1
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Russ BE, Barugahare A, Dakle P, Tsyganov K, Quon S, Yu B, Li J, Lee JKC, Olshansky M, He Z, Harrison PF, See M, Nussing S, Morey AE, Udupa VA, Bennett TJ, Kallies A, Murre C, Collas P, Powell D, Goldrath AW, Turner SJ. Active maintenance of CD8 + T cell naivety through regulation of global genome architecture. Cell Rep 2023; 42:113301. [PMID: 37858463 PMCID: PMC10679840 DOI: 10.1016/j.celrep.2023.113301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/07/2023] [Accepted: 10/03/2023] [Indexed: 10/21/2023] Open
Abstract
The differentiation of naive CD8+ T lymphocytes into cytotoxic effector and memory CTL results in large-scale changes in transcriptional and phenotypic profiles. Little is known about how large-scale changes in genome organization underpin these transcriptional programs. We use Hi-C to map changes in the spatial organization of long-range genome contacts within naive, effector, and memory virus-specific CD8+ T cells. We observe that the architecture of the naive CD8+ T cell genome is distinct from effector and memory genome configurations, with extensive changes within discrete functional chromatin domains associated with effector/memory differentiation. Deletion of BACH2, or to a lesser extent, reducing SATB1 DNA binding, within naive CD8+ T cells results in a chromatin architecture more reminiscent of effector/memory states. This suggests that key transcription factors within naive CD8+ T cells act to restrain T cell differentiation by actively enforcing a unique naive chromatin state.
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Affiliation(s)
- Brendan E Russ
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia.
| | - Adele Barugahare
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia; Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Pushkar Dakle
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Kirril Tsyganov
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia; Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Sara Quon
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Bingfei Yu
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Jasmine Li
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia; Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Jason K C Lee
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Moshe Olshansky
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Zhaohren He
- Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Paul F Harrison
- Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Michael See
- Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Simone Nussing
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Alison E Morey
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Vibha A Udupa
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Taylah J Bennett
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Axel Kallies
- Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Cornelis Murre
- Department of Molecular Biology, University of California, San Diego, San Diego, CA, USA
| | - Phillipe Collas
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway; Department of Immunology and Transfusion Medicine, Oslo University Hospital, Oslo, Norway
| | - David Powell
- Bioinformatics Platform, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Ananda W Goldrath
- Department of Biological Sciences, University of California, San Diego, San Diego, CA, USA
| | - Stephen J Turner
- Department of Microbiology, Immunity Theme, Biomedical Discovery Institute, Monash University, Clayton, VIC, Australia.
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2
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Pandupuspitasari NS, Khan FA, Huang C, Ali A, Yousaf MR, Shakeel F, Putri EM, Negara W, Muktiani A, Prasetiyono BWHE, Kustiawan L, Wahyuni DS. Recent advances in chromosome capture techniques unraveling 3D genome architecture in germ cells, health, and disease. Funct Integr Genomics 2023; 23:214. [PMID: 37386239 DOI: 10.1007/s10142-023-01146-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023]
Abstract
In eukaryotes, the genome does not emerge in a specific shape but rather as a hierarchial bundle within the nucleus. This multifaceted genome organization consists of multiresolution cellular structures, such as chromosome territories, compartments, and topologically associating domains, which are frequently defined by architecture, design proteins including CTCF and cohesin, and chromatin loops. This review briefly discusses the advances in understanding the basic rules of control, chromatin folding, and functional areas in early embryogenesis. With the use of chromosome capture techniques, the latest advancements in technologies for visualizing chromatin interactions come close to revealing 3D genome formation frameworks with incredible detail throughout all genomic levels, including at single-cell resolution. The possibility of detecting variations in chromatin architecture might open up new opportunities for disease diagnosis and prevention, infertility treatments, therapeutic approaches, desired exploration, and many other application scenarios.
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Affiliation(s)
- Nuruliarizki Shinta Pandupuspitasari
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia.
| | - Faheem Ahmed Khan
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Chunjie Huang
- Institute of Reproductive Medicine, School of Medicine, Nantong University, Nantong, 226001, China
| | - Azhar Ali
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Muhammad Rizwan Yousaf
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Farwa Shakeel
- Laboratory of Molecular Biology and Genomics, Faculty of Science and Technology, University of Central Punjab, Lahore, Pakistan
| | - Ezi Masdia Putri
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Windu Negara
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
| | - Anis Muktiani
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia
| | - Bambang Waluyo Hadi Eko Prasetiyono
- Laboratory of Feed Technology, Animal Science Department, Faculty of Animal and Agricultural Sciences Universitas Diponegoro, Semarang, Indonesia
| | - Limbang Kustiawan
- Laboratory of Animal Nutrition and Feed Science, Animal Science Department, Faculty of Animal and Agricultural Sciences, Universitas Diponegoro, Semarang, Indonesia
| | - Dimar Sari Wahyuni
- Research Center for Animal Husbandry, National Research and Innovation Agency, Bogor, Indonesia
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3
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Hernández-Romero IA, Valdes VJ. De Novo Polycomb Recruitment and Repressive Domain Formation. EPIGENOMES 2022; 6:25. [PMID: 35997371 PMCID: PMC9397058 DOI: 10.3390/epigenomes6030025] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 11/29/2022] Open
Abstract
Every cell of an organism shares the same genome; even so, each cellular lineage owns a different transcriptome and proteome. The Polycomb group proteins (PcG) are essential regulators of gene repression patterning during development and homeostasis. However, it is unknown how the repressive complexes, PRC1 and PRC2, identify their targets and elicit new Polycomb domains during cell differentiation. Classical recruitment models consider the pre-existence of repressive histone marks; still, de novo target binding overcomes the absence of both H3K27me3 and H2AK119ub. The CpG islands (CGIs), non-core proteins, and RNA molecules are involved in Polycomb recruitment. Nonetheless, it is unclear how de novo targets are identified depending on the physiological context and developmental stage and which are the leading players stabilizing Polycomb complexes at domain nucleation sites. Here, we examine the features of de novo sites and the accessory elements bridging its recruitment and discuss the first steps of Polycomb domain formation and transcriptional regulation, comprehended by the experimental reconstruction of the repressive domains through time-resolved genomic analyses in mammals.
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Affiliation(s)
| | - Victor Julian Valdes
- Department of Cell Biology and Development, Institute of Cellular Physiology (IFC), National Autonomous University of Mexico (UNAM), Mexico City 04510, Mexico
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4
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Voortman L, Anderson C, Urban E, Yuan L, Tran S, Neuhaus-Follini A, Derrick J, Gregor T, Johnston RJ. Temporally dynamic antagonism between transcription and chromatin compaction controls stochastic photoreceptor specification in flies. Dev Cell 2022; 57:1817-1832.e5. [PMID: 35835116 PMCID: PMC9378680 DOI: 10.1016/j.devcel.2022.06.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 05/09/2022] [Accepted: 06/20/2022] [Indexed: 01/12/2023]
Abstract
Stochastic mechanisms diversify cell fates during development. How cells randomly choose between two or more fates remains poorly understood. In the Drosophila eye, the random mosaic of two R7 photoreceptor subtypes is determined by expression of the transcription factor Spineless (Ss). We investigated how cis-regulatory elements and trans factors regulate nascent transcriptional activity and chromatin compaction at the ss gene locus during R7 development. The ss locus is in a compact state in undifferentiated cells. An early enhancer drives transcription in all R7 precursors, and the locus opens. In differentiating cells, transcription ceases and the ss locus stochastically remains open or compacts. In SsON R7s, ss is open and competent for activation by a late enhancer, whereas in SsOFF R7s, ss is compact, and repression prevents expression. Our results suggest that a temporally dynamic antagonism, in which transcription drives large-scale decompaction and then compaction represses transcription, controls stochastic fate specification.
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Affiliation(s)
- Lukas Voortman
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Caitlin Anderson
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Elizabeth Urban
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Luorongxin Yuan
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sang Tran
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | | | - Josh Derrick
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Thomas Gregor
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA; Joseph Henry Laboratories of Physics, the Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Developmental and Stem Cell Biology, UMR3738, Institut Pasteur, 75015 Paris, France
| | - Robert J Johnston
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
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5
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Núñez-Martínez HN, Recillas-Targa F. Emerging Functions of lncRNA Loci beyond the Transcript Itself. Int J Mol Sci 2022; 23:ijms23116258. [PMID: 35682937 PMCID: PMC9181104 DOI: 10.3390/ijms23116258] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 05/14/2022] [Accepted: 05/30/2022] [Indexed: 02/04/2023] Open
Abstract
Thousands of long noncoding RNAs (lncRNAs) are actively transcribed in mammalian genomes. This class of RNAs has important regulatory functions in a broad range of cellular processes and diseases. Numerous lncRNAs have been demonstrated to mediate gene regulation through RNA-based mechanisms. Simultaneously, non-functional lncRNA transcripts derived from the activity of lncRNA loci have been identified, which underpin the notion that a considerable fraction of lncRNA loci exert regulatory functions through mechanisms associated with the production or the activity of lncRNA loci beyond the synthesized transcripts. We particularly distinguish two main RNA-independent components associated with regulatory effects; the act of transcription and the activity of DNA regulatory elements. We describe the experimental approaches to distinguish and understand the functional mechanisms derived from lncRNA loci. These scenarios reveal emerging mechanisms important to understanding the lncRNA implications in genome biology.
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6
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From genotype to phenotype: genetics of mammalian long non-coding RNAs in vivo. Nat Rev Genet 2022; 23:229-243. [PMID: 34837040 DOI: 10.1038/s41576-021-00427-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2021] [Indexed: 12/14/2022]
Abstract
Genome-wide sequencing has led to the discovery of thousands of long non-coding RNA (lncRNA) loci in the human genome, but evidence of functional significance has remained controversial for many lncRNAs. Genetically engineered model organisms are considered the gold standard for linking genotype to phenotype. Recent advances in CRISPR-Cas genome editing have led to a rapid increase in the use of mouse models to more readily survey lncRNAs for functional significance. Here, we review strategies to investigate the physiological relevance of lncRNA loci by highlighting studies that have used genetic mouse models to reveal key in vivo roles for lncRNAs, from fertility to brain development. We illustrate how an investigative approach, starting with whole-gene deletion followed by transcription termination and/or transgene rescue strategies, can provide definitive evidence for the in vivo function of mammalian lncRNAs.
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7
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SINEUPs: a novel toolbox for RNA therapeutics. Essays Biochem 2021; 65:775-789. [PMID: 34623427 PMCID: PMC8564737 DOI: 10.1042/ebc20200114] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 07/22/2021] [Accepted: 08/23/2021] [Indexed: 12/17/2022]
Abstract
RNA molecules have emerged as a new class of promising therapeutics to expand the range of druggable targets in the genome. In addition to ‘canonical’ protein-coding mRNAs, the emerging richness of sense and antisense long non-coding RNAs (lncRNAs) provides a new reservoir of molecular tools for RNA-based drugs. LncRNAs are composed of modular structural domains with specific activities involving the recruitment of protein cofactors or directly interacting with nucleic acids. A single therapeutic RNA transcript can then be assembled combining domains with defined secondary structures and functions, and antisense sequences specific for the RNA/DNA target of interest. As the first representative molecules of this new pharmacology, we have identified SINEUPs, a new functional class of natural antisense lncRNAs that increase the translation of partially overlapping mRNAs. Their activity is based on the combination of two domains: an embedded mouse inverted SINEB2 element that enhances mRNA translation (effector domain) and an overlapping antisense region that provides specificity for the target sense transcript (binding domain). By genetic engineering, synthetic SINEUPs can potentially target any mRNA of interest increasing translation and therefore the endogenous level of the encoded protein. In this review, we describe the state-of-the-art knowledge of SINEUPs and discuss recent publications showing their potential application in diseases where a physiological increase of endogenous protein expression can be therapeutic.
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8
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Abstract
We have known for decades that long noncoding RNAs (lncRNAs) can play essential functions across most forms of life. The maintenance of chromosome length requires an lncRNA (e.g., hTERC) and two lncRNAs in the ribosome that are required for protein synthesis. Thus, lncRNAs can represent powerful RNA machines. More recently, it has become clear that mammalian genomes encode thousands more lncRNAs. Thus, we raise the question: Which, if any, of these lncRNAs could also represent RNA-based machines? Here we synthesize studies that are beginning to address this question by investigating fundamental properties of lncRNA genes, revealing new insights into the RNA structure-function relationship, determining cis- and trans-acting lncRNAs in vivo, and generating new developments in high-throughput screening used to identify functional lncRNAs. Overall, these findings provide a context toward understanding the molecular grammar underlying lncRNA biology.
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Affiliation(s)
- John L Rinn
- BioFrontiers Institute, Department of Biochemistry, University of Colorado, Boulder, Colorado 80303, USA;
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, California 94305, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, USA
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9
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Alecki C, Chiwara V, Sanz LA, Grau D, Arias Pérez O, Boulier EL, Armache KJ, Chédin F, Francis NJ. RNA-DNA strand exchange by the Drosophila Polycomb complex PRC2. Nat Commun 2020; 11:1781. [PMID: 32286294 PMCID: PMC7156742 DOI: 10.1038/s41467-020-15609-x] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 03/17/2020] [Indexed: 12/21/2022] Open
Abstract
Polycomb Group (PcG) proteins form memory of transient transcriptional repression that is necessary for development. In Drosophila, DNA elements termed Polycomb Response Elements (PREs) recruit PcG proteins. How PcG activities are targeted to PREs to maintain repressed states only in appropriate developmental contexts has been difficult to elucidate. PcG complexes modify chromatin, but also interact with both RNA and DNA, and RNA is implicated in PcG targeting and function. Here we show that R-loops form at many PREs in Drosophila embryos, and correlate with repressive states. In vitro, both PRC1 and PRC2 can recognize R-loops and open DNA bubbles. Unexpectedly, we find that PRC2 drives formation of RNA-DNA hybrids, the key component of R-loops, from RNA and dsDNA. Our results identify R-loop formation as a feature of Drosophila PREs that can be recognized by PcG complexes, and RNA-DNA strand exchange as a PRC2 activity that could contribute to R-loop formation.
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Affiliation(s)
- Célia Alecki
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Département de biochimie et médecine moléculaire Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - Victoria Chiwara
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Lionel A Sanz
- Department of Molecular and Cellular Biology and Genome Center, 1 Shields Avenue, University of California, Davis, Davis, CA, 95616, USA
| | - Daniel Grau
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Osvaldo Arias Pérez
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
- Natural Sciences and Engineering Postgraduate, Universidad Autonoma Metropolitana, Cuajimalpa, Mexico City, Mexico
| | - Elodie L Boulier
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada
| | - Karim-Jean Armache
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology and Genome Center, 1 Shields Avenue, University of California, Davis, Davis, CA, 95616, USA
| | - Nicole J Francis
- Institut de recherches cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC, H2W 1R7, Canada.
- Département de biochimie et médecine moléculaire Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada.
- Division of Experimental Medicine, McGill University, 1001 Decarie Boulevard, Montreal, QC, H4A 3J1, Canada.
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10
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Techlo TR, Rasmussen AH, Møller PL, Bøttcher M, Winther S, Davidsson OB, Olofsson IA, Chalmer MA, Kogelman LJA, Nyegaard M, Olesen J, Hansen TF. Familial analysis reveals rare risk variants for migraine in regulatory regions. Neurogenetics 2020; 21:149-157. [PMID: 32076896 PMCID: PMC7283211 DOI: 10.1007/s10048-020-00606-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 02/07/2020] [Indexed: 01/08/2023]
Abstract
The most recent genome-wide association study of migraine increased the total number of known migraine risk loci to 38. Still, most of the heritability of migraine remains unexplained, and it has been suggested that rare gene dysregulatory variants play an important role in migraine etiology. Addressing the missing heritability of migraine, we aim to fine-map signals from the known migraine risk loci to regulatory mechanisms and associate these to downstream genic targets. We analyzed a large cohort of whole-genome sequenced patients from extended migraine pedigrees (1040 individuals from 155 families). We test for association between rare variants segregating in regulatory regions with migraine. The findings were replicated in an independent case-control cohort (2027 migraineurs, 1650 controls). We report an increased burden of rare variants in one CpG island and three polycomb group response elements near four migraine risk loci. We found that the association is independent of the common risk variants in the loci. The regulatory regions are suggested to affect different genes than those originally tagged by the index SNPs of the migraine loci. Families with familial clustering of migraine have an increased burden of rare variants in regulatory regions near known migraine risk loci, with effects that are independent of the variants in the loci. The possible regulatory targets suggest different genes than those originally tagged by the index SNPs of the migraine loci.
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Affiliation(s)
- Tanya Ramdal Techlo
- Danish Headache Center, Department of Neurology, Rigshospitalet, Nordstjernevej 40, DK-2600, Glostrup, Denmark
| | - Andreas Høiberg Rasmussen
- Danish Headache Center, Department of Neurology, Rigshospitalet, Nordstjernevej 40, DK-2600, Glostrup, Denmark
| | - Peter L Møller
- Department of Biomedicine, Aarhus University, Hoegh-Guldbergs Gade 10, Aarhus, Denmark
| | - Morten Bøttcher
- Department of Cardiology, Hospital Unit West Jutland, Herning, Denmark
| | - Simon Winther
- Department of Cardiology, Hospital Unit West Jutland, Herning, Denmark.,Department of Cardiology, Aarhus University Hospital, Skejby, Aarhus, Denmark
| | - Olafur B Davidsson
- Danish Headache Center, Department of Neurology, Rigshospitalet, Nordstjernevej 40, DK-2600, Glostrup, Denmark
| | - Isa A Olofsson
- Danish Headache Center, Department of Neurology, Rigshospitalet, Nordstjernevej 40, DK-2600, Glostrup, Denmark
| | - Mona Ameri Chalmer
- Danish Headache Center, Department of Neurology, Rigshospitalet, Nordstjernevej 40, DK-2600, Glostrup, Denmark
| | - Lisette J A Kogelman
- Danish Headache Center, Department of Neurology, Rigshospitalet, Nordstjernevej 40, DK-2600, Glostrup, Denmark
| | - Mette Nyegaard
- Department of Biomedicine, Aarhus University, Hoegh-Guldbergs Gade 10, Aarhus, Denmark
| | - Jes Olesen
- Danish Headache Center, Department of Neurology, Rigshospitalet, Nordstjernevej 40, DK-2600, Glostrup, Denmark
| | - Thomas Folkmann Hansen
- Danish Headache Center, Department of Neurology, Rigshospitalet, Nordstjernevej 40, DK-2600, Glostrup, Denmark. .,Institute for Biological Psychiatry, Mental Health Center Sct. Hans, Roskilde, Denmark. .,Novo Nordic Foundation Centre for Protein Research, Copenhagen University, Copenhagen, Denmark.
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11
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Lee H, Zhang Z, Krause HM. Long Noncoding RNAs and Repetitive Elements: Junk or Intimate Evolutionary Partners? Trends Genet 2019; 35:892-902. [PMID: 31662190 DOI: 10.1016/j.tig.2019.09.006] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/22/2019] [Accepted: 09/13/2019] [Indexed: 12/27/2022]
Abstract
Our recent ability to sequence entire genomes, along with all of their transcribed RNAs, has led to the surprising finding that only ∼1% of the human genome is used to encode proteins. This finding has led to vigorous debate over the functional importance of the transcribed but untranslated portions of the genome. Currently, scientists tend to assume coding genes are functional until proven not to be, while the opposite is true for noncoding genes. This review takes a new look at the evidence for and against widespread noncoding gene functionality. We focus in particular on long noncoding RNA (noncoding RNAs longer than 200 nucleotides) genes and their 'junk' associates, transposable elements, and satellite repeats. Taken together, the suggestion put forward is that more of this junk DNA may be functional than nonfunctional and that noncoding RNAs and transposable elements act symbiotically to drive evolution.
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Affiliation(s)
- Hyunmin Lee
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Zhaolei Zhang
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Henry M Krause
- Donnelly Centre, University of Toronto, Toronto, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada.
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12
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Debrand E, Chakalova L, Miles J, Dai YF, Goyenechea B, Dye S, Osborne CS, Horton A, Harju-Baker S, Pink RC, Caley D, Carter DRF, Peterson KR, Fraser P. An intergenic non-coding RNA promoter required for histone modifications in the human β-globin chromatin domain. PLoS One 2019; 14:e0217532. [PMID: 31412036 PMCID: PMC6693763 DOI: 10.1371/journal.pone.0217532] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/22/2019] [Indexed: 12/05/2022] Open
Abstract
Transcriptome analyses show a surprisingly large proportion of the mammalian genome is transcribed; much more than can be accounted for by genes and introns alone. Most of this transcription is non-coding in nature and arises from intergenic regions, often overlapping known protein-coding genes in sense or antisense orientation. The functional relevance of this widespread transcription is unknown. Here we characterize a promoter responsible for initiation of an intergenic transcript located approximately 3.3 kb and 10.7 kb upstream of the adult-specific human β-globin genes. Mutational analyses in β-YAC transgenic mice show that alteration of intergenic promoter activity results in ablation of H3K4 di- and tri-methylation and H3 hyperacetylation extending over a 30 kb region immediately downstream of the initiation site, containing the adult δ- and β-globin genes. This results in dramatically decreased expression of the adult genes through position effect variegation in which the vast majority of definitive erythroid cells harbor inactive adult globin genes. In contrast, expression of the neighboring ε- and γ-globin genes is completely normal in embryonic erythroid cells, indicating a developmentally specific variegation of the adult domain. Our results demonstrate a role for intergenic non-coding RNA transcription in the propagation of histone modifications over chromatin domains and epigenetic control of β-like globin gene transcription during development.
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Affiliation(s)
- Emmanuel Debrand
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Lyubomira Chakalova
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Joanne Miles
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Yan-Feng Dai
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Beatriz Goyenechea
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Sandra Dye
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Cameron S. Osborne
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Alice Horton
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
| | - Susanna Harju-Baker
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Ryan C. Pink
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Daniel Caley
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - David R. F. Carter
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, United Kingdom
| | - Kenneth R. Peterson
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Peter Fraser
- Laboratory of Chromatin and Gene Expression, The Babraham Institute, Babraham Research Campus, Cambridge, United Kingdom
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13
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lncRNA transcriptional initiation induces chromatin remodeling within a limited range in the fission yeast fbp1 promoter. Sci Rep 2019; 9:299. [PMID: 30670704 PMCID: PMC6342983 DOI: 10.1038/s41598-018-36049-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 11/01/2018] [Indexed: 11/23/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) transcribed across gene promoters have been detected. These regulate transcription by mechanisms that have not been fully elucidated. We herein show that the chromatin configuration is altered into an accessible state within 290 bp downstream from the initiation site of metabolic-stress-induced lncRNAs (mlonRNAs) in the promoter of the fission yeast fbp1 gene, whose transcription is massively induced upon glucose starvation. Chromatin upstream from fbp1 is progressively altered into an open configuration, as a cascade of transcription of three overlapping mlonRNA species (-a, -b and -c in order) occurs with transcriptional initiation sites progressing 5′ to 3′ upstream of the fbp1 promoter. Initiation of the shortest mlonRNA (mlonRNA-c) induces chromatin remodeling around a transcription factor-binding site and subsequent massive induction of fbp1. We identify the cis-element required for mlonRNA-c initiation, and by changing the distance between mlonRNA-initiation site and the transcription factor-binding site, we show that mlonRNA-initiation effectively induces chromatin remodeling in a limited distance within 290 bp. These results indicate that mlonRNAs are transcribed across the fbp1 promoter as a short-range inducer for local chromatin alterations, and suggest that strict chromatin modulation is archived via stepwise mlonRNA-initiations.
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14
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Kaikkonen MU, Adelman K. Emerging Roles of Non-Coding RNA Transcription. Trends Biochem Sci 2018; 43:654-667. [DOI: 10.1016/j.tibs.2018.06.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 05/07/2018] [Accepted: 06/03/2018] [Indexed: 12/14/2022]
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15
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Zhao PA, Rivera-Mulia JC, Gilbert DM. Replication Domains: Genome Compartmentalization into Functional Replication Units. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1042:229-257. [DOI: 10.1007/978-981-10-6955-0_11] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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16
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Isoda T, Moore AJ, He Z, Chandra V, Aida M, Denholtz M, Piet van Hamburg J, Fisch KM, Chang AN, Fahl SP, Wiest DL, Murre C. Non-coding Transcription Instructs Chromatin Folding and Compartmentalization to Dictate Enhancer-Promoter Communication and T Cell Fate. Cell 2017; 171:103-119.e18. [PMID: 28938112 DOI: 10.1016/j.cell.2017.09.001] [Citation(s) in RCA: 213] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 06/24/2017] [Accepted: 08/30/2017] [Indexed: 01/01/2023]
Abstract
It is now established that Bcl11b specifies T cell fate. Here, we show that in developing T cells, the Bcl11b enhancer repositioned from the lamina to the nuclear interior. Our search for factors that relocalized the Bcl11b enhancer identified a non-coding RNA named ThymoD (thymocyte differentiation factor). ThymoD-deficient mice displayed a block at the onset of T cell development and developed lymphoid malignancies. We found that ThymoD transcription promoted demethylation at CTCF bound sites and activated cohesin-dependent looping to reposition the Bcl11b enhancer from the lamina to the nuclear interior and to juxtapose the Bcl11b enhancer and promoter into a single-loop domain. These large-scale changes in nuclear architecture were associated with the deposition of activating epigenetic marks across the loop domain, plausibly facilitating phase separation. These data indicate how, during developmental progression and tumor suppression, non-coding transcription orchestrates chromatin folding and compartmentalization to direct with high precision enhancer-promoter communication.
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Affiliation(s)
- Takeshi Isoda
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Amanda J Moore
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Zhaoren He
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Vivek Chandra
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Masatoshi Aida
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Matthew Denholtz
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Jan Piet van Hamburg
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kathleen M Fisch
- Center for Computational Biology & Bioinformatics, Institute for Genomic Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Aaron N Chang
- Center for Computational Biology & Bioinformatics, Institute for Genomic Medicine, Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA
| | - Shawn P Fahl
- Blood Cell Development and Function, Fox Chase Cancer Center, 333 Cottman Avenue, PA, Philadelphia, PA 19111, USA
| | - David L Wiest
- Blood Cell Development and Function, Fox Chase Cancer Center, 333 Cottman Avenue, PA, Philadelphia, PA 19111, USA
| | - Cornelis Murre
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
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17
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The New RNA World: Growing Evidence for Long Noncoding RNA Functionality. Trends Genet 2017; 33:665-676. [DOI: 10.1016/j.tig.2017.08.002] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 08/01/2017] [Accepted: 08/02/2017] [Indexed: 12/18/2022]
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18
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Abstract
Eukaryotic genomes are rich in transcription units encoding "long noncoding RNAs" (lncRNAs). The purpose of all this transcription is unclear since most lncRNAs are quickly targeted for destruction during synthesis or shortly thereafter. As debates continue over the functional significance of many specific lncRNAs, support grows for the notion that the act of transcription rather than the RNA product itself is functionally important in many cases. Indeed, this alternative mechanism might better explain how low-abundance lncRNAs transcribed from noncoding DNA function in organisms. Here, we highlight some of the recently emerging features that distinguish coding from noncoding transcription and discuss how these differences might have important implications for the functional consequences of noncoding transcription.
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19
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Abstract
The question of how noncoding RNAs are involved in Polycomb group (PcG) and Trithorax group (TrxG) regulation has been on an extraordinary journey over the last three decades. Favored models have risen and fallen, and healthy debates have swept back and forth. The field has recently reached a critical mass of compelling data that throws light on several previously unresolved issues. The time is ripe for a fruitful combination of these findings with two other long-running avenues of research, namely the biochemical properties of the PcG/TrxG system and the application of theoretical mathematical models toward an understanding of the system's regulatory properties. I propose that integrating our current knowledge of noncoding RNA into a quantitative biochemical and theoretical framework for PcG and TrxG regulation has the potential to reconcile several apparently conflicting models and identifies fascinating questions for future research.
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Affiliation(s)
- Leonie Ringrose
- Integrated Research Institute for Life Sciences, Humboldt-Universität zu Berlin, 10115 Berlin, Germany;
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20
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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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21
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Abstract
There is growing evidence that transcription and nuclear organization are tightly linked. Yet, whether transcription of thousands of long noncoding RNAs (lncRNAs) could play a role in this packaging process remains elusive. Although some lncRNAs have been found to have clear roles in nuclear architecture (e.g., FIRRE, NEAT1, XIST, and others), the vast majority remain poorly understood. In this Perspective, we highlight how the act of transcription can affect nuclear architecture. We synthesize several recent findings into a proposed model where the transcription of lncRNAs can serve as guide-posts for shaping genome organization. This model is similar to the game "cat's cradle," where the shape of a string is successively changed by opening up new sites for finger placement. Analogously, transcription of lncRNAs could serve as "grip holds" for nuclear proteins to pull the genome into new positions. This model could explain general lncRNA properties such as low abundance and tissue specificity. Overall, we propose a general framework for how the act of lncRNA transcription could play a role in organizing the 3D genome.
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Affiliation(s)
- Marta Melé
- Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, MA 02138, USA
| | - John L Rinn
- Harvard Stem Cell and Regenerative Biology Department, Harvard University, Cambridge, MA 02138, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, MA 02138, USA; Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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22
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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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23
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Chromatin-enriched lncRNAs can act as cell-type specific activators of proximal gene transcription. Nat Struct Mol Biol 2017. [PMID: 28628087 PMCID: PMC5682930 DOI: 10.1038/nsmb.3424] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We recently described a new class of long noncoding RNA defined by especially tight chromatin association, whose presence is strongly correlated with expression of nearby genes in HEK293 cells. Here we critically examine the generality and cis-enhancer mechanism of this class of chromatin enriched RNA (cheRNA). CheRNA are largely cell-type specific, and remain the most effective chromatin signature for predicting cis-gene transcription in all cell types examined. Targeted depletion of three cheRNAs decreases gene expression of their neighbors, indicating potential co-activator function. Single-molecule FISH of one cheRNA-distal target gene pair suggests spatial overlap consistent with a role in chromosome looping. In another example, the cheRNA HIDALGO stimulates the fetal hemoglobin HBG1 gene during erythroid differentiation by promoting contacts to a downstream enhancer. Our results suggest that many cheRNAs activate proximal, lineage-specific gene transcription.
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24
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Chetverina DA, Elizar’ev PV, Lomaev DV, Georgiev PG, Erokhin MM. Control of the gene activity by polycomb and trithorax group proteins in Drosophila. RUSS J GENET+ 2017. [DOI: 10.1134/s1022795417020028] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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25
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Transcription of the non-coding RNA upperhand controls Hand2 expression and heart development. Nature 2016; 539:433-436. [PMID: 27783597 DOI: 10.1038/nature20128] [Citation(s) in RCA: 260] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 09/29/2016] [Indexed: 12/28/2022]
Abstract
HAND2 is an ancestral regulator of heart development and one of four transcription factors that control the reprogramming of fibroblasts into cardiomyocytes. Deletion of Hand2 in mice results in right ventricle hypoplasia and embryonic lethality. Hand2 expression is tightly regulated by upstream enhancers that reside within a super-enhancer delineated by histone H3 acetyl Lys27 (H3K27ac) modifications. Here we show that transcription of a Hand2-associated long non-coding RNA, which we named upperhand (Uph), is required to maintain the super-enhancer signature and elongation of RNA polymerase II through the Hand2 enhancer locus. Blockade of Uph transcription, but not knockdown of the mature transcript, abolished Hand2 expression, causing right ventricular hypoplasia and embryonic lethality in mice. Given the substantial number of uncharacterized promoter-associated long non-coding RNAs encoded by the mammalian genome, the Uph-Hand2 regulatory partnership offers a mechanism by which divergent non-coding transcription can establish a permissive chromatin environment.
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26
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Kahn TG, Dorafshan E, Schultheis D, Zare A, Stenberg P, Reim I, Pirrotta V, Schwartz YB. Interdependence of PRC1 and PRC2 for recruitment to Polycomb Response Elements. Nucleic Acids Res 2016; 44:10132-10149. [PMID: 27557709 PMCID: PMC5137424 DOI: 10.1093/nar/gkw701] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 07/26/2016] [Accepted: 07/28/2016] [Indexed: 12/31/2022] Open
Abstract
Polycomb Group (PcG) proteins are epigenetic repressors essential for control of development and cell differentiation. They form multiple complexes of which PRC1 and PRC2 are evolutionary conserved and obligatory for repression. The targeting of PRC1 and PRC2 is poorly understood and was proposed to be hierarchical and involve tri-methylation of histone H3 (H3K27me3) and/or monoubiquitylation of histone H2A (H2AK118ub). Here, we present a strict test of this hypothesis using the Drosophila model. We discover that neither H3K27me3 nor H2AK118ub is required for targeting PRC complexes to Polycomb Response Elements (PREs). We find that PRC1 can bind PREs in the absence of PRC2 but at many PREs PRC2 requires PRC1 to be targeted. We show that one role of H3K27me3 is to allow PcG complexes anchored at PREs to interact with surrounding chromatin. In contrast, the bulk of H2AK118ub is unrelated to PcG repression. These findings radically change our view of how PcG repression is targeted and suggest that PRC1 and PRC2 can communicate independently of histone modifications.
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Affiliation(s)
- Tatyana G Kahn
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
| | - Eshagh Dorafshan
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
| | - Dorothea Schultheis
- Friedrich-Alexander University of Erlangen-Nürnberg, Department of Biology, Division of Developmental Biology, Erlangen, D-91058, Germany
| | - Aman Zare
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
| | - Per Stenberg
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden.,Division of CBRN Defense and Security, Swedish Defense Research Agency, FOI, Umeå, 906 21, Sweden
| | - Ingolf Reim
- Friedrich-Alexander University of Erlangen-Nürnberg, Department of Biology, Division of Developmental Biology, Erlangen, D-91058, Germany
| | - Vincenzo Pirrotta
- Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA
| | - Yuri B Schwartz
- Department of Molecular Biology, Umeå University, Umeå, 901 87, Sweden
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27
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Hosogane M, Funayama R, Shirota M, Nakayama K. Lack of Transcription Triggers H3K27me3 Accumulation in the Gene Body. Cell Rep 2016; 16:696-706. [PMID: 27396330 DOI: 10.1016/j.celrep.2016.06.034] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 05/07/2016] [Accepted: 06/05/2016] [Indexed: 10/21/2022] Open
Abstract
Trimethylated H3K27 (H3K27me3) is associated with transcriptional repression, and its abundance in chromatin is frequently altered in cancer. However, it has remained unclear how genomic regions modified by H3K27me3 are specified and formed. We previously showed that downregulation of transcription by oncogenic Ras signaling precedes upregulation of H3K27me3 level. Here, we show that lack of transcription as a result of deletion of the transcription start site of a gene is sufficient to increase H3K27me3 content in the gene body. We further found that histone deacetylation mediates Ras-induced gene silencing and subsequent H3K27me3 accumulation. The H3K27me3 level increased gradually after Ras activation, requiring at least 35 days to achieve saturation. Such maximal accumulation of H3K27me3 was reversed by forced induction of transcription with the dCas9-activator system. Thus, our results indicate that changes in H3K27me3 level, especially in the body of a subset of genes, are triggered by changes in transcriptional activity itself.
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Affiliation(s)
- Masaki Hosogane
- Department of Cell Proliferation, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Ryo Funayama
- Department of Cell Proliferation, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Matsuyuki Shirota
- Division of Interdisciplinary Medical Sciences, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan
| | - Keiko Nakayama
- Department of Cell Proliferation, United Center for Advanced Research and Translational Medicine, Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai 980-8575, Japan.
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28
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Beltran M, Yates CM, Skalska L, Dawson M, Reis FP, Viiri K, Fisher CL, Sibley CR, Foster BM, Bartke T, Ule J, Jenner RG. The interaction of PRC2 with RNA or chromatin is mutually antagonistic. Genome Res 2016; 26:896-907. [PMID: 27197219 PMCID: PMC4937559 DOI: 10.1101/gr.197632.115] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 05/05/2016] [Indexed: 12/17/2022]
Abstract
Polycomb repressive complex 2 (PRC2) modifies chromatin to maintain genes in a repressed state during development. PRC2 is primarily associated with CpG islands at repressed genes and also possesses RNA binding activity. However, the RNAs that bind PRC2 in cells, the subunits that mediate these interactions, and the role of RNA in PRC2 recruitment to chromatin all remain unclear. By performing iCLIP for PRC2 in comparison with other RNA binding proteins, we show here that PRC2 binds nascent RNA at essentially all active genes. Although interacting with RNA promiscuously, PRC2 binding is enriched at specific locations within RNAs, primarily exon–intron boundaries and the 3′ UTR. Deletion of other PRC2 subunits reveals that SUZ12 is sufficient to establish this RNA binding profile. Contrary to prevailing models, we also demonstrate that the interaction of PRC2 with RNA or chromatin is mutually antagonistic in cells and in vitro. RNA degradation in cells triggers PRC2 recruitment to CpG islands at active genes. Correspondingly, the release of PRC2 from chromatin in cells increases RNA binding. Consistent with this, RNA and nucleosomes compete for PRC2 binding in vitro. We propose that RNA prevents PRC2 recruitment to chromatin at active genes and that mutual antagonism between RNA and chromatin underlies the pattern of PRC2 chromatin association across the genome.
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Affiliation(s)
- Manuel Beltran
- UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Christopher M Yates
- UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Lenka Skalska
- UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Marcus Dawson
- UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Filipa P Reis
- UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Keijo Viiri
- UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Cynthia L Fisher
- UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Christopher R Sibley
- Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, Queen Square, London WC1N 3BG, United Kingdom
| | - Benjamin M Foster
- MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, United Kingdom
| | - Till Bartke
- MRC Clinical Sciences Centre, Imperial College London, London W12 0NN, United Kingdom
| | - Jernej Ule
- Department of Molecular Neuroscience, UCL Institute of Neurology, University College London, Queen Square, London WC1N 3BG, United Kingdom
| | - Richard G Jenner
- UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
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29
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Rougemaille M, Libri D. Control of cryptic transcription in eukaryotes. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 702:122-31. [PMID: 21713682 DOI: 10.1007/978-1-4419-7841-7_10] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Over the last few years, the development of large-scale technologies has radically modified our conception of genome-wide transcriptional control by unveiling an unexpected high complexity of the eukaryotic transcriptome. In organisms ranging from yeast to human, a considerable number of novel small RNA species have been discovered in regions that were previously thought to be incompatible with high levels of transcription. Intriguingly, these transcripts, which are rapidly targeted for degradation by the exosome, appear to be devoid of any coding potential and may be the consequence of unwanted transcription events. However, the notion that an important fraction of these RNAs represent by-products of regulatory transcription is progressively emerging. In this chapter, we discuss the recent advances made in our understanding of the shape of the eukaryotic transcriptome. We also focus on the molecular mechanisms that cells exploit to prevent cryptic transcripts from interfering with the expression of protein-coding genes. Finally, we summarize data obtained in different systems suggesting that such RNAs may play a critical role in the regulation of gene expression as well as the evolution of genomes.
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Affiliation(s)
- Mathieu Rougemaille
- LEA Laboratory of Nuclear RNA Metabolism, Centre de Génétique Moléculaire, CNRS-UPR2167, Gif-sur-Yvette, France,
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30
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Chicken genome modelling for the benefit of science. WORLD POULTRY SCI J 2016. [DOI: 10.1017/s0043933915002652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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31
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Erokhin MM, Davydova AI, Lomaev DV, Georgiev PG, Chetverina DA. The effect of transcription on enhancer activity in Drosophila melanogaster. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416010051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Affiliation(s)
- Victoria H. Meller
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202; , ,
| | - Sonal S. Joshi
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202; , ,
| | - Nikita Deshpande
- Department of Biological Sciences, Wayne State University, Detroit, Michigan 48202; , ,
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33
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Transcription through Polycomb response elements does not induce a switch from repression to activation. Proc Natl Acad Sci U S A 2015; 112:14755-6. [PMID: 26567151 DOI: 10.1073/pnas.1520102112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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34
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Chen PB, Chen HV, Acharya D, Rando OJ, Fazzio TG. R loops regulate promoter-proximal chromatin architecture and cellular differentiation. Nat Struct Mol Biol 2015; 22:999-1007. [PMID: 26551076 PMCID: PMC4677832 DOI: 10.1038/nsmb.3122] [Citation(s) in RCA: 127] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 10/09/2015] [Indexed: 12/11/2022]
Abstract
Numerous chromatin-remodeling factors are regulated by interactions with RNA, although the contexts and functions of RNA binding are poorly understood. Here we show that R-loops, RNA:DNA hybrids consisting of nascent transcripts hybridized to template DNA, modulate the binding of two key chromatin regulatory complexes, Tip60–p400 and polycomb repressive complex 2 (PRC2) in mouse embryonic stem cells (ESCs). Like PRC2, the Tip60–p400 histone acetyltransferase complex binds to nascent transcripts, but unlike PRC2, transcription promotes chromatin binding by Tip60–p400. Interestingly, we observed higher Tip60–p400 and lower PRC2 levels at genes marked by promoter-proximal R-loops. Furthermore, disruption of R-loops broadly reduced Tip60–p400 and increased PRC2 occupancy genome-wide. Consistent with these alterations, ESCs with reduced R-loops exhibited impaired differentiation. These results show that R-loops act both positively and negatively to modulate the recruitment of key pluripotency regulators.
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Affiliation(s)
- Poshen B Chen
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Hsiuyi V Chen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Diwash Acharya
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Thomas G Fazzio
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts, USA.,Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, USA
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35
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Austenaa L, Barozzi I, Simonatto M, Masella S, Della Chiara G, Ghisletti S, Curina A, de Wit E, Bouwman B, de Pretis S, Piccolo V, Termanini A, Prosperini E, Pelizzola M, de Laat W, Natoli G. Transcription of Mammalian cis-Regulatory Elements Is Restrained by Actively Enforced Early Termination. Mol Cell 2015; 60:460-74. [DOI: 10.1016/j.molcel.2015.09.018] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 08/13/2015] [Accepted: 09/17/2015] [Indexed: 12/12/2022]
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36
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Hox miRNA regulation within the Drosophila Bithorax complex: Patterning behavior. Mech Dev 2015; 138 Pt 2:151-159. [PMID: 26311219 DOI: 10.1016/j.mod.2015.08.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 08/14/2015] [Accepted: 08/17/2015] [Indexed: 01/02/2023]
Abstract
The study of Drosophila Hox genes, located in the Antennapedia complex (ANT-C) and Bithorax complex (BX-C), has provided fundamental insights into mechanisms of how the segments of the animal body plan are specified. Notably, even though the analysis of the BX-C formally began over a century ago, surprises continue to emerge regarding its regulation and function. Even simply the gene content of the BX-C has been regularly revised in past years, especially with regard to non-coding RNAs (ncRNAs), including microRNAs. In this perspective, we review the history of studies of non-coding transcription in the BX-C, and highlight recent studies of its miRNAs that provide new insights into their tissue-specific roles in Hox gene regulation. In particular, we have demonstrated unexpected importance of endogenous BX-C miRNAs to restrict the spatial accumulation of Hox proteins and their TALE cofactors in the ventral nerve cord, and link this to aberrant neural differentiation and reproductive behavior. These findings open new directions on studying Hox miRNA function, and we speculate that further understanding of their roles in insect models may provide new leads for studying the enigmatic biological functions of analogous miRNAs located in vertebrate Hox clusters.
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37
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Javeed N, Tardi NJ, Maher M, Singari S, Edwards KA. Controlled expression of Drosophila homeobox loci using the Hostile takeover system. Dev Dyn 2015; 244:808-25. [PMID: 25820349 PMCID: PMC4449281 DOI: 10.1002/dvdy.24279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Revised: 03/12/2015] [Accepted: 03/16/2015] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Hostile takeover (Hto) is a Drosophila protein trapping system that allows the investigator to both induce a gene and tag its product. The Hto transposon carries a GAL4-regulated promoter expressing an exon encoding a FLAG-mCherry tag. Upon expression, the Hto exon can splice to a downstream genomic exon, generating a fusion transcript and tagged protein. RESULTS Using rough-eye phenotypic screens, Hto inserts were recovered at eight homeobox or Pax loci: cut, Drgx/CG34340, Pox neuro, araucan, shaven/D-Pax2, Zn finger homeodomain 2, Sex combs reduced (Scr), and the abdominal-A region. The collection yields diverse misexpression phenotypes. Ectopic Drgx was found to alter the cytoskeleton and cell adhesion in ovary follicle cells. Hto expression of cut, araucan, or shaven gives phenotypes similar to those of the corresponding UAS-cDNA constructs. The cut and Pox neuro phenotypes are suppressed by the corresponding RNAi constructs. The Scr and abdominal-A inserts do not make fusion proteins, but may act by chromatin- or RNA-based mechanisms. CONCLUSIONS Hto can effectively express tagged homeodomain proteins from their endogenous loci; the Minos vector allows inserts to be obtained even in transposon cold-spots. Hto screens may recover homeobox genes at high rates because they are particularly sensitive to misexpression.
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Affiliation(s)
- Naureen Javeed
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Nicholas J. Tardi
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Maggie Maher
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Swetha Singari
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
| | - Kevin A. Edwards
- School of Biological Sciences, Illinois State University, Normal, IL 61790, USA
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38
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Grossniklaus U, Paro R. Transcriptional silencing by polycomb-group proteins. Cold Spring Harb Perspect Biol 2014; 6:a019331. [PMID: 25367972 DOI: 10.1101/cshperspect.a019331] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Polycomb-group (PcG) genes encode chromatin proteins involved in stable and heritable transcriptional silencing. PcG proteins participate in distinct multimeric complexes that deposit, or bind to, specific histone modifications (e.g., H3K27me3 and H2AK119ub1) to prevent gene activation and maintain repressed chromatin domains. PcG proteins are evolutionary conserved and play a role in processes ranging from vernalization and seed development in plants, over X-chromosome inactivation in mammals, to the maintenance of stem cell identity. PcG silencing is medically relevant as it is often observed in human disorders, including cancer, and tissue regeneration, which involve the reprogramming of PcG-controlled target genes.
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Affiliation(s)
- Ueli Grossniklaus
- Institute of Plant Biology and Zürich-Basel Plant Science Center, University of Zürich, CH-8008 Zürich, Switzerland
| | - Renato Paro
- Department of Biosystems Science and Engineering, ETH Zürich, 4058 Basel, Switzerland
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39
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Kunej T, Obsteter J, Pogacar Z, Horvat S, Calin GA. The decalog of long non-coding RNA involvement in cancer diagnosis and monitoring. Crit Rev Clin Lab Sci 2014; 51:344-57. [PMID: 25123609 DOI: 10.3109/10408363.2014.944299] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Long non-coding RNAs (lncRNAs) are transcripts without protein-coding capacity; initially regarded as "transcriptional noise", lately they have emerged as essential factors in both cell biology and mechanisms of disease. In this article, we present basic knowledge of lncRNA molecular mechanisms, associated physiological processes and cancer association, as well as their diagnostic and therapeutic value in the form of a decalog: (1) Non-coding RNAs (ncRNAs) are transcripts without protein-coding capacity divided by size (short and long ncRNAs), function (housekeeping RNA and regulatory RNA) and direction of transcription (sense/antisense, bidirectional, intronic and intergenic), containing a broad range of molecules with diverse properties and functions, such as messenger RNA, transfer RNA, microRNA and long non-coding RNAs. (2) Long non-coding RNAs are implicated in many molecular mechanisms, such as transcriptional regulation, post-transcriptional regulation and processing of other short ncRNAs. (3) Long non-coding RNAs play an important role in many physiological processes such as X-chromosome inactivation, cell differentiation, immune response and apoptosis. (4) Long non-coding RNAs have been linked to hallmarks of cancer: (a) sustaining proliferative signaling; (b) evading growth suppressors; (c) enabling replicative immortality; (d) activating invasion and metastasis; (e) inducing angiogenesis; (f) resisting cell death; and (g) reprogramming energy metabolism. (5) Regarding their impact on cancer cells, lncRNAs are divided into two groups: oncogenic and tumor-suppressor lncRNAs. (6) Studies of lncRNA involvement in cancer usually analyze deregulated expression patterns at the RNA level as well as the effects of single nucleotide polymorphisms and copy number variations at the DNA level. (7) Long non-coding RNAs have potential as novel biomarkers due to tissue-specific expression patterns, efficient detection in body fluids and high stability. (8) LncRNAs serve as novel biomarkers for diagnostic, prognostic and monitoring purposes. (9) Tissue specificity of lncRNAs enables the development of selective therapeutic options. (10) Long non-coding RNAs are emerging as commercial biomarkers and therapeutic agents.
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Affiliation(s)
- Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana , Domzale , Slovenia
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40
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Abstract
The study of long noncoding RNAs (lncRNAs) is still in its infancy with more putative RNAs identified than those with ascribed functions. Defined as transcripts that are longer than 200 nucleotides without a coding sequence, their numbers are on the rise and may well challenge protein coding transcripts in number and diversity. lncRNAs are often expressed at low levels and their sequences are frequently poorly conserved, making it unclear if they are transcriptional noise or bonafide effectors. Despite these limitations, inroads into their functions are being made and it is clear they make a contribution in regulating all aspects of biology. The early verdict on their activity, however, suggests the majority function as chromatin modifiers. A good proportion show a connection to disease highlighting their importance and the need to determine their function. The focus of this review is on lncRNAs which influence developmental processes which in itself covers a large range of known activities.
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Affiliation(s)
- Jamila I Horabin
- Department of Biomedical Sciences, College of Medicine, Florida State University, Rm 3300-G, 1115 W. Call St., Tallahassee, FL, 32306-4300, USA,
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41
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Riising EM, Comet I, Leblanc B, Wu X, Johansen JV, Helin K. Gene silencing triggers polycomb repressive complex 2 recruitment to CpG islands genome wide. Mol Cell 2014; 55:347-60. [PMID: 24999238 DOI: 10.1016/j.molcel.2014.06.005] [Citation(s) in RCA: 304] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 04/14/2014] [Accepted: 05/28/2014] [Indexed: 01/24/2023]
Abstract
Polycomb group (PcG) proteins are required for normal differentiation and development and are frequently deregulated in cancer. PcG proteins are involved in gene silencing; however, their role in initiation and maintenance of transcriptional repression is not well defined. Here, we show that knockout of the Polycomb repressive complex 2 (PRC2) does not lead to significant gene expression changes in mouse embryonic stem cells (mESCs) and that it is dispensable for initiating silencing of target genes during differentiation. Transcriptional inhibition in mESCs is sufficient to induce genome-wide ectopic PRC2 recruitment to endogenous PcG target genes found in other tissues. PRC2 binding analysis shows that it is restricted to nucleosome-free CpG islands (CGIs) of untranscribed genes. Our results show that it is the transcriptional state that governs PRC2 binding, and we propose that it binds by default to nontranscribed CGI genes to maintain their silenced state and to protect cell identity.
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Affiliation(s)
- Eva Madi Riising
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Itys Comet
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Benjamin Leblanc
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark; The Danish Stem Cell Center (DanStem), Blegdamsvej 3, 2200 Copenhagen, Denmark
| | - Xudong Wu
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Jens Vilstrup Johansen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark; The Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Kristian Helin
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark; Centre for Epigenetics, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark; The Danish Stem Cell Center (DanStem), Blegdamsvej 3, 2200 Copenhagen, Denmark.
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42
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Abstract
Enhancer elements regulate the tissue- and developmental-stage-specific expression of genes. Recent estimates suggest that there are more than 50,000 enhancers in mammalian cells. At least a subset of enhancers has been shown to recruit RNA polymerase II transcription complexes and to generate enhancer transcripts. Here, we provide an overview of enhancer function and discuss how transcription of enhancers or enhancer-generated transcripts could contribute to the regulation of gene expression during development and differentiation.
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43
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Gummalla M, Galetti S, Maeda RK, Karch F. Hox gene regulation in the central nervous system of Drosophila. Front Cell Neurosci 2014; 8:96. [PMID: 24795565 PMCID: PMC4005941 DOI: 10.3389/fncel.2014.00096] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 03/14/2014] [Indexed: 12/20/2022] Open
Abstract
Hox genes specify the structures that form along the anteroposterior (AP) axis of bilateria. Within the genome, they often form clusters where, remarkably enough, their position within the clusters reflects the relative positions of the structures they specify along the AP axis. This correspondence between genomic organization and gene expression pattern has been conserved through evolution and provides a unique opportunity to study how chromosomal context affects gene regulation. In Drosophila, a general rule, often called “posterior dominance,” states that Hox genes specifying more posterior structures repress the expression of more anterior Hox genes. This rule explains the apparent spatial complementarity of Hox gene expression patterns in Drosophila. Here we review a noticeable exception to this rule where the more-posteriorly expressed Abd-B Hox gene fails to repress the more-anterior abd-A gene in cells of the central nervous system (CNS). While Abd-B is required to repress ectopic expression of abd-A in the posterior epidermis, abd-A repression in the posterior CNS is accomplished by a different mechanism that involves a large 92 kb long non-coding RNA (lncRNA) encoded by the intergenic region separating abd-A and Abd-B (the iab8ncRNA). Dissection of this lncRNA revealed that abd-A is repressed by the lncRNA using two redundant mechanisms. The first mechanism is mediated by a microRNA (mir-iab-8) encoded by intronic sequence within the large iab8-ncRNA. Meanwhile, the second mechanism seems to involve transcriptional interference by the long iab-8 ncRNA on the abd-A promoter. Recent work demonstrating CNS-specific regulation of genes by ncRNAs in Drosophila, seem to highlight a potential role for the iab-8-ncRNA in the evolution of the Drosophila Hox complexes.
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Affiliation(s)
- Maheshwar Gummalla
- Department of Genetics and Evolution, University of Geneva Geneva, Switzerland ; Institute of Biochemistry, University of Medicine - University of Göttingen Göttingen, Germany
| | - Sandrine Galetti
- Department of Genetics and Evolution, University of Geneva Geneva, Switzerland
| | - Robert K Maeda
- Department of Genetics and Evolution, University of Geneva Geneva, Switzerland
| | - François Karch
- Department of Genetics and Evolution, University of Geneva Geneva, Switzerland
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44
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Homeotic gene regulation: a paradigm for epigenetic mechanisms underlying organismal development. Subcell Biochem 2014; 61:177-207. [PMID: 23150252 DOI: 10.1007/978-94-007-4525-4_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The organization of eukaryotic genome into chromatin within the nucleus eventually dictates the cell type specific expression pattern of genes. This higher order of chromatin organization is established during development and dynamically maintained throughout the life span. Developmental mechanisms are conserved in bilaterians and hence they have body plan in common, which is achieved by regulatory networks controlling cell type specific gene expression. Homeotic genes are conserved in metazoans and are crucial for animal development as they specify cell type identity along the anterior-posterior body axis. Hox genes are the best studied in the context of epigenetic regulation that has led to significant understanding of the organismal development. Epigenome specific regulation is brought about by conserved chromatin modulating factors like PcG/trxG proteins during development and differentiation. Here we discuss the conserved epigenetic mechanisms relevant to homeotic gene regulation in metazoans.
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45
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A genetic program theory of aging using an RNA population model. Ageing Res Rev 2014; 13:46-54. [PMID: 24263168 DOI: 10.1016/j.arr.2013.11.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 11/08/2013] [Indexed: 12/11/2022]
Abstract
Aging is a common characteristic of multicellular eukaryotes. Copious hypotheses have been proposed to explain the mechanisms of aging, but no single theory is generally acceptable. In this article, we refine the RNA population gene activating model (Lv et al., 2003) based on existing reports as well as on our own latest findings. We propose the RNA population model as a genetic theory of aging. The new model can also be applied to differentiation and tumorigenesis and could explain the biological significance of non-coding DNA, RNA, and repetitive sequence DNA. We provide evidence from the literature as well as from our own findings for the roles of repetitive sequences in gene activation. In addition, we predict several phenomena related to aging and differentiation based on this model.
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46
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Arbel-Goren R, Tal A, Stavans J. Phenotypic noise: effects of post-transcriptional regulatory processes affecting mRNA. WILEY INTERDISCIPLINARY REVIEWS-RNA 2013; 5:197-207. [PMID: 24259395 DOI: 10.1002/wrna.1209] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 10/28/2013] [Accepted: 10/29/2013] [Indexed: 11/10/2022]
Abstract
The inherently stochastic nature of biomolecular processes is one of the main sources giving rise to cell-to-cell variations in protein and mRNA abundance, termed noise. Noise in isogenic populations can enhance survival under adverse conditions and stress, and has therefore played a fundamental role in evolution. On the other hand, noise may have detrimental effects and therefore cells must also display robustness to fluctuations and possess mechanisms of control in order to function properly. Noise can be introduced at every step in the cascade of intermediate events resulting in the production of functional proteins. While initial studies of noise focused on stochasticity introduced at the transcriptional level, recent years have witnessed a gradual shift of emphasis into the effects that post-transcriptional processes have on phenotypic noise. Here, we survey the insights that have been gained on the effects of processes that modify RNA transcript populations on phenotypic noise, including regulation by noncoding RNAs in prokaryotes and eukaryotes, alternative splicing and transcriptional interference.
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Affiliation(s)
- Rinat Arbel-Goren
- Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
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47
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Schorderet P, Lonfat N, Darbellay F, Tschopp P, Gitto S, Soshnikova N, Duboule D. A genetic approach to the recruitment of PRC2 at the HoxD locus. PLoS Genet 2013; 9:e1003951. [PMID: 24244202 PMCID: PMC3820793 DOI: 10.1371/journal.pgen.1003951] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 09/27/2013] [Indexed: 01/01/2023] Open
Abstract
Polycomb group (PcG) proteins are essential for the repression of key factors during early development. In Drosophila, the polycomb repressive complexes (PRC) associate with defined polycomb response DNA elements (PREs). In mammals, however, the mechanisms underlying polycomb recruitment at targeted loci are poorly understood. We have used an in vivo approach to identify DNA sequences of importance for the proper recruitment of polycomb proteins at the HoxD locus. We report that various genomic re-arrangements of the gene cluster do not strongly affect PRC2 recruitment and that relatively small polycomb interacting sequences appear necessary and sufficient to confer polycomb recognition and targeting to ectopic loci. In addition, a high GC content, while not sufficient to recruit PRC2, may help its local spreading. We discuss the importance of PRC2 recruitment over Hox gene clusters in embryonic stem cells, for their subsequent coordinated transcriptional activation during development. Hox genes are essential for the proper organization of structures along the developing vertebrate body axis. These genes must be activated at a precise time and their premature transcription is deleterious to the organism. Early on, Hox gene clusters are covered by Polycomb Repressive protein Complexes (PRCs), which help keep these genes silent. However, the mechanism(s) that selectively recruit PRCs to these particular genomic loci remains elusive. We have used a collection of mutant mice carrying a set of deletions inside and outside the HoxD cluster to try and detect the presence of any DNA sequence of particular importance in this mechanism. We conclude that a range of low affinity sequences synergize to recruit PRCs over the gene cluster, which makes this process very robust and resistant to genetic perturbations.
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Affiliation(s)
- Patrick Schorderet
- National Research Center ‘Frontiers in Genetics’, Geneva, Switzerland
- School of Life Sciences, Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Nicolas Lonfat
- School of Life Sciences, Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Fabrice Darbellay
- National Research Center ‘Frontiers in Genetics’, Geneva, Switzerland
- School of Life Sciences, Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Patrick Tschopp
- National Research Center ‘Frontiers in Genetics’, Geneva, Switzerland
- Department of Genetics and Evolution, University of Geneva, Sciences III, Geneva, Switzerland
| | - Sandra Gitto
- National Research Center ‘Frontiers in Genetics’, Geneva, Switzerland
- Department of Genetics and Evolution, University of Geneva, Sciences III, Geneva, Switzerland
| | - Natalia Soshnikova
- National Research Center ‘Frontiers in Genetics’, Geneva, Switzerland
- School of Life Sciences, Federal Institute of Technology (EPFL), Lausanne, Switzerland
| | - Denis Duboule
- National Research Center ‘Frontiers in Genetics’, Geneva, Switzerland
- School of Life Sciences, Federal Institute of Technology (EPFL), Lausanne, Switzerland
- Department of Genetics and Evolution, University of Geneva, Sciences III, Geneva, Switzerland
- * E-mail: ,
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48
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Miyazaki H, Higashimoto K, Yada Y, Endo TA, Sharif J, Komori T, Matsuda M, Koseki Y, Nakayama M, Soejima H, Handa H, Koseki H, Hirose S, Nishioka K. Ash1l methylates Lys36 of histone H3 independently of transcriptional elongation to counteract polycomb silencing. PLoS Genet 2013; 9:e1003897. [PMID: 24244179 PMCID: PMC3820749 DOI: 10.1371/journal.pgen.1003897] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 09/03/2013] [Indexed: 12/27/2022] Open
Abstract
Molecular mechanisms for the establishment of transcriptional memory are poorly understood. 5,6-dichloro-1-D-ribofuranosyl-benzimidazole (DRB) is a P-TEFb kinase inhibitor that artificially induces the poised RNA polymerase II (RNAPII), thereby manifesting intermediate steps for the establishment of transcriptional activation. Here, using genetics and DRB, we show that mammalian Absent, small, or homeotic discs 1-like (Ash1l), a member of the trithorax group proteins, methylates Lys36 of histone H3 to promote the establishment of Hox gene expression by counteracting Polycomb silencing. Importantly, we found that Ash1l-dependent Lys36 di-, tri-methylation of histone H3 in a coding region and exclusion of Polycomb group proteins occur independently of transcriptional elongation in embryonic stem (ES) cells, although both were previously thought to be consequences of transcription. Genome-wide analyses of histone H3 Lys36 methylation under DRB treatment have suggested that binding of the retinoic acid receptor (RAR) to a certain genomic region promotes trimethylation in the RAR-associated gene independent of its ongoing transcription. Moreover, DRB treatment unveils a parallel response between Lys36 methylation of histone H3 and occupancy of either Tip60 or Mof in a region-dependent manner. We also found that Brg1 is another key player involved in the response. Our results uncover a novel regulatory cascade orchestrated by Ash1l with RAR and provide insights into mechanisms underlying the establishment of the transcriptional activation that counteracts Polycomb silencing.
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Affiliation(s)
- Hitomi Miyazaki
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga City, Saga, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi City, Saitama, Japan
| | - Ken Higashimoto
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga City, Saga, Japan
| | - Yukari Yada
- Division of Gene Expression, Department of Developmental Genetics, National Institute of Genetics, 1111 Yata, Mishima City, Shizuoka, Japan
| | - Takaho A. Endo
- RIKEN Center for Integrative Medical Sciences, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, Japan
| | - Jafar Sharif
- RIKEN Center for Integrative Medical Sciences, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, Japan
| | - Toshiharu Komori
- Division of Gene Expression, Department of Developmental Genetics, National Institute of Genetics, 1111 Yata, Mishima City, Shizuoka, Japan
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama City, Kanagawa, Japan
| | - Masashi Matsuda
- RIKEN Center for Integrative Medical Sciences, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, Japan
| | - Yoko Koseki
- RIKEN Center for Integrative Medical Sciences, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, Japan
| | - Manabu Nakayama
- Laboratory of Medical Genomics, Department of Human Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu City, Chiba, Japan
| | - Hidenobu Soejima
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga City, Saga, Japan
| | - Hiroshi Handa
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259 Nagatsuta, Yokohama City, Kanagawa, Japan
| | - Haruhiko Koseki
- RIKEN Center for Integrative Medical Sciences, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi City, Saitama, Japan
| | - Susumu Hirose
- Division of Gene Expression, Department of Developmental Genetics, National Institute of Genetics, 1111 Yata, Mishima City, Shizuoka, Japan
| | - Kenichi Nishioka
- Division of Molecular Genetics and Epigenetics, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga City, Saga, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi City, Saitama, Japan
- Division of Gene Expression, Department of Developmental Genetics, National Institute of Genetics, 1111 Yata, Mishima City, Shizuoka, Japan
- * E-mail:
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49
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Abstract
The regulation of gene expression by non-coding RNAs (ncRNAs) has become a new paradigm in biology. RNA-mediated gene silencing pathways have been studied extensively, revealing diverse epigenetic and posttranscriptional mechanisms. In contrast, the roles of ncRNAs in activating gene expression remains poorly understood. In this review, we summarize the current knowledge of gene activation by small RNAs, long non-coding RNAs, and enhancer-derived RNAs, with an emphasis on epigenetic mechanisms.
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Affiliation(s)
- Alan L Jiao
- Department of Molecular, Cellular and Developmental Biology; Yale University; New Haven, CT USA
| | - Frank J Slack
- Department of Molecular, Cellular and Developmental Biology; Yale University; New Haven, CT USA
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Kaneko S, Son J, Shen SS, Reinberg D, Bonasio R. PRC2 binds active promoters and contacts nascent RNAs in embryonic stem cells. Nat Struct Mol Biol 2013; 20:1258-64. [PMID: 24141703 PMCID: PMC3839660 DOI: 10.1038/nsmb.2700] [Citation(s) in RCA: 245] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 09/26/2013] [Indexed: 01/09/2023]
Abstract
EZH2 is the catalytic subunit of PRC2, a central epigenetic repressor essential for development processes in vivo and for the differentiation of embryonic stem cells (ESCs) in vitro. The biochemical function of PRC2 in depositing repressive H3K27me3 marks is well understood, but how it is regulated and directed to specific genes before and during differentiation remains unknown. Here, we report that PRC2 binds at low levels to a majority of promoters in mouse ESCs, including many that are active and devoid of H3K27me3. Using in vivo RNA–protein crosslinking, we show that EZH2 directly binds to the 5′ of nascent RNAs transcribed from a subset of these promoters and that these binding events correlate with decreased H3K27me3. Our findings suggest a molecular mechanism by which PRC2 senses the transcriptional state of the cell and translates it into epigenetic information.
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Affiliation(s)
- Syuzo Kaneko
- 1] Howard Hughes Medical Institute, New York University School of Medicine, New York, New York, USA. [2] Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, New York, USA
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