trained Immunity Carried by Non-immune Cells. Front Microbiol 2019; 9:3225. [PMID: 30692968 PMCID: PMC6340064 DOI: 10.3389/fmicb.2018.03225] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/11/2018] [Indexed: 12/21/2022] Open
Abstract
“Trained immunity” is a term proposed by Netea to describe the ability of an organism to develop an exacerbated immunological response to protect against a second infection independent of the adaptative immunity. This immunological memory can last from 1 week to several months and is only described in innate immune cells such as monocytes, macrophages, and natural killer cells. Paradoxically, the lifespan of these cells in the blood is shorter than the duration of trained immunity. This observation suggested that trained immunity could be carried by long lifespan cells such as stem cells and non-immune cells like fibroblasts. It is now evident that in addition to performing their putative function in the development and maintenance of tissue homeostasis, non-immune cells also play an important role in the response to pathogens by producing anti-microbial factors, with long-term inflammation suggesting that non-immune cells can be trained to confer long-lasting immunological memory. This review provides a summary of the current relevant knowledge about the cells which possess immunological memory and discusses the possibility that non-immune cells may carry immunological memory and mechanisms that might be involved.
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Affiliation(s)
- Attoumani Hamada
- IRD, MEPHI, Institut Hospitalier Universitaire Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Cédric Torre
- IRD, MEPHI, Institut Hospitalier Universitaire Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Michel Drancourt
- IRD, MEPHI, Institut Hospitalier Universitaire Méditerranée Infection, Aix-Marseille University, Marseille, France
| | - Eric Ghigo
- IRD, MEPHI, Institut Hospitalier Universitaire Méditerranée Infection, Aix-Marseille University, Marseille, France
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112
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Ruiz JL, Yerbanga RS, Lefèvre T, Ouedraogo JB, Corces VG, Gómez-Díaz E. Chromatin changes in Anopheles gambiae induced by Plasmodium falciparum infection. Epigenetics Chromatin 2019; 12:5. [PMID: 30616642 PMCID: PMC6322293 DOI: 10.1186/s13072-018-0250-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 12/19/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Infection by the human malaria parasite leads to important changes in mosquito phenotypic traits related to vector competence. However, we still lack a clear understanding of the underlying mechanisms and, in particular, of the epigenetic basis for these changes. We have examined genome-wide distribution maps of H3K27ac, H3K9ac, H3K9me3 and H3K4me3 by ChIP-seq and the transcriptome by RNA-seq, of midguts from Anopheles gambiae mosquitoes blood-fed uninfected and infected with natural isolates of the human malaria parasite Plasmodium falciparum in Burkina Faso. RESULTS We report 15,916 regions containing differential histone modification enrichment between infected and uninfected, of which 8339 locate at promoters and/or intersect with genes. The functional annotation of these regions allowed us to identify infection-responsive genes showing differential enrichment in various histone modifications, such as CLIP proteases, antimicrobial peptides-encoding genes, and genes related to melanization responses and the complement system. Further, the motif analysis of regions differentially enriched in various histone modifications predicts binding sites that might be involved in the cis-regulation of these regions, such as Deaf1, Pangolin and Dorsal transcription factors (TFs). Some of these TFs are known to regulate immunity gene expression in Drosophila and are involved in the Notch and JAK/STAT signaling pathways. CONCLUSIONS The analysis of malaria infection-induced chromatin changes in mosquitoes is important not only to identify regulatory elements and genes underlying mosquito responses to P. falciparum infection, but also for possible applications to the genetic manipulation of mosquitoes and to other mosquito-borne systems.
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Affiliation(s)
- José L. Ruiz
- Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas, 41092 Seville, Spain
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas, 18016 Granada, Spain
| | - Rakiswendé S. Yerbanga
- Institut de Recherche en Sciences de la Santé (IRSS), 01 BP 171, Bobo Dioulasso, Burkina Faso
| | - Thierry Lefèvre
- Institut de Recherche en Sciences de la Santé (IRSS), 01 BP 171, Bobo Dioulasso, Burkina Faso
- MIVEGEC, IRD, CNRS, University of Montpellier, Montpellier, France
| | - Jean B. Ouedraogo
- Institut de Recherche en Sciences de la Santé (IRSS), 01 BP 171, Bobo Dioulasso, Burkina Faso
| | - Victor G. Corces
- Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322 USA
| | - Elena Gómez-Díaz
- Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas, 41092 Seville, Spain
- Instituto de Parasitología y Biomedicina López-Neyra (IPBLN), Consejo Superior de Investigaciones Científicas, 18016 Granada, Spain
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113
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De S, Cheng Y, Sun MA, Gehred ND, Kassis JA. Structure and function of an ectopic Polycomb chromatin domain. SCIENCE ADVANCES 2019; 5:eaau9739. [PMID: 30662949 PMCID: PMC6326746 DOI: 10.1126/sciadv.aau9739] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 11/28/2018] [Indexed: 05/14/2023]
Abstract
Polycomb group proteins (PcGs) drive target gene repression and form large chromatin domains. In Drosophila, DNA elements known as Polycomb group response elements (PREs) recruit PcGs to the DNA. We have shown that, within the invected-engrailed (inv-en) Polycomb domain, strong, constitutive PREs are dispensable for Polycomb domain structure and function. We suggest that the endogenous chromosomal location imparts stability to this Polycomb domain. To test this possibility, a 79-kb en transgene was inserted into other chromosomal locations. This transgene is functional and forms a Polycomb domain. The spreading of the H3K27me3 repressive mark, characteristic of PcG domains, varies depending on the chromatin context of the transgene. Unlike at the endogenous locus, deletion of the strong, constitutive PREs from the transgene leads to both loss- and gain-of function phenotypes, demonstrating the important role of these regulatory elements. Our data show that chromatin context plays an important role in Polycomb domain structure and function.
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114
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Probing the Function of Metazoan Histones with a Systematic Library of H3 and H4 Mutants. Dev Cell 2018; 48:406-419.e5. [PMID: 30595536 DOI: 10.1016/j.devcel.2018.11.047] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 09/15/2018] [Accepted: 11/28/2018] [Indexed: 11/21/2022]
Abstract
Replication-dependent histone genes often reside in tandemly arrayed gene clusters, hindering systematic loss-of-function analyses. Here, we used CRISPR/Cas9 and the attP/attB double-integration system to alter numbers and sequences of histone genes in their original genomic context in Drosophila melanogaster. As few as 8 copies of the histone gene unit supported embryo development and adult viability, whereas flies with 20 copies were indistinguishable from wild-types. By hierarchical assembly, 40 alanine-substitution mutations (covering all known modified residues in histones H3 and H4) were introduced and characterized. Mutations at multiple residues compromised viability, fertility, and DNA-damage responses. In particular, H4K16 was necessary for expression of male X-linked genes, male viability, and maintenance of ovarian germline stem cells, whereas H3K27 was essential for late embryogenesis. Simplified mosaic analysis showed that H3R26 is required for H3K27 trimethylation. We have developed a powerful strategy and valuable reagents to systematically probe histone functions in D. melanogaster.
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115
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Abstract
Inheritance of genomic DNA underlies the vast majority of biological inheritance, yet it has been clear for decades that additional epigenetic information can be passed on to future generations. Here, we review major model systems for transgenerational epigenetic inheritance via the germline in multicellular organisms. In addition to surveying examples of epivariation that may arise stochastically or in response to unknown stimuli, we also discuss the induction of heritable epigenetic changes by genetic or environmental perturbations. Mechanistically, we discuss the increasingly well-understood molecular pathways responsible for epigenetic inheritance, with a focus on the unusual features of the germline epigenome.
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Affiliation(s)
- Ana Bošković
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Oliver J. Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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116
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Greenstein RA, Al-Sady B. Epigenetic fates of gene silencing established by heterochromatin spreading in cell identity and genome stability. Curr Genet 2018; 65:423-428. [PMID: 30390097 DOI: 10.1007/s00294-018-0901-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 10/24/2018] [Accepted: 10/27/2018] [Indexed: 01/20/2023]
Abstract
Heterochromatin spreading, the propagation of repressive chromatin along the chromosome, is a reaction critical to genome stability and defense, as well as maintenance of unique cell fates. Here, we discuss the intrinsic properties of the spreading reaction and circumstances under which its products, formed distal to DNA-encoded nucleation sites, can be epigenetically maintained. Finally, we speculate that the epigenetic properties of heterochromatin evolved together with the need to stabilize cellular identity.
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Affiliation(s)
- R A Greenstein
- Department of Microbiology and Immunology, George Williams Hooper Foundation, University of California San Francisco, San Francisco, CA, 94143, USA.,TETRAD Graduate Program, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Bassem Al-Sady
- Department of Microbiology and Immunology, George Williams Hooper Foundation, University of California San Francisco, San Francisco, CA, 94143, USA.
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117
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Reverón-Gómez N, González-Aguilera C, Stewart-Morgan KR, Petryk N, Flury V, Graziano S, Johansen JV, Jakobsen JS, Alabert C, Groth A. Accurate Recycling of Parental Histones Reproduces the Histone Modification Landscape during DNA Replication. Mol Cell 2018; 72:239-249.e5. [PMID: 30146316 PMCID: PMC6202308 DOI: 10.1016/j.molcel.2018.08.010] [Citation(s) in RCA: 149] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 06/25/2018] [Accepted: 08/07/2018] [Indexed: 12/22/2022]
Abstract
Chromatin organization is disrupted genome-wide during DNA replication. On newly synthesized DNA, nucleosomes are assembled from new naive histones and old modified histones. It remains unknown whether the landscape of histone post-translational modifications (PTMs) is faithfully copied during DNA replication or the epigenome is perturbed. Here we develop chromatin occupancy after replication (ChOR-seq) to determine histone PTM occupancy immediately after DNA replication and across the cell cycle. We show that H3K4me3, H3K36me3, H3K79me3, and H3K27me3 positional information is reproduced with high accuracy on newly synthesized DNA through histone recycling. Quantitative ChOR-seq reveals that de novo methylation to restore H3K4me3 and H3K27me3 levels occurs across the cell cycle with mark- and locus-specific kinetics. Collectively, this demonstrates that accurate parental histone recycling preserves positional information and allows PTM transmission to daughter cells while modification of new histones gives rise to complex epigenome fluctuations across the cell cycle that could underlie cell-to-cell heterogeneity.
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Affiliation(s)
- Nazaret Reverón-Gómez
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Cristina González-Aguilera
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kathleen R Stewart-Morgan
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Nataliya Petryk
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Valentin Flury
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Simona Graziano
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jens Vilstrup Johansen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Janus Schou Jakobsen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Constance Alabert
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark; The Novo Nordisk Center for Protein Research (CPR), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, 2200 Copenhagen, Denmark.
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118
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Ortega E, Rengachari S, Ibrahim Z, Hoghoughi N, Gaucher J, Holehouse AS, Khochbin S, Panne D. Transcription factor dimerization activates the p300 acetyltransferase. Nature 2018; 562:538-544. [PMID: 30323286 PMCID: PMC6914384 DOI: 10.1038/s41586-018-0621-1] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 08/15/2018] [Indexed: 01/08/2023]
Abstract
The transcriptional coactivator p300 is a histone lysine acetyltransferase that is typically recruited to transcriptional enhancers and regulates gene expression by acetylating chromatin. Here we show that p300 activation directly depends on the activation and oligomerisation status of transcription factor (TF) ligands. Using two model TFs, IRF3 and STAT1, we demonstrate that TF dimerization enables trans-autoacetylation of p300 in a highly conserved and intrinsically disordered autoinhibitory lysine-rich loop (AIL), resulting in HAT activation. We describe a p300 crystal structure in which the AIL invades the active site of a neighbouring HAT domain thus revealing a snap-shot of a trans-autoacetylation reaction intermediate. Substrate access to the active site involves rearrangement of an autoinhibitory RING domain. Our data explain how cellular signalling, TF activation and dimerization controls p300 activation thus explaining why gene transcription is associated with chromatin acetylation.
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Affiliation(s)
- Esther Ortega
- European Molecular Biology Laboratory, Grenoble, France
| | - Srinivasan Rengachari
- European Molecular Biology Laboratory, Grenoble, France.,Max Planck Institute for Biophysical Chemistry, Department of Molecular Biology, Göttingen, Germany
| | - Ziad Ibrahim
- European Molecular Biology Laboratory, Grenoble, France.,Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Naghmeh Hoghoughi
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Jonathan Gaucher
- European Molecular Biology Laboratory, Grenoble, France.,Université Grenoble Alpes, INSERM U1042, HP2 Laboratory, Grenoble, France
| | - Alex S Holehouse
- Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO, USA
| | - Saadi Khochbin
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Daniel Panne
- European Molecular Biology Laboratory, Grenoble, France. .,Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK.
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119
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Yen YP, Hsieh WF, Tsai YY, Lu YL, Liau ES, Hsu HC, Chen YC, Liu TC, Chang M, Li J, Lin SP, Hung JH, Chen JA. Dlk1-Dio3 locus-derived lncRNAs perpetuate postmitotic motor neuron cell fate and subtype identity. eLife 2018; 7:38080. [PMID: 30311912 PMCID: PMC6221546 DOI: 10.7554/elife.38080] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 10/11/2018] [Indexed: 12/28/2022] Open
Abstract
The mammalian imprinted Dlk1-Dio3 locus produces multiple long non-coding RNAs (lncRNAs) from the maternally inherited allele, including Meg3 (i.e., Gtl2) in the mammalian genome. Although this locus has well-characterized functions in stem cell and tumor contexts, its role during neural development is unknown. By profiling cell types at each stage of embryonic stem cell-derived motor neurons (ESC~MNs) that recapitulate spinal cord development, we uncovered that lncRNAs expressed from the Dlk1-Dio3 locus are predominantly and gradually enriched in rostral motor neurons (MNs). Mechanistically, Meg3 and other Dlk1-Dio3 locus-derived lncRNAs facilitate Ezh2/Jarid2 interactions. Loss of these lncRNAs compromises the H3K27me3 landscape, leading to aberrant expression of progenitor and caudal Hox genes in postmitotic MNs. Our data thus illustrate that these lncRNAs in the Dlk1-Dio3 locus, particularly Meg3, play a critical role in maintaining postmitotic MN cell fate by repressing progenitor genes and they shape MN subtype identity by regulating Hox genes. When a gene is active, its DNA sequence is ‘transcribed’ to form a molecule of RNA. Many of these RNAs act as templates for making proteins. But for some genes, the protein molecules are not their final destinations. Their RNA molecules instead help to control gene activity, which can alter the behaviour or the identity of a cell. For example, experiments performed in individual cells suggest that so-called long non-coding RNAs (or lncRNAs for short) guide how stem cells develop into different types of mature cells. However, it is not clear whether lncRNAs play the same critical role in embryos. Yen et al. used embryonic stem cells to model how motor neurons develop in the spinal cord of mouse embryos. This revealed that motor neurons produce large amounts of a specific group of lncRNAs, particularly one called Meg3. Further experiments showed that motor neurons in mouse embryos that lack Meg3 do not correctly silence a set of genes called the Hox genes, which are crucial for laying out the body plans of many different animal embryos. These neurons also incorrectly continue to express genes that are normally active in an early phase of the stem-like cells that make motor neurons. There is wide interest in how lncRNAs help to regulate embryonic development. With this new knowledge of how Meg3 regulates the activity of Hox genes in motor neurons, research could now be directed toward investigating whether lncRNAs help other tissues to develop in a similar way.
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Affiliation(s)
- Ya-Ping Yen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China.,Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Wen-Fu Hsieh
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Ya-Yin Tsai
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Ya-Lin Lu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Ee Shan Liau
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Ho-Chiang Hsu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Yen-Chung Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Ting-Chun Liu
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Mien Chang
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
| | - Joye Li
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Shau-Ping Lin
- Institute of Biotechnology, College of Bio-Resources and Agriculture, National Taiwan University, Taipei, Taiwan, Republic of China
| | - Jui-Hung Hung
- Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, Taiwan, Republic of China.,Department of Computer Science, National Chiao Tung University, Hsinchu, Taiwan, Republic of China
| | - Jun-An Chen
- Institute of Molecular Biology, Academia Sinica, Taipei, Taiwan, Republic of China
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120
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Yu C, Gan H, Serra-Cardona A, Zhang L, Gan S, Sharma S, Johansson E, Chabes A, Xu RM, Zhang Z. A mechanism for preventing asymmetric histone segregation onto replicating DNA strands. Science 2018; 361:1386-1389. [PMID: 30115745 PMCID: PMC6597248 DOI: 10.1126/science.aat8849] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 07/30/2018] [Indexed: 12/11/2022]
Abstract
How parental histone (H3-H4)2 tetramers, the primary carriers of epigenetic modifications, are transferred onto leading and lagging strands of DNA replication forks for epigenetic inheritance remains elusive. Here we show that parental (H3-H4)2 tetramers are assembled into nucleosomes onto both leading and lagging strands, with a slight preference for lagging strands. The lagging-strand preference increases markedly in budding yeast cells lacking Dpb3 and Dpb4, two subunits of the leading strand DNA polymerase, Pol ε, owing to the impairment of parental (H3-H4)2 transfer to leading strands. Dpb3-Dpb4 binds H3-H4 in vitro and participates in the inheritance of heterochromatin. These results indicate that different proteins facilitate the transfer of parental (H3-H4)2 onto leading versus lagging strands and that Dbp3-Dpb4 plays an important role in this poorly understood process.
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Affiliation(s)
- Chuanhe Yu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Haiyun Gan
- Institute for Cancer Genetics, Department of Pediatrics and Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Albert Serra-Cardona
- Institute for Cancer Genetics, Department of Pediatrics and Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Lin Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Songlin Gan
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, SE 90187 Umeå, Sweden
| | - Erik Johansson
- Department of Medical Biochemistry and Biophysics, Umeå University, SE 90187 Umeå, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, SE 90187 Umeå, Sweden
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Department of Pediatrics and Genetics and Development, Columbia University, New York, NY 10032, USA.
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121
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Gan H, Serra-Cardona A, Hua X, Zhou H, Labib K, Yu C, Zhang Z. The Mcm2-Ctf4-Polα Axis Facilitates Parental Histone H3-H4 Transfer to Lagging Strands. Mol Cell 2018; 72:140-151.e3. [PMID: 30244834 DOI: 10.1016/j.molcel.2018.09.001] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 08/27/2018] [Accepted: 08/30/2018] [Indexed: 12/20/2022]
Abstract
Although essential for epigenetic inheritance, the transfer of parental histone (H3-H4)2 tetramers that contain epigenetic modifications to replicating DNA strands is poorly understood. Here, we show that the Mcm2-Ctf4-Polα axis facilitates the transfer of parental (H3-H4)2 tetramers to lagging-strand DNA at replication forks. Mutating the conserved histone-binding domain of the Mcm2 subunit of the CMG (Cdc45-MCM-GINS) DNA helicase, which translocates along the leading-strand template, results in a marked enrichment of parental (H3-H4)2 on leading strand, due to the impairment of the transfer of parental (H3-H4)2 to lagging strands. Similar effects are observed in Ctf4 and Polα primase mutants that disrupt the connection of the CMG helicase to Polα that resides on lagging-strand template. Our results support a model whereby parental (H3-H4)2 complexes displaced from nucleosomes by DNA unwinding at replication forks are transferred by the CMG-Ctf4-Polα complex to lagging-strand DNA for nucleosome assembly at the original location.
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Affiliation(s)
- Haiyun Gan
- Institute for Cancer Genetics, Department of Pediatrics and Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Albert Serra-Cardona
- Institute for Cancer Genetics, Department of Pediatrics and Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Xu Hua
- Institute for Cancer Genetics, Department of Pediatrics and Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Hui Zhou
- Institute for Cancer Genetics, Department of Pediatrics and Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Karim Labib
- MRC Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Chuanhe Yu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA.
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Department of Pediatrics and Genetics and Development, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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122
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Patten DK, Corleone G, Győrffy B, Perone Y, Slaven N, Barozzi I, Erdős E, Saiakhova A, Goddard K, Vingiani A, Shousha S, Pongor LS, Hadjiminas DJ, Schiavon G, Barry P, Palmieri C, Coombes RC, Scacheri P, Pruneri G, Magnani L. Enhancer mapping uncovers phenotypic heterogeneity and evolution in patients with luminal breast cancer. Nat Med 2018; 24:1469-1480. [PMID: 30038216 PMCID: PMC6130800 DOI: 10.1038/s41591-018-0091-x] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 05/14/2018] [Indexed: 12/31/2022]
Abstract
The degree of intrinsic and interpatient phenotypic heterogeneity and its role in tumor evolution is poorly understood. Phenotypic drifts can be transmitted via inheritable transcriptional programs. Cell-type specific transcription is maintained through the activation of epigenetically defined regulatory regions including promoters and enhancers. Here we have annotated the epigenome of 47 primary and metastatic estrogen-receptor (ERα)-positive breast cancer clinical specimens and inferred phenotypic heterogeneity from the regulatory landscape, identifying key regulatory elements commonly shared across patients. Shared regions contain a unique set of regulatory information including the motif for transcription factor YY1. We identify YY1 as a critical determinant of ERα transcriptional activity promoting tumor growth in most luminal patients. YY1 also contributes to the expression of genes mediating resistance to endocrine treatment. Finally, we used H3K27ac levels at active enhancer elements as a surrogate of intra-tumor phenotypic heterogeneity to track the expansion and contraction of phenotypic subpopulations throughout breast cancer progression. By tracking the clonality of SLC9A3R1-positive cells, a bona fide YY1-ERα-regulated gene, we show that endocrine therapies select for phenotypic clones under-represented at diagnosis. Collectively, our data show that epigenetic mechanisms significantly contribute to phenotypic heterogeneity and evolution in systemically treated breast cancer patients.
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Affiliation(s)
- Darren K Patten
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Giacomo Corleone
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Balázs Győrffy
- MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
- Semmelweis University, 2nd Deptartment of Pediatrics, Budapest, Hungary
| | - Ylenia Perone
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Neil Slaven
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Iros Barozzi
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Edina Erdős
- Department of Biochemistry and Molecular Biology, Genomic Medicine and Bioinformatic Core Facility, University of Debrecen, Debrecen, Hungary
| | - Alina Saiakhova
- Department of Genetics and Genome Sciences, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Kate Goddard
- Department of Breast and General Surgery, Charing Cross Hospital, Imperial College Healthcare NHS Trust, London, UK
| | - Andrea Vingiani
- Department of Pathology, European Institute of Oncology, Milan, Italy
| | - Sami Shousha
- Centre for Pathology, Department of Medicine, Imperial College London, London, UK
| | - Lőrinc Sándor Pongor
- MTA TTK Lendület Cancer Biomarker Research Group, Institute of Enzymology, Hungarian Academy of Sciences, Budapest, Hungary
| | - Dimitri J Hadjiminas
- Centre for Pathology, Department of Medicine, Imperial College London, London, UK
| | | | - Peter Barry
- Department of Breast Surgery, The Royal Marsden NHS Foundation Trust, Sutton, UK
| | - Carlo Palmieri
- Institute of Translational Medicine University of Liverpool, Clatterbridge Cancer Centre, NHS Foundation Trust, and Royal Liverpool University Hospital, Liverpool, Merseyside, UK
| | - Raul C Coombes
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK
| | - Peter Scacheri
- Department of Genetics and Genome Sciences, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, USA
| | - Giancarlo Pruneri
- Pathology Department, Fondazione IRCCS Istituto Nazionale Tumori and University of Milan, School of Medicine, Milan, Italy
| | - Luca Magnani
- Department of Surgery and Cancer, The Imperial Centre for Translational and Experimental Medicine, Imperial College London, London, UK.
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123
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Affiliation(s)
- Danny Reinberg
- Howard Hughes Medical Institute, New York University (NYU) School of Medicine, New York, NY, USA. .,Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY, USA.,Chaires Blaise Pascal, Genetics and Development Biology, Institut Curie, Paris, France
| | - Lynne D Vales
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY, USA
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124
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Rechavi O, Lev I. Principles of Transgenerational Small RNA Inheritance in Caenorhabditis elegans. Curr Biol 2018; 27:R720-R730. [PMID: 28743023 DOI: 10.1016/j.cub.2017.05.043] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Examples of transgenerational inheritance of environmental responses are rapidly accumulating. In Caenorhabditis elegans nematodes, such heritable information transmits across generations in the form of RNA-dependent RNA polymerase-amplified small RNAs. Regulatory small RNAs enable sequence-specific gene regulation, and unlike chromatin modifications, can move between tissues, and escape from immediate germline reprogramming. In this review, we discuss the path that small RNAs take from the soma to the germline, and elaborate on the mechanisms that maintain or erase parental small RNA responses after a specific number of generations. We focus on the intricate interactions between heritable small RNAs and histone modifications, deposited on specific loci. A trace of heritable chromatin marks, in particular trimethylation of histone H3 lysine 9, is deposited on RNAi-targeted loci. However, how these modifications regulate RNAi or small RNA inheritance was until recently unclear. Integrating the very latest literature, we suggest that changes to histone marks may instigate transgenerational gene regulation indirectly, by affecting the biogenesis of heritable small RNAs. Inheritance of small RNAs could spread adaptive ancestral responses.
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Affiliation(s)
- Oded Rechavi
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School for Neuroscience, Tel Aviv University, Tel Aviv, Israel 69978.
| | - Itamar Lev
- Department of Neurobiology, Wise Faculty of Life Sciences and Sagol School for Neuroscience, Tel Aviv University, Tel Aviv, Israel 69978.
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125
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Epigenetic inheritance mediated by coupling of RNAi and histone H3K9 methylation. Nature 2018; 558:615-619. [PMID: 29925950 PMCID: PMC6312107 DOI: 10.1038/s41586-018-0239-3] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 04/30/2018] [Indexed: 02/06/2023]
Abstract
Histone posttranslational modifications (PTMs) are associated with epigenetic states that form the basis for cell type specific gene expression1,2. Once established, histone PTMs can be maintained by positive feedback involving enzymes that recognize and catalyze the same modification on newly deposited histones. Recent studies suggest that in wild-type cells, histone PTM-based positive feedback is too weak to mediate epigenetic inheritance in the absence of other inputs3–7. RNAi-mediated histone H3 lysine 9 methylation (H3K9me) and heterochromatin formation define a potential epigenetic inheritance mechanism in which positive feedback involving small interfering RNA (siRNA) amplification can be directly coupled to histone PTM positive feedback8–14. However, it remains unknown whether such a coupling of two feedback loops can maintain epigenetic silencing independently of DNA sequence and in the absence of enabling mutations that disrupt genome-wide chromatin structure or transcription15–17. Here using fission yeast S. pombe, we show that siRNA-induced H3K9me and silencing of a euchromatic gene can be epigenetically inherited in cis during multiple mitotic and meiotic cell divisions in wild-type cells. This inheritance involves the spreading of secondary siRNAs and H3K9me3 to the targeted gene and surrounding areas and requires both RNAi and H3K9me, suggesting that siRNA and H3K9me positive feedback loops act synergistically to maintain silencing. In contrast, when maintained solely by histone PTM positive feedback, silencing is erased by H3K9 demethylation promoted by Epe1, or by interallelic interactions following mating to cells containing an expressed epiallele even in the absence of Epe1. These findings demonstrate that the RNAi machinery can mediate transgenerational epigenetic inheritance independently of DNA sequence or enabling mutations and reveal a role for the coupling of siRNA and H3K9me positive feedback loops in protection of epigenetic alleles from erasure.
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126
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The chromatin basis of neurodevelopmental disorders: Rethinking dysfunction along the molecular and temporal axes. Prog Neuropsychopharmacol Biol Psychiatry 2018; 84:306-327. [PMID: 29309830 DOI: 10.1016/j.pnpbp.2017.12.013] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 12/19/2017] [Accepted: 12/24/2017] [Indexed: 12/13/2022]
Abstract
The complexity of the human brain emerges from a long and finely tuned developmental process orchestrated by the crosstalk between genome and environment. Vis à vis other species, the human brain displays unique functional and morphological features that result from this extensive developmental process that is, unsurprisingly, highly vulnerable to both genetically and environmentally induced alterations. One of the most striking outcomes of the recent surge of sequencing-based studies on neurodevelopmental disorders (NDDs) is the emergence of chromatin regulation as one of the two domains most affected by causative mutations or Copy Number Variations besides synaptic function, whose involvement had been largely predicted for obvious reasons. These observations place chromatin dysfunction at the top of the molecular pathways hierarchy that ushers in a sizeable proportion of NDDs and that manifest themselves through synaptic dysfunction and recurrent systemic clinical manifestation. Here we undertake a conceptual investigation of chromatin dysfunction in NDDs with the aim of systematizing the available evidence in a new framework: first, we tease out the developmental vulnerabilities in human corticogenesis as a structuring entry point into the causation of NDDs; second, we provide a much needed clarification of the multiple meanings and explanatory frameworks revolving around "epigenetics", highlighting those that are most relevant for the analysis of these disorders; finally we go in-depth into paradigmatic examples of NDD-causing chromatin dysregulation, with a special focus on human experimental models and datasets.
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Zhang Y, Zhang X, Shi J, Tuorto F, Li X, Liu Y, Liebers R, Zhang L, Qu Y, Qian J, Pahima M, Liu Y, Yan M, Cao Z, Lei X, Cao Y, Peng H, Liu S, Wang Y, Zheng H, Woolsey R, Quilici D, Zhai Q, Li L, Zhou T, Yan W, Lyko F, Zhang Y, Zhou Q, Duan E, Chen Q. Dnmt2 mediates intergenerational transmission of paternally acquired metabolic disorders through sperm small non-coding RNAs. Nat Cell Biol 2018; 20:535-540. [PMID: 29695786 PMCID: PMC5926820 DOI: 10.1038/s41556-018-0087-2] [Citation(s) in RCA: 265] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 03/19/2018] [Indexed: 12/29/2022]
Abstract
The discovery of RNAs (for example, messenger RNAs, non-coding RNAs) in sperm has opened the possibility that sperm may function by delivering additional paternal information aside from solely providing the DNA 1 . Increasing evidence now suggests that sperm small non-coding RNAs (sncRNAs) can mediate intergenerational transmission of paternally acquired phenotypes, including mental stress2,3 and metabolic disorders4-6. How sperm sncRNAs encode paternal information remains unclear, but the mechanism may involve RNA modifications. Here we show that deletion of a mouse tRNA methyltransferase, DNMT2, abolished sperm sncRNA-mediated transmission of high-fat-diet-induced metabolic disorders to offspring. Dnmt2 deletion prevented the elevation of RNA modifications (m5C, m2G) in sperm 30-40 nt RNA fractions that are induced by a high-fat diet. Also, Dnmt2 deletion altered the sperm small RNA expression profile, including levels of tRNA-derived small RNAs and rRNA-derived small RNAs, which might be essential in composing a sperm RNA 'coding signature' that is needed for paternal epigenetic memory. Finally, we show that Dnmt2-mediated m5C contributes to the secondary structure and biological properties of sncRNAs, implicating sperm RNA modifications as an additional layer of paternal hereditary information.
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Affiliation(s)
- Yunfang Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
- University of Chinese Academy of Sciences, Beijing, China
| | - Xudong Zhang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Junchao Shi
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Francesca Tuorto
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Xin Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yusheng Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Reinhard Liebers
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Liwen Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yongcun Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jingjing Qian
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Maya Pahima
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Ying Liu
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Menghong Yan
- Key Laboratory of Nutrition and Metabolism, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Zhonghong Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, Shandong University of Technology, Zibo, China
| | - Xiaohua Lei
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yujing Cao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Hongying Peng
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Shichao Liu
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Yue Wang
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Huili Zheng
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Rebekah Woolsey
- Nevada Proteomics Center, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - David Quilici
- Nevada Proteomics Center, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Qiwei Zhai
- Key Laboratory of Nutrition and Metabolism, Chinese Academy of Sciences Center for Excellence in Molecular Cell Science, Institute for Nutritional Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Lei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Wei Yan
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Enkui Duan
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.
| | - Qi Chen
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, NV, USA.
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128
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Rimel JK, Taatjes DJ. The essential and multifunctional TFIIH complex. Protein Sci 2018; 27:1018-1037. [PMID: 29664212 PMCID: PMC5980561 DOI: 10.1002/pro.3424] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 04/04/2018] [Accepted: 04/05/2018] [Indexed: 12/19/2022]
Abstract
TFIIH is a 10‐subunit complex that regulates RNA polymerase II (pol II) transcription but also serves other important biological roles. Although much remains unknown about TFIIH function in eukaryotic cells, much progress has been made even in just the past few years, due in part to technological advances (e.g. cryoEM and single molecule methods) and the development of chemical inhibitors of TFIIH enzymes. This review focuses on the major cellular roles for TFIIH, with an emphasis on TFIIH function as a regulator of pol II transcription. We describe the structure of TFIIH and its roles in pol II initiation, promoter‐proximal pausing, elongation, and termination. We also discuss cellular roles for TFIIH beyond transcription (e.g. DNA repair, cell cycle regulation) and summarize small molecule inhibitors of TFIIH and diseases associated with defects in TFIIH structure and function.
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Affiliation(s)
- Jenna K Rimel
- Department of Chemistry & Biochemistry, University of Colorado, Boulder, Colorado, 80303
| | - Dylan J Taatjes
- Department of Chemistry & Biochemistry, University of Colorado, Boulder, Colorado, 80303
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129
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Zhang Y, Zhang X, Shi J, Tuorto F, Li X, Liu Y, Liebers R, Zhang L, Qu Y, Qian J, Pahima M, Liu Y, Yan M, Cao Z, Lei X, Cao Y, Peng H, Liu S, Wang Y, Zheng H, Woolsey R, Quilici D, Zhai Q, Li L, Zhou T, Yan W, Lyko F, Zhang Y, Zhou Q, Duan E, Chen Q. Dnmt2 mediates intergenerational transmission of paternally acquired metabolic disorders through sperm small non-coding RNAs. Nat Cell Biol 2018. [DOI: doi.org/10.1038/s41556-018-0087-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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130
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Zhu J, Ordway AJ, Weber L, Buddika K, Kumar JP. Polycomb group (PcG) proteins and Pax6 cooperate to inhibit in vivo reprogramming of the developing Drosophila eye. Development 2018; 145:dev160754. [PMID: 29530880 PMCID: PMC5963869 DOI: 10.1242/dev.160754] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 03/01/2018] [Indexed: 01/01/2023]
Abstract
How different cells and tissues commit to and determine their fates has been a central question in developmental biology since the seminal embryological experiments conducted by Wilhelm Roux and Hans Driesch in sea urchins and frogs. Here, we demonstrate that Polycomb group (PcG) proteins maintain Drosophila eye specification by suppressing the activation of alternative fate choices. The loss of PcG in the developing eye results in a cellular reprogramming event in which the eye is redirected to a wing fate. This fate transformation occurs with either the individual loss of Polycomb proteins or the simultaneous reduction of the Pleiohomeotic repressive complex and Pax6. Interestingly, the requirement for retinal selector genes is limited to Pax6, as the removal of more downstream members does not lead to the eye-wing transformation. We also show that distinct PcG complexes are required during different developmental windows throughout eye formation. These findings build on earlier observations that the eye can be reprogrammed to initiate head epidermis, antennal and leg development.
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Affiliation(s)
- Jinjin Zhu
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Alison J Ordway
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Lena Weber
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Kasun Buddika
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Justin P Kumar
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
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131
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Abstract
Heterochromatin is a key architectural feature of eukaryotic chromosomes, which endows particular genomic domains with specific functional properties. The capacity of heterochromatin to restrain the activity of mobile elements, isolate DNA repair in repetitive regions and ensure accurate chromosome segregation is crucial for maintaining genomic stability. Nucleosomes at heterochromatin regions display histone post-translational modifications that contribute to developmental regulation by restricting lineage-specific gene expression. The mechanisms of heterochromatin establishment and of heterochromatin maintenance are separable and involve the ability of sequence-specific factors bound to nascent transcripts to recruit chromatin-modifying enzymes. Heterochromatin can spread along the chromatin from nucleation sites. The propensity of heterochromatin to promote its own spreading and inheritance is counteracted by inhibitory factors. Because of its importance for chromosome function, heterochromatin has key roles in the pathogenesis of various human diseases. In this Review, we discuss conserved principles of heterochromatin formation and function using selected examples from studies of a range of eukaryotes, from yeast to human, with an emphasis on insights obtained from unicellular model organisms.
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132
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Wang C, Zhu B, Xiong J. Recruitment and reinforcement: maintaining epigenetic silencing. SCIENCE CHINA-LIFE SCIENCES 2018; 61:515-522. [PMID: 29564598 DOI: 10.1007/s11427-018-9276-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 01/16/2018] [Indexed: 01/07/2023]
Abstract
Cells need to appropriately balance transcriptional stability and adaptability in order to maintain their identities while responding robustly to various stimuli. Eukaryotic cells use an elegant "epigenetic" system to achieve this functionality. "Epigenetics" is referred to as heritable information beyond the DNA sequence, including histone and DNA modifications, ncRNAs and other chromatin-related components. Here, we review the mechanisms of the epigenetic inheritance of a repressive chromatin state, with an emphasis on recent progress in the field. We emphasize that (i) epigenetic information is inherited in a relatively stable but imprecise fashion; (ii) multiple cis and trans factors are involved in the maintenance of epigenetic information during mitosis; and (iii) the maintenance of a repressive epigenetic state requires both recruitment and self-reinforcement mechanisms. These mechanisms crosstalk with each other and form interconnected feedback loops to shape a stable epigenetic system while maintaining certain degrees of flexibility.
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Affiliation(s)
- Chengzhi Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Xiong
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
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133
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Højfeldt JW, Laugesen A, Willumsen BM, Damhofer H, Hedehus L, Tvardovskiy A, Mohammad F, Jensen ON, Helin K. Accurate H3K27 methylation can be established de novo by SUZ12-directed PRC2. Nat Struct Mol Biol 2018; 25:225-232. [PMID: 29483650 PMCID: PMC5842896 DOI: 10.1038/s41594-018-0036-6] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 01/18/2018] [Indexed: 01/07/2023]
Abstract
Polycomb repressive complex 2 (PRC2) catalyzes methylation on lysine 27 of histone H3 (H3K27) and is required for maintaining transcriptional patterns and cellular identity, but the specification and maintenance of genomic PRC2 binding and H3K27 methylation patterns remain incompletely understood. Epigenetic mechanisms have been proposed, wherein pre-existing H3K27 methylation directs recruitment and regulates the catalytic activity of PRC2 to support its own maintenance. Here we investigate whether such mechanisms are required for specifying H3K27 methylation patterns in mouse embryonic stem cells (mESCs). Through re-expression of PRC2 subunits in PRC2-knockout cells that have lost all H3K27 methylation, we demonstrate that methylation patterns can be accurately established de novo. We find that regional methylation kinetics correlate with original methylation patterns even in their absence, and specification of the genomic PRC2 binding pattern is retained and specifically dependent on the PRC2 core subunit SUZ12. Thus, the H3K27 methylation patterns in mESCs are not dependent on self-autonomous epigenetic inheritance.
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Affiliation(s)
- Jonas W Højfeldt
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anne Laugesen
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Berthe M Willumsen
- Cell Biology and Physiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Helene Damhofer
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lin Hedehus
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrey Tvardovskiy
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
- Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Faizaan Mohammad
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
- The Novo Nordisk Foundation Center for Stem Cell Biology (DanStem), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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134
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Khan S, Iqbal M, Tariq M, Baig SM, Abbas W. Epigenetic regulation of HIV-1 latency: focus on polycomb group (PcG) proteins. Clin Epigenetics 2018; 10:14. [PMID: 29441145 PMCID: PMC5800276 DOI: 10.1186/s13148-018-0441-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/05/2018] [Indexed: 01/10/2023] Open
Abstract
HIV-1 latency allows the virus to persist until reactivation, in a transcriptionally silent form in its cellular reservoirs despite the presence of effective cART. Such viral persistence represents a major barrier to HIV eradication since treatment interruption leads to rebound plasma viremia. Polycomb group (PcG) proteins have recently got a considerable attention in regulating HIV-1 post-integration latency as they are involved in the repression of proviral gene expression through the methylation of histones. This epigenetic regulation plays an important role in the establishment and maintenance of HIV-1 latency. In fact, PcG proteins act in complexes and modulate the epigenetic signatures of integrated HIV-1 promoter. Key role played by PcG proteins in the molecular control of HIV-1 latency has led to hypothesize that PcG proteins may represent a valuable target for future HIV-1 therapy in purging HIV-1 reservoirs. In this regard, various small molecules have been synthesized or explored to specifically block the epigenetic activity of PcG. In this review, we will highlight the possible therapeutic approaches to achieve either a functional or sterilizing cure of HIV-1 infection with special focus on histone methylation by PcG proteins together with current and novel pharmacological approaches to reactivate HIV-1 from latency that could ultimately lead towards a better clearance of viral latent reservoirs.
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Affiliation(s)
- Sheraz Khan
- Health Biotechnology Division (HBD), National Institute for Biotechnology and Genetic Engineering (NIBGE), PO Box 577, Jhang road, Faisalabad, 38000 Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Mazhar Iqbal
- Health Biotechnology Division (HBD), National Institute for Biotechnology and Genetic Engineering (NIBGE), PO Box 577, Jhang road, Faisalabad, 38000 Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Muhammad Tariq
- Department of Biology (Epigenetics group), SBA School of Science and Engineering, LUMS, Lahore, 54792 Pakistan
| | - Shahid M. Baig
- Health Biotechnology Division (HBD), National Institute for Biotechnology and Genetic Engineering (NIBGE), PO Box 577, Jhang road, Faisalabad, 38000 Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
| | - Wasim Abbas
- Health Biotechnology Division (HBD), National Institute for Biotechnology and Genetic Engineering (NIBGE), PO Box 577, Jhang road, Faisalabad, 38000 Pakistan
- Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan
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135
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Michieletto D, Chiang M, Colì D, Papantonis A, Orlandini E, Cook PR, Marenduzzo D. Shaping epigenetic memory via genomic bookmarking. Nucleic Acids Res 2018; 46:83-93. [PMID: 29190361 PMCID: PMC5758908 DOI: 10.1093/nar/gkx1200] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/06/2017] [Accepted: 11/19/2017] [Indexed: 12/18/2022] Open
Abstract
Reconciling the stability of epigenetic patterns with the rapid turnover of histone modifications and their adaptability to external stimuli is an outstanding challenge. Here, we propose a new biophysical mechanism that can establish and maintain robust yet plastic epigenetic domains via genomic bookmarking (GBM). We model chromatin as a recolourable polymer whose segments bear non-permanent histone marks (or colours) which can be modified by 'writer' proteins. The three-dimensional chromatin organisation is mediated by protein bridges, or 'readers', such as Polycomb Repressive Complexes and Transcription Factors. The coupling between readers and writers drives spreading of biochemical marks and sustains the memory of local chromatin states across replication and mitosis. In contrast, GBM-targeted perturbations destabilise the epigenetic patterns. Strikingly, we demonstrate that GBM alone can explain the full distribution of Polycomb marks in a whole Drosophila chromosome. We finally suggest that our model provides a starting point for an understanding of the biophysics of cellular differentiation and reprogramming.
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Affiliation(s)
- Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Michael Chiang
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
| | - Davide Colì
- Dipartimento di Fisica e Astronomia and Sezione INFN, Università di Padova, Via Marzolo 8, Padova 35131, Italy
| | - Argyris Papantonis
- Centre for Molecular Medicine, University of Cologne, Robert-Koch-Str. 21, D-50931, Cologne, DE, Germany
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia and Sezione INFN, Università di Padova, Via Marzolo 8, Padova 35131, Italy
| | - Peter R Cook
- The Sir William Dunn School of Pathology, South Parks Road, Oxford OX1 3RE, UK
| | - Davide Marenduzzo
- School of Physics and Astronomy, University of Edinburgh, Peter Guthrie Tait Road, Edinburgh EH9 3FD, UK
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136
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Histone Demethylase Activity of Utx Is Essential for Viability and Regulation of HOX Gene Expression in Drosophila. Genetics 2017; 208:633-637. [PMID: 29247011 PMCID: PMC5788527 DOI: 10.1534/genetics.117.300421] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/12/2017] [Indexed: 12/12/2022] Open
Abstract
The trimethylation of histone H3 at lysine 27 (H3K27me3) by Polycomb Repressive Complex 2 (PRC2) is essential for the repression of Polycomb target genes. However, the role of enzymatic demethylation of H3K27me3 by the KDM6-family demethylases Utx, Uty, and JmjD3 is less clear. Studies in both mice and worms led to the proposal that KDM6 proteins, but not their H3K27me3 demethylase activity, is critical for normal development. Here, we investigated the requirement of the demethylase activity of the single KDM6 family member Utx in Drosophila. We generated Drosophila expressing a full-length but catalytically inactive Utx protein and found that these mutants show the same phenotypes as animals lacking the Utx protein. Specifically, animals lacking maternally deposited active Utx demethylase in the early embryo show stochastic loss of HOX gene expression that appears to be propagated in a clonal fashion. This suggests that Utx demethylase activity is critical for the removal of ectopic H3K27 trimethylation from active HOX genes during the onset of zygotic gene transcription, and thereby prevents the inappropriate installment of long-term repression by Polycomb. Conversely, maternally deposited catalytically active Utx protein suffices to permit animals that lack zygotic expression of enzymatically active Utx to develop into morphologically normal adults, which eclose from the pupal case but die shortly thereafter. Utx demethylase activity is therefore also essential to sustain viability in adult flies. Together, these analyses identify the earliest embryonic stages and the adult stage as two phases during the Drosophila life cycle that critically require H3K27me3 demethylase activity.
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137
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Pereira A, Paro R. Pho dynamically interacts with Spt5 to facilitate transcriptional switches at the hsp70 locus. Epigenetics Chromatin 2017; 10:57. [PMID: 29208012 PMCID: PMC5718073 DOI: 10.1186/s13072-017-0166-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/29/2017] [Indexed: 11/10/2022] Open
Abstract
Background Numerous target genes of the Polycomb group (PcG) are transiently activated by a stimulus and subsequently repressed. However, mechanisms by which PcG proteins regulate such target genes remain elusive. Results We employed the heat shock-responsive hsp70 locus in Drosophila to study the chromatin dynamics of PRC1 and its interplay with known regulators of the locus before, during and after heat shock. We detected mutually exclusive binding patterns for HSF and PRC1 at the hsp70 locus. We found that Pleiohomeotic (Pho), a DNA-binding PcG member, dynamically interacts with Spt5, an elongation factor. The dynamic interaction switch between Pho and Spt5 is triggered by the recruitment of HSF to chromatin. Mutation in the protein–protein interaction domain (REPO domain) of Pho interferes with the dynamics of its interaction with Spt5. The transcriptional kinetics of the heat shock response is negatively affected by a mutation in the REPO domain of Pho. Conclusions We propose that a dynamic interaction switch between PcG proteins and an elongation factor enables stress-inducible genes to efficiently switch between ON/OFF states in the presence/absence of the activating stimulus. Electronic supplementary material The online version of this article (10.1186/s13072-017-0166-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Allwyn Pereira
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland
| | - Renato Paro
- Department of Biosystems Science and Engineering, ETH Zurich, 4058, Basel, Switzerland. .,Faculty of Sciences, University of Basel, 4056, Basel, Switzerland.
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138
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Velanis CN, Goodrich J. Vernalization and Epigenetic Inheritance: A Game of Histones. Curr Biol 2017; 27:R1324-R1326. [DOI: 10.1016/j.cub.2017.10.048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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139
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Abstract
Collinear regulation of Hox genes in space and time has been an outstanding question ever since the initial work of Ed Lewis in 1978. Here we discuss recent advances in our understanding of this phenomenon in relation to novel concepts associated with large-scale regulation and chromatin structure during the development of both axial and limb patterns. We further discuss how this sequential transcriptional activation marks embryonic stem cell-like axial progenitors in mammals and, consequently, how a temporal genetic system is further translated into spatial coordinates via the fate of these progenitors. In this context, we argue the benefit and necessity of implementing this unique mechanism as well as the difficulty in evolving an alternative strategy to deliver this critical positional information.
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Affiliation(s)
- Jacqueline Deschamps
- Hubrecht Institute, University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Denis Duboule
- School of Life Sciences, Ecole Polytechnique Fédérale, Lausanne, 1015 Lausanne, Switzerland.,Department of Genetics and Evolution, University of Geneva, 1211 Geneva 4, Switzerland
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140
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Utf1 contributes to intergenerational epigenetic inheritance of pluripotency. Sci Rep 2017; 7:14612. [PMID: 29097685 PMCID: PMC5668265 DOI: 10.1038/s41598-017-14426-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 10/10/2017] [Indexed: 12/27/2022] Open
Abstract
Undifferentiated embryonic cell transcription factor 1 (Utf1) is expressed in pluripotent embryonic stem cells (ESCs) and primordial germ cells (PGCs). Utf1 expression is directly controlled by pluripotency factors Oct4 and Sox2, which form a ternary complex with the Utf1 enhancer. The Utf1 protein plays a role in chromatin organization and epigenetic control of bivalent gene expression in ESCs in vitro, where it promotes effective cell differentiation during exit from pluripotency. The function of Utf1 in PGCs in vivo, however, is not known. Here, we report that proper development of Utf1 null embryos almost entirely depends on the presence of functional Utf1 alleles in the parental germline. This indicates that Utf1’s proposed epigenetic role in ESC pluripotency in vitro may be linked to intergenerational epigenetic inheritance in vivo. One component - or at least facilitator - of the relevant epigenetic mark appears to be Utf1 itself, since Utf1-driven tomato reporter and Utf1 are detected in mature germ cells. We also provide initial evidence for a reduced adult testis size in Utf1 null mice. Our findings thus point at unexpected functional links between the core ESC pluripotency factor network and epigenetic inheritance of pluripotency.
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141
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Reid MA, Dai Z, Locasale JW. The impact of cellular metabolism on chromatin dynamics and epigenetics. Nat Cell Biol 2017; 19:1298-1306. [PMID: 29058720 PMCID: PMC5886854 DOI: 10.1038/ncb3629] [Citation(s) in RCA: 332] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/15/2017] [Indexed: 12/12/2022]
Abstract
The substrates used to modify nucleic acids and chromatin are affected by nutrient availability and the activity of metabolic pathways. Thus, cellular metabolism constitutes a fundamental component of chromatin status and thereby of genome regulation. Here we describe the biochemical and genetic principles of how metabolism can influence chromatin biology and epigenetics, discuss the functional roles of this interplay in developmental and cancer biology, and present future directions in this rapidly emerging area.
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Affiliation(s)
- Michael A. Reid
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, 27710, USA
| | - Ziwei Dai
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, 27710, USA
| | - Jason W. Locasale
- Department of Pharmacology and Cancer Biology, Duke Cancer Institute, Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, North Carolina, 27710, USA
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142
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Abstract
This Perspective discusses a recent study by Erceg et al. (2017) regarding regulated gene silencing by Polycomb group (PcG) proteins. It focuses on characterizing Polycomb response elements (PREs) and their dual functions in Drosophila. Development requires the expression of master regulatory genes necessary to specify a cell lineage. Equally significant is the stable and heritable silencing of master regulators that would specify alternative lineages. This regulated gene silencing is carried out by Polycomb group (PcG) proteins, which must be correctly recruited only to the subset of their target loci that requires lineage-specific silencing. A recent study by Erceg and colleagues (pp. 590–602) expands on a key aspect of that targeting: The same DNA elements that recruit PcG complexes to a repressed locus also encode transcriptional enhancers that function in different lineages where that locus must be expressed. Thus, PcG targeting elements overlap with enhancers.
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Affiliation(s)
- Elizabeth S Jaensch
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA
| | - Sharmistha Kundu
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA
| | - Robert E Kingston
- Department of Molecular Biology, Massachusetts General Hospital, Boston, Massachusetts, 02114, USA
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143
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Erdel F. How Communication Between Nucleosomes Enables Spreading and Epigenetic Memory of Histone Modifications. Bioessays 2017; 39. [PMID: 29034500 DOI: 10.1002/bies.201700053] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 09/04/2017] [Indexed: 11/08/2022]
Abstract
Nucleosomes "talk" to each other about their modification state to form extended domains of modified histones independently of the underlying DNA sequence. At the same time, DNA elements promote modification of nucleosomes in their vicinity. How do these site-specific and histone-based activities act together to regulate spreading of histone modifications along the genome? How do they enable epigenetic memory to preserve cell identity? Many models for the dynamics of repressive histone modifications emphasize the role of strong positive feedback loops, which reinforce histone modifications by recruiting histone modifiers to preexisting modifications. Recent experiments question that repressive histone modifications are self-sustained independently of their genomic context, thereby indicating that histone-based feedback is relatively weak. In the present review, current models for the dynamics of histone modifications are compared and it is suggested that limitation of histone-based feedback is key to intrinsic confinement of spreading and coexistence of short- and long-term memory at different genomic loci. See also the video abstract here: https://youtu.be/3bxr_xDEZfQ.
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Affiliation(s)
- Fabian Erdel
- Division of Chromatin Networks, German Cancer Research Center (DKFZ) and BioQuant, Im Neuenheimer Feld 280, Heidelberg, 69120, Germany
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144
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Jiang D, Berger F. DNA replication-coupled histone modification maintains Polycomb gene silencing in plants. Science 2017; 357:1146-1149. [PMID: 28818970 DOI: 10.1126/science.aan4965] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/09/2017] [Indexed: 01/01/2023]
Abstract
Propagation of patterns of gene expression through the cell cycle requires prompt restoration of epigenetic marks after the twofold dilution caused by DNA replication. Here we show that the transcriptional repressive mark H3K27me3 (histone H3 lysine 27 trimethylation) is restored in replicating plant cells through DNA replication-coupled modification of histone variant H3.1. Plants evolved a mechanism for efficient K27 trimethylation on H3.1, which is essential for inheritance of the silencing memory from mother to daughter cells. We illustrate how this mechanism establishes H3K27me3-mediated silencing during the developmental transition to flowering. Our study reveals a mechanism responsible for transmission of H3K27me3 in plant cells through cell divisions, enabling H3K27me3 to function as an epigenetic mark.
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Affiliation(s)
- Danhua Jiang
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
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145
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Abstract
Polycomb Group (PcG) proteins epigenetically repress key developmental genes and thereby control alternative cell fates. PcG proteins act as complexes that can modify histones and these histone modifications play a role in transmitting the “memory” of the repressed state as cells divide. Here we consider mainstream models that link histone modifications to hierarchical recruitment of PcG complexes and compare them to results of a direct test of interdependence between PcG complexes for recruitment to Drosophila genes. The direct test indicates that PcG complexes do not rely on histone modifications to recognize their target genes but use them to stabilize the interactions within large chromatin domains. It also shows that multiple strategies are used to coordinate the targeting of PcG complexes to different genes, which may make the repression of these genes more or less robust.
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Affiliation(s)
- Eshagh Dorafshan
- a Department of Molecular Biology , Umeå University , Umeå , Sweden
| | - Tatyana G Kahn
- a Department of Molecular Biology , Umeå University , Umeå , Sweden
| | - Yuri B Schwartz
- a Department of Molecular Biology , Umeå University , Umeå , Sweden
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146
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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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147
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Acharya S, Hartmann M, Erhardt S. Chromatin-associated noncoding RNAs in development and inheritance. WILEY INTERDISCIPLINARY REVIEWS-RNA 2017; 8. [PMID: 28840663 DOI: 10.1002/wrna.1435] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Revised: 06/30/2017] [Accepted: 07/03/2017] [Indexed: 12/13/2022]
Abstract
Noncoding RNAs (ncRNAs) have emerged as crucial players in chromatin regulation. Their diversity allows them to partake in the regulation of numerous cellular processes across species. During development, long and short ncRNAs act in conjunction with each other where long ncRNAs (lncRNAs) are best understood in establishing appropriate gene expression patterns, while short ncRNAs (sRNAs) are known to establish constitutive heterochromatin and suppress mobile elements. Additionally, increasing evidence demonstrates roles of sRNAs in several typically lncRNA-mediated processes such as dosage compensation, indicating a complex regulatory network of noncoding RNAs. Together, various ncRNAs establish many mitotically heritable epigenetic marks during development. Additionally, they participate in mechanisms that regulate maintenance of these epigenetic marks during the lifespan of the organism. Interestingly, some epigenetic traits are transmitted to the next generation(s) via paramutations or transgenerational inheritance mediated by sRNAs. In this review, we give an overview of the various functions and regulations of ncRNAs and the mechanisms they employ in the establishment and maintenance of epigenetic marks and multi-generational transmission of epigenetic traits. WIREs RNA 2017, 8:e1435. doi: 10.1002/wrna.1435 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Sreemukta Acharya
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, and CellNetworks, Im Neuenheimer Feld 282, Heidelberg, Germany
| | - Mark Hartmann
- Regulation of Cellular Differentiation Group, Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Sylvia Erhardt
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, and CellNetworks, Im Neuenheimer Feld 282, Heidelberg, Germany
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148
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Kassis JA, Kennison JA, Tamkun JW. Polycomb and Trithorax Group Genes in Drosophila. Genetics 2017; 206:1699-1725. [PMID: 28778878 PMCID: PMC5560782 DOI: 10.1534/genetics.115.185116] [Citation(s) in RCA: 142] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Accepted: 05/15/2017] [Indexed: 01/08/2023] Open
Abstract
Polycomb group (PcG) and Trithorax group (TrxG) genes encode important regulators of development and differentiation in metazoans. These two groups of genes were discovered in Drosophila by their opposing effects on homeotic gene (Hox) expression. PcG genes collectively behave as genetic repressors of Hox genes, while the TrxG genes are necessary for HOX gene expression or function. Biochemical studies showed that many PcG proteins are present in two protein complexes, Polycomb repressive complexes 1 and 2, which repress transcription via chromatin modifications. TrxG proteins activate transcription via a variety of mechanisms. Here we summarize the large body of genetic and biochemical experiments in Drosophila on these two important groups of genes.
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Affiliation(s)
- Judith A Kassis
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - James A Kennison
- Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892
| | - John W Tamkun
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, California 95064
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149
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Johnson WL, Straight AF. RNA-mediated regulation of heterochromatin. Curr Opin Cell Biol 2017; 46:102-109. [PMID: 28614747 PMCID: PMC5729926 DOI: 10.1016/j.ceb.2017.05.004] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 05/16/2017] [Accepted: 05/22/2017] [Indexed: 02/09/2023]
Abstract
The formation of condensed, transcriptionally repressed heterochromatin is essential for controlling gene expression throughout development, silencing parasitic DNA elements, and for genome stability and inheritance. Cells employ diverse mechanisms for controlling heterochromatin states through proteins that modify DNA and histones. An emerging theme is that chromatin-associated RNAs play important roles in regulating heterochromatin proteins by controlling their initial recruitment to chromatin, their stable association with chromatin, their spread along chromatin, or their enzymatic activity. Major challenges for the field include not only identifying regulatory RNAs, but understanding the underlying biochemical mechanisms for how RNAs associate with chromatin, the specificity of interactions between heterochromatin proteins and RNA, and how these binding events manifest in cells to orchestrate RNA-mediated regulation of heterochromatin.
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Affiliation(s)
- Whitney L Johnson
- Department of Biochemistry, Stanford University Medical School, Stanford, CA 94305, United States
| | - Aaron F Straight
- Department of Biochemistry, Stanford University Medical School, Stanford, CA 94305, United States.
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150
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Abstract
New work reports that both derepressed and hyper-repressed chromatin states in animals can be transmitted to progeny for many generations. Transmission depends on genomic architecture and histone modifications.
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Affiliation(s)
- Vincenzo Pirrotta
- Molecular Biology and Biochemistry, Rutgers University, Piscataway, New Jersey, USA
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