1
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Peraldi R, Kmita M. 40 years of the homeobox: mechanisms of Hox spatial-temporal collinearity in vertebrates. Development 2024; 151:dev202508. [PMID: 39167089 DOI: 10.1242/dev.202508] [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] [Indexed: 08/23/2024]
Abstract
Animal body plans are established during embryonic development by the Hox genes. This patterning process relies on the differential expression of Hox genes along the head-to-tail axis. Hox spatial collinearity refers to the relationship between the organization of Hox genes in clusters and the differential Hox expression, whereby the relative order of the Hox genes within a cluster mirrors the spatial sequence of expression in the developing embryo. In vertebrates, the cluster organization is also associated with the timing of Hox activation, which harmonizes Hox expression with the progressive emergence of axial tissues. Thereby, in vertebrates, Hox temporal collinearity is intimately linked to Hox spatial collinearity. Understanding the mechanisms contributing to Hox temporal and spatial collinearity is thus key to the comprehension of vertebrate patterning. Here, we provide an overview of the main discoveries pertaining to the mechanisms of Hox spatial-temporal collinearity.
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Affiliation(s)
- Rodrigue Peraldi
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada
- Programme de Biologie Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
| | - Marie Kmita
- Genetics and Development Research Unit, Institut de Recherches Cliniques de Montréal, Montréal, Québec H2W 1R7, Canada
- Programme de Biologie Moléculaire, Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Département de Médecine, Université de Montréal, Montréal, Québec H3C 3J7, Canada
- Department of Experimental Medicine, McGill University, Montreal, Quebec H4A 3J1, Canada
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2
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Yancoskie M, Khaleghi R, Gururajan A, Raghunathan A, Gupta A, Diethelm S, Maritz C, Sturla S, Krishnan M, Naegeli H. ASH1L guards cis-regulatory elements against cyclobutane pyrimidine dimer induction. Nucleic Acids Res 2024; 52:8254-8270. [PMID: 38884271 PMCID: PMC11317172 DOI: 10.1093/nar/gkae517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/29/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024] Open
Abstract
The histone methyltransferase ASH1L, first discovered for its role in transcription, has been shown to accelerate the removal of ultraviolet (UV) light-induced cyclobutane pyrimidine dimers (CPDs) by nucleotide excision repair. Previous reports demonstrated that CPD excision is most efficient at transcriptional regulatory elements, including enhancers, relative to other genomic sites. Therefore, we analyzed DNA damage maps in ASH1L-proficient and ASH1L-deficient cells to understand how ASH1L controls enhancer stability. This comparison showed that ASH1L protects enhancer sequences against the induction of CPDs besides stimulating repair activity. ASH1L reduces CPD formation at C-containing but not at TT dinucleotides, and no protection occurs against pyrimidine-(6,4)-pyrimidone photoproducts or cisplatin crosslinks. The diminished CPD induction extends to gene promoters but excludes retrotransposons. This guardian role against CPDs in regulatory elements is associated with the presence of H3K4me3 and H3K27ac histone marks, which are known to interact with the PHD and BRD motifs of ASH1L, respectively. Molecular dynamics simulations identified a DNA-binding AT hook of ASH1L that alters the distance and dihedral angle between neighboring C nucleotides to disfavor dimerization. The loss of this protection results in a higher frequency of C->T transitions at enhancers of skin cancers carrying ASH1L mutations compared to ASH1L-intact counterparts.
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Affiliation(s)
- Michelle N Yancoskie
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
| | - Reihaneh Khaleghi
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
| | - Anirvinya Gururajan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Aadarsh Raghunathan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Aryan Gupta
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Sarah Diethelm
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
| | - Corina Maritz
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zurich, Zurich 8092, Switzerland
| | - Marimuthu Krishnan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
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3
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Jayakrishnan M, Havlová M, Veverka V, Regnard C, Becker P. Genomic context-dependent histone H3K36 methylation by three Drosophila methyltransferases and implications for dedicated chromatin readers. Nucleic Acids Res 2024; 52:7627-7649. [PMID: 38813825 PMCID: PMC11260483 DOI: 10.1093/nar/gkae449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/03/2024] [Accepted: 05/28/2024] [Indexed: 05/31/2024] Open
Abstract
Methylation of histone H3 at lysine 36 (H3K36me3) marks active chromatin. The mark is interpreted by epigenetic readers that assist transcription and safeguard the integrity of the chromatin fiber. The chromodomain protein MSL3 binds H3K36me3 to target X-chromosomal genes in male Drosophila for dosage compensation. The PWWP-domain protein JASPer recruits the JIL1 kinase to active chromatin on all chromosomes. Unexpectedly, depletion of K36me3 had variable, locus-specific effects on the interactions of those readers. This observation motivated a systematic and comprehensive study of K36 methylation in a defined cellular model. Contrasting prevailing models, we found that K36me1, K36me2 and K36me3 each contribute to distinct chromatin states. A gene-centric view of the changing K36 methylation landscape upon depletion of the three methyltransferases Set2, NSD and Ash1 revealed local, context-specific methylation signatures. Set2 catalyzes K36me3 predominantly at transcriptionally active euchromatin. NSD places K36me2/3 at defined loci within pericentric heterochromatin and on weakly transcribed euchromatic genes. Ash1 deposits K36me1 at regions with enhancer signatures. The genome-wide mapping of MSL3 and JASPer suggested that they bind K36me2 in addition to K36me3, which was confirmed by direct affinity measurement. This dual specificity attracts the readers to a broader range of chromosomal locations and increases the robustness of their actions.
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Affiliation(s)
- Muhunden Jayakrishnan
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-Universität, Munich, Germany
| | - Magdalena Havlová
- Institute of Organic Chemistry and Biochemistry (IOCB) of the Czech Academy of Sciences, Prague, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry (IOCB) of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Catherine Regnard
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-Universität, Munich, Germany
| | - Peter B Becker
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-Universität, Munich, Germany
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4
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Anyetei-Anum CS, Leatham-Jensen MP, Fox GC, Smith BR, Krajewski K, Strahl BD, Dowen JM, Matera AG, Duronio RJ, McKay DJ. Dual roles of histone H3 lysine-4 in antagonizing Polycomb group function and promoting target gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600669. [PMID: 38979215 PMCID: PMC11230394 DOI: 10.1101/2024.06.25.600669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Tight control over cell identity gene expression is necessary for proper adult form and function. The opposing activities of Polycomb and trithorax complexes determine the ON/OFF state of targets like the Hox genes. Trithorax encodes a methyltransferase specific to histone H3 lysine-4 (H3K4). However, there is no direct evidence that H3K4 regulates Polycomb group target genes in vivo . Here, we demonstrate two key roles for replication-dependent histone H3.2K4 in target control. We find that H3.2K4 antagonizes Polycomb group catalytic activity and that it is required for proper target gene activation. We conclude that H3.2K4 directly regulates expression of Polycomb targets.
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5
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Wenger A, Biran A, Alcaraz N, Redó-Riveiro A, Sell AC, Krautz R, Flury V, Reverón-Gómez N, Solis-Mezarino V, Völker-Albert M, Imhof A, Andersson R, Brickman JM, Groth A. Symmetric inheritance of parental histones governs epigenome maintenance and embryonic stem cell identity. Nat Genet 2023; 55:1567-1578. [PMID: 37666988 PMCID: PMC10484787 DOI: 10.1038/s41588-023-01476-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/17/2023] [Indexed: 09/06/2023]
Abstract
Modified parental histones are segregated symmetrically to daughter DNA strands during replication and can be inherited through mitosis. How this may sustain the epigenome and cell identity remains unknown. Here we show that transmission of histone-based information during DNA replication maintains epigenome fidelity and embryonic stem cell plasticity. Asymmetric segregation of parental histones H3-H4 in MCM2-2A mutants compromised mitotic inheritance of histone modifications and globally altered the epigenome. This included widespread spurious deposition of repressive modifications, suggesting elevated epigenetic noise. Moreover, H3K9me3 loss at repeats caused derepression and H3K27me3 redistribution across bivalent promoters correlated with misexpression of developmental genes. MCM2-2A mutation challenged dynamic transitions in cellular states across the cell cycle, enhancing naïve pluripotency and reducing lineage priming in G1. Furthermore, developmental competence was diminished, correlating with impaired exit from pluripotency. Collectively, this argues that epigenetic inheritance of histone modifications maintains a correctly balanced and dynamic chromatin landscape able to support mammalian cell differentiation.
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Affiliation(s)
- Alice Wenger
- Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- Lexogen GmbH, Vienna, Austria
| | - Alva Biran
- Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Nicolas Alcaraz
- Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Alba Redó-Riveiro
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Annika Charlotte Sell
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark
| | - Robert Krautz
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Valentin Flury
- Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | - Nazaret Reverón-Gómez
- Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
| | | | - Moritz Völker-Albert
- EpiQMAx GmbH, Planegg, Germany
- Faculty of Medicine, Biomedical Center, Protein Analysis Unit, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Axel Imhof
- Faculty of Medicine, Biomedical Center, Protein Analysis Unit, Ludwig-Maximilians-Universität München, Planegg, Germany
| | - Robin Andersson
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Joshua M Brickman
- Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), University of Copenhagen, Copenhagen, Denmark.
| | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark.
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark.
- Department of Cellular and Molecular Medicine (ICMM), University of Copenhagen, Copenhagen, Denmark.
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6
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Fal K, Berr A, Le Masson M, Faigenboim A, Pano E, Ishkhneli N, Moyal NL, Villette C, Tomkova D, Chabouté ME, Williams LE, Carles CC. Lysine 27 of histone H3.3 is a fine modulator of developmental gene expression and stands as an epigenetic checkpoint for lignin biosynthesis in Arabidopsis. THE NEW PHYTOLOGIST 2023; 238:1085-1100. [PMID: 36779574 DOI: 10.1111/nph.18666] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/28/2022] [Indexed: 06/18/2023]
Abstract
Chromatin is a dynamic platform within which gene expression is controlled by epigenetic modifications, notably targeting amino acid residues of histone H3. Among them is lysine 27 of H3 (H3K27), the trimethylation of which by the Polycomb Repressive Complex 2 (PRC2) is instrumental in regulating spatiotemporal patterns of key developmental genes. H3K27 is also subjected to acetylation and is found at sites of active transcription. Most information on the function of histone residues and their associated modifications in plants was obtained from studies of loss-of-function mutants for the complexes that modify them. To decrypt the genuine function of H3K27, we expressed a non-modifiable variant of H3 at residue K27 (H3.3K27A ) in Arabidopsis, and developed a multi-scale approach combining in-depth phenotypical and cytological analyses, with transcriptomics and metabolomics. We uncovered that the H3.3K27A variant causes severe developmental defects, part of them are reminiscent of PRC2 mutants, part of them are new. They include early flowering, increased callus formation and short stems with thicker xylem cell layer. This latest phenotype correlates with mis-regulation of phenylpropanoid biosynthesis. Overall, our results reveal novel roles of H3K27 in plant cell fates and metabolic pathways, and highlight an epigenetic control point for elongation and lignin composition of the stem.
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Affiliation(s)
- Kateryna Fal
- Plant and Cell Physiology Lab, IRIG-DBSCI-LPCV, CEA, Grenoble Alpes University - CNRS - INRAE - CEA, 17 rue des Martyrs, bât. C2, 38054, Grenoble Cedex 9, France
| | - Alexandre Berr
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France
| | - Marie Le Masson
- Plant and Cell Physiology Lab, IRIG-DBSCI-LPCV, CEA, Grenoble Alpes University - CNRS - INRAE - CEA, 17 rue des Martyrs, bât. C2, 38054, Grenoble Cedex 9, France
| | - Adi Faigenboim
- Institute of Plant Sciences, ARO Volcani Center, PO Box 15159, Rishon LeZion, 7528809, Israel
| | - Emeline Pano
- Plant and Cell Physiology Lab, IRIG-DBSCI-LPCV, CEA, Grenoble Alpes University - CNRS - INRAE - CEA, 17 rue des Martyrs, bât. C2, 38054, Grenoble Cedex 9, France
| | - Nickolay Ishkhneli
- Robert H. Smith Institute of Plant Sciences & Genetics in Agriculture - Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Netta-Lee Moyal
- Robert H. Smith Institute of Plant Sciences & Genetics in Agriculture - Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Claire Villette
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France
| | - Denisa Tomkova
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France
| | - Marie-Edith Chabouté
- Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, 12 rue du Général Zimmer, 67084, Strasbourg Cedex, France
| | - Leor Eshed Williams
- Robert H. Smith Institute of Plant Sciences & Genetics in Agriculture - Hebrew University of Jerusalem, Rehovot, 76100, Israel
| | - Cristel C Carles
- Plant and Cell Physiology Lab, IRIG-DBSCI-LPCV, CEA, Grenoble Alpes University - CNRS - INRAE - CEA, 17 rue des Martyrs, bât. C2, 38054, Grenoble Cedex 9, France
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7
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Yancoskie MN, Maritz C, van Eijk P, Reed SH, Naegeli H. To incise or not and where: SET-domain methyltransferases know. Trends Biochem Sci 2023; 48:321-330. [PMID: 36357311 DOI: 10.1016/j.tibs.2022.10.003] [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: 07/22/2022] [Revised: 10/10/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022]
Abstract
The concept of the histone code posits that histone modifications regulate gene functions once interpreted by epigenetic readers. A well-studied case is trimethylation of lysine 4 of histone H3 (H3K4me3), which is enriched at gene promoters. However, H3K4me3 marks are not needed for the expression of most genes, suggesting extra roles, such as influencing the 3D genome architecture. Here, we highlight an intriguing analogy between the H3K4me3-dependent induction of double-strand breaks in several recombination events and the impact of this same mark on DNA incisions for the repair of bulky lesions. We propose that Su(var)3-9, Enhancer-of-zeste and Trithorax (SET)-domain methyltransferases generate H3K4me3 to guide nucleases into chromatin spaces, the favorable accessibility of which ensures that DNA break intermediates are readily processed, thereby safeguarding genome stability.
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Affiliation(s)
- Michelle N Yancoskie
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Corina Maritz
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Patrick van Eijk
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Simon H Reed
- Institute of Cancer and Genetics, School of Medicine, Cardiff University, Cardiff, UK
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland.
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8
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Salzler HR, Vandadi V, McMichael BD, Brown JC, Boerma SA, Leatham-Jensen MP, Adams KM, Meers MP, Simon JM, Duronio RJ, McKay DJ, Matera AG. Distinct roles for canonical and variant histone H3 lysine-36 in Polycomb silencing. SCIENCE ADVANCES 2023; 9:eadf2451. [PMID: 36857457 PMCID: PMC9977188 DOI: 10.1126/sciadv.adf2451] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 01/31/2023] [Indexed: 05/26/2023]
Abstract
Polycomb complexes regulate cell type-specific gene expression programs through heritable silencing of target genes. Trimethylation of histone H3 lysine 27 (H3K27me3) is essential for this process. Perturbation of H3K36 is thought to interfere with H3K27me3. We show that mutants of Drosophila replication-dependent (H3.2K36R) or replication-independent (H3.3K36R) histone H3 genes generally maintain Polycomb silencing and reach later stages of development. In contrast, combined (H3.3K36RH3.2K36R) mutants display widespread Hox gene misexpression and fail to develop past the first larval stage. Chromatin profiling revealed that the H3.2K36R mutation disrupts H3K27me3 levels broadly throughout silenced domains, whereas these regions are mostly unaffected in H3.3K36R animals. Analysis of H3.3 distributions showed that this histone is enriched at presumptive Polycomb response elements located outside of silenced domains but relatively depleted from those inside. We conclude that H3.2 and H3.3 K36 residues collaborate to repress Hox genes using different mechanisms.
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Affiliation(s)
- Harmony R. Salzler
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Vasudha Vandadi
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Benjamin D. McMichael
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - John C. Brown
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Sally A. Boerma
- Department of Biology, Carleton College, Northfield, MN, USA
| | - Mary P. Leatham-Jensen
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Kirsten M. Adams
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Michael P. Meers
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
| | - Jeremy M. Simon
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Robert J. Duronio
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Daniel J. McKay
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - A. Gregory Matera
- Integrative Program for Biological and Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
- Department of Biology, University of North Carolina, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
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9
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Epigenetic factor competition reshapes the EMT landscape. Proc Natl Acad Sci U S A 2022; 119:e2210844119. [PMID: 36215492 PMCID: PMC9586264 DOI: 10.1073/pnas.2210844119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The emergence of and transitions between distinct phenotypes in isogenic cells can be attributed to the intricate interplay of epigenetic marks, external signals, and gene-regulatory elements. These elements include chromatin remodelers, histone modifiers, transcription factors, and regulatory RNAs. Mathematical models known as gene-regulatory networks (GRNs) are an increasingly important tool to unravel the workings of such complex networks. In such models, epigenetic factors are usually proposed to act on the chromatin regions directly involved in the expression of relevant genes. However, it has been well-established that these factors operate globally and compete with each other for targets genome-wide. Therefore, a perturbation of the activity of a regulator can redistribute epigenetic marks across the genome and modulate the levels of competing regulators. In this paper, we propose a conceptual and mathematical modeling framework that incorporates both local and global competition effects between antagonistic epigenetic regulators, in addition to local transcription factors, and show the counterintuitive consequences of such interactions. We apply our approach to recent experimental findings on the epithelial-mesenchymal transition (EMT). We show that it can explain the puzzling experimental data, as well as provide verifiable predictions.
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10
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Verma A, Arya R, Brahmachari V. Identification of a polycomb responsive region in human HoxA cluster and its long-range interaction with polycomb enriched genomic regions. Gene 2022; 845:146832. [PMID: 36007803 DOI: 10.1016/j.gene.2022.146832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 08/15/2022] [Accepted: 08/18/2022] [Indexed: 11/04/2022]
Abstract
Polycomb and Trithorax group proteins (PcG, TrxG) epigenetically regulate developmental genes. These proteins bind with specific DNA elements, the Polycomb Response Element (PRE). Apart from mutations in polycomb/ trithorax proteins, altered cis-elements like PRE underlie the modified function and thus disease etiology. PREs are well studied in Drosophila, while only a few human PREs have been reported. We have identified a polycomb responsive DNA element, hPRE-HoxA3, in the intron of the HoxA3 gene. The hPRE-HoxA3 represses luciferase reporter activity in a PcG-dependent manner. The endogenous hPRE-HoxA3 element recruits PcG proteins and is enriched with repressive H3K27me3 marks, demonstrating that hPRE-HoxA3 is a part of the PcG-dependent gene regulatory network. Furthermore, it interacts with D11-12, the well-known PRE in the human Hox cluster. hPRE-Hox3 is a part of the 3-dimensional chromosomal domain organization as it is involved in the long-range interaction with other PcG enriched regions of Hox A, B, C, and D clusters.
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Affiliation(s)
- Akanksha Verma
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi-110007, India.
| | - Richa Arya
- Current address- Cytogenetics Laboratory, Department of Zoology, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
| | - Vani Brahmachari
- Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi-110007, India
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11
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Taylor-Papadimitriou J, Burchell JM. Histone Methylases and Demethylases Regulating Antagonistic Methyl Marks: Changes Occurring in Cancer. Cells 2022; 11:1113. [PMID: 35406676 PMCID: PMC8997813 DOI: 10.3390/cells11071113] [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: 02/16/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 02/06/2023] Open
Abstract
Epigenetic regulation of gene expression is crucial to the determination of cell fate in development and differentiation, and the Polycomb (PcG) and Trithorax (TrxG) groups of proteins, acting antagonistically as complexes, play a major role in this regulation. Although originally identified in Drosophila, these complexes are conserved in evolution and the components are well defined in mammals. Each complex contains a protein with methylase activity (KMT), which can add methyl groups to a specific lysine in histone tails, histone 3 lysine 27 (H3K27), by PcG complexes, and H3K4 and H3K36 by TrxG complexes, creating transcriptionally repressive or active marks, respectively. Histone demethylases (KDMs), identified later, added a new dimension to histone methylation, and mutations or changes in levels of expression are seen in both methylases and demethylases and in components of the PcG and TrX complexes across a range of cancers. In this review, we focus on both methylases and demethylases governing the methylation state of the suppressive and active marks and consider their action and interaction in normal tissues and in cancer. A picture is emerging which indicates that the changes which occur in cancer during methylation of histone lysines can lead to repression of genes, including tumour suppressor genes, or to the activation of oncogenes. Methylases or demethylases, which are themselves tumour suppressors, are highly mutated. Novel targets for cancer therapy have been identified and a methylase (KMT6A/EZH2), which produces the repressive H3K27me3 mark, and a demethylase (KDM1A/LSD1), which demethylates the active H3K4me2 mark, are now under clinical evaluation.
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12
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Hanna CW, Huang J, Belton C, Reinhardt S, Dahl A, Andrews S, Stewart A, Kranz A, Kelsey G. OUP accepted manuscript. Nucleic Acids Res 2022; 50:1993-2004. [PMID: 35137160 PMCID: PMC8887468 DOI: 10.1093/nar/gkac051] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 01/14/2022] [Accepted: 01/25/2022] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | | | - Susanne Reinhardt
- Dresden Concept Genome Center, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, 01307, Germany
| | - Andreas Dahl
- Dresden Concept Genome Center, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, 01307, Germany
| | - Simon Andrews
- Bioinformatics Group, Babraham Institute, Cambridge CB22 3AT, UK
| | - A Francis Stewart
- Genomics, Center for Molecular and Cellular Bioengineering, Biotechnology Center, Technische Universität Dresden, 01307, Germany
- Max-Planck-Institute for Cell Biology and Genetics, Dresden 01307, Germany
| | - Andrea Kranz
- Correspondence may also be addressed to Andrea Kranz.
| | - Gavin Kelsey
- To whom correspondence should be addressed. Tel: +44 1223 496332;
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13
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Yan Y, Tian M, Li M, Zhou G, Chen Q, Xu M, Hu Y, Luo W, Guo X, Zhang C, Xie H, Wu QF, Xiong W, Liu S, Guan JS. ASH1L haploinsufficiency results in autistic-like phenotypes in mice and links Eph receptor gene to autism spectrum disorder. Neuron 2022; 110:1156-1172.e9. [DOI: 10.1016/j.neuron.2021.12.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/23/2021] [Accepted: 12/27/2021] [Indexed: 12/12/2022]
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14
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MLL1 is required for maintenance of intestinal stem cells. PLoS Genet 2021; 17:e1009250. [PMID: 34860830 PMCID: PMC8641872 DOI: 10.1371/journal.pgen.1009250] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 10/30/2021] [Indexed: 12/12/2022] Open
Abstract
Epigenetic mechanisms are gatekeepers for the gene expression patterns that establish and maintain cellular identity in mammalian development, stem cells and adult homeostasis. Amongst many epigenetic marks, methylation of histone 3 lysine 4 (H3K4) is one of the most widely conserved and occupies a central position in gene expression. Mixed lineage leukemia 1 (MLL1/KMT2A) is the founding mammalian H3K4 methyltransferase. It was discovered as the causative mutation in early onset leukemia and subsequently found to be required for the establishment of definitive hematopoiesis and the maintenance of adult hematopoietic stem cells. Despite wide expression, the roles of MLL1 in non-hematopoietic tissues remain largely unexplored. To bypass hematopoietic lethality, we used bone marrow transplantation and conditional mutagenesis to discover that the most overt phenotype in adult Mll1-mutant mice is intestinal failure. MLL1 is expressed in intestinal stem cells (ISCs) and transit amplifying (TA) cells but not in the villus. Loss of MLL1 is accompanied by loss of ISCs and a differentiation bias towards the secretory lineage with increased numbers and enlargement of goblet cells. Expression profiling of sorted ISCs revealed that MLL1 is required to promote expression of several definitive intestinal transcription factors including Pitx1, Pitx2, Foxa1, Gata4, Zfp503 and Onecut2, as well as the H3K27me3 binder, Bahcc1. These results were recapitulated using conditional mutagenesis in intestinal organoids. The stem cell niche in the crypt includes ISCs in close association with Paneth cells. Loss of MLL1 from ISCs promoted transcriptional changes in Paneth cells involving metabolic and stress responses. Here we add ISCs to the MLL1 repertoire and observe that all known functions of MLL1 relate to the properties of somatic stem cells, thereby highlighting the suggestion that MLL1 is a master somatic stem cell regulator.
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15
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Shaheen N, Akhtar J, Umer Z, Khan MHF, Bakhtiari MH, Saleem M, Faisal A, Tariq M. Polycomb Requires Chaperonin Containing TCP-1 Subunit 7 for Maintaining Gene Silencing in Drosophila. Front Cell Dev Biol 2021; 9:727972. [PMID: 34660585 PMCID: PMC8517254 DOI: 10.3389/fcell.2021.727972] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
In metazoans, heritable states of cell type-specific gene expression patterns linked with specialization of various cell types constitute transcriptional cellular memory. Evolutionarily conserved Polycomb group (PcG) and trithorax group (trxG) proteins contribute to the transcriptional cellular memory by maintaining heritable patterns of repressed and active expression states, respectively. Although chromatin structure and modifications appear to play a fundamental role in maintenance of repression by PcG, the precise targeting mechanism and the specificity factors that bind PcG complexes to defined regions in chromosomes remain elusive. Here, we report a serendipitous discovery that uncovers an interplay between Polycomb (Pc) and chaperonin containing T-complex protein 1 (TCP-1) subunit 7 (CCT7) of TCP-1 ring complex (TRiC) chaperonin in Drosophila. CCT7 interacts with Pc at chromatin to maintain repressed states of homeotic and non-homeotic targets of PcG, which supports a strong genetic interaction observed between Pc and CCT7 mutants. Depletion of CCT7 results in dissociation of Pc from chromatin and redistribution of an abundant amount of Pc in cytoplasm. We propose that CCT7 is an important modulator of Pc, which helps Pc recruitment at chromatin, and compromising CCT7 can directly influence an evolutionary conserved epigenetic network that supervises the appropriate cellular identities during development and homeostasis of an organism.
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Affiliation(s)
- Najma Shaheen
- Epigenetics and Gene Regulation Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Jawad Akhtar
- Epigenetics and Gene Regulation Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Zain Umer
- Epigenetics and Gene Regulation Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Haider Farooq Khan
- Epigenetics and Gene Regulation Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Mahnoor Hussain Bakhtiari
- Epigenetics and Gene Regulation Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Murtaza Saleem
- Department of Physics, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Amir Faisal
- Cancer Therapeutics Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Tariq
- Epigenetics and Gene Regulation Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
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16
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Shaukat A, Khan MHF, Ahmad H, Umer Z, Tariq M. Interplay Between BALL and CREB Binding Protein Maintains H3K27 Acetylation on Active Genes in Drosophila. Front Cell Dev Biol 2021; 9:740866. [PMID: 34650987 PMCID: PMC8509297 DOI: 10.3389/fcell.2021.740866] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/07/2021] [Indexed: 12/22/2022] Open
Abstract
CREB binding protein (CBP) is a multifunctional transcriptional co-activator that interacts with a variety of transcription factors and acts as a histone acetyltransferase. In Drosophila, CBP mediated acetylation of histone H3 lysine 27 (H3K27ac) is a known hallmark of gene activation regulated by trithorax group proteins (trxG). Recently, we have shown that a histone kinase Ballchen (BALL) substantially co-localizes with H3K27ac at trxG target loci and is required to maintain gene activation in Drosophila. Here, we report a previously unknown interaction between BALL and CBP, which positively regulates H3K27ac. Analysis of genome-wide binding profile of BALL and CBP reveals major overlap and their co-localization at actively transcribed genes. We show that BALL biochemically interacts with CBP and depletion of BALL results in drastic reduction in H3K27ac. Together, these results demonstrate a previously unknown synergy between BALL and CBP and reveals a potentially new pathway required to maintain gene activation during development.
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Affiliation(s)
- Ammad Shaukat
- Epigenetics and Gene Regulation Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Haider Farooq Khan
- Epigenetics and Gene Regulation Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Hina Ahmad
- Epigenetics and Gene Regulation Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Zain Umer
- Epigenetics and Gene Regulation Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Tariq
- Epigenetics and Gene Regulation Laboratory, Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
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17
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Lindehell H, Glotov A, Dorafshan E, Schwartz YB, Larsson J. The role of H3K36 methylation and associated methyltransferases in chromosome-specific gene regulation. SCIENCE ADVANCES 2021; 7:eabh4390. [PMID: 34597135 PMCID: PMC10938550 DOI: 10.1126/sciadv.abh4390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
In Drosophila, two chromosomes require special mechanisms to balance their transcriptional output to the rest of the genome. These are the male-specific lethal complex targeting the male X chromosome and Painting of fourth targeting chromosome 4. Here, we explore the role of histone H3 methylated at lysine-36 (H3K36) and the associated methyltransferases—Set2, NSD, and Ash1—in these two chromosome-specific systems. We show that the loss of Set2 impairs the MSL complex–mediated dosage compensation; however, the effect is not recapitulated by H3K36 replacement and indicates an alternative target of Set2. Unexpectedly, balanced transcriptional output from the fourth chromosome requires intact H3K36 and depends on the additive functions of NSD and Ash1. We conclude that H3K36 methylation and the associated methyltransferases are important factors to balance transcriptional output of the male X chromosome and the fourth chromosome. Furthermore, our study highlights the pleiotropic effects of these enzymes.
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Affiliation(s)
- Henrik Lindehell
- Department of Molecular Biology, Umeå University, SE-90187 Umeå, Sweden
| | - Alexander Glotov
- Department of Molecular Biology, Umeå University, SE-90187 Umeå, Sweden
| | - Eshagh Dorafshan
- Department of Molecular Biology, Umeå University, SE-90187 Umeå, Sweden
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18
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The Trithorax group protein ASH1 requires a combination of BAH domain and AT hooks, but not the SET domain, for mitotic chromatin binding and survival. Chromosoma 2021; 130:215-234. [PMID: 34331109 PMCID: PMC8426247 DOI: 10.1007/s00412-021-00762-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 07/03/2021] [Accepted: 07/06/2021] [Indexed: 11/20/2022]
Abstract
The Drosophila Trithorax group (TrxG) protein ASH1 remains associated with mitotic chromatin through mechanisms that are poorly understood. ASH1 dimethylates histone H3 at lysine 36 via its SET domain. Here, we identify domains of the TrxG protein ASH1 that are required for mitotic chromatin attachment in living Drosophila. Quantitative live imaging demonstrates that ASH1 requires AT hooks and the BAH domain but not the SET domain for full chromatin binding in metaphase, and that none of these domains are essential for interphase binding. Genetic experiments show that disruptions of the AT hooks and the BAH domain together, but not deletion of the SET domain alone, are lethal. Transcriptional profiling demonstrates that intact ASH1 AT hooks and the BAH domain are required to maintain expression levels of a specific set of genes, including several involved in cell identity and survival. This study identifies in vivo roles for specific ASH1 domains in mitotic binding, gene regulation, and survival that are distinct from its functions as a histone methyltransferase.
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19
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Zhang F, Zhao X, Jiang R, Wang Y, Wang X, Gu Y, Xu L, Ye J, Chen CD, Guo S, Zhang D, Zhao D. Identification of Jmjd3 as an Essential Epigenetic Regulator of Hox Gene Temporal Collinear Activation for Body Axial Patterning in Mice. Front Cell Dev Biol 2021; 9:642931. [PMID: 34368113 PMCID: PMC8333871 DOI: 10.3389/fcell.2021.642931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 06/23/2021] [Indexed: 11/13/2022] Open
Abstract
Body axial patterning develops via a rostral-to-caudal sequence and relies on the temporal colinear activation of Hox genes. However, the underlying mechanism of Hox gene temporal colinear activation remains largely elusive. Here, with small-molecule inhibitors and conditional gene knockout mice, we identified Jmjd3, a subunit of TrxG, as an essential regulator of temporal colinear activation of Hox genes with its H3K27me3 demethylase activity. We demonstrated that Jmjd3 not only initiates but also maintains the temporal collinear expression of Hox genes. However, we detected no antagonistic roles between Jmjd3 and Ezh2, a core subunit of PcG repressive complex 2, during the processes of axial skeletal patterning. Our findings provide new insights into the regulation of Hox gene temporal collinear activation for body axial patterning in mice.
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Affiliation(s)
- Feng Zhang
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital, Fourth Military Medical University, Xi'an, China.,Department of Pathology, Air Force Medical Center (Air Force General Hospital), Chinese People's Liberation Army, Beijing, China
| | - Xiong Zhao
- Department of Orthopedics, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Runmin Jiang
- Department of Thoracic Surgery, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - Yuying Wang
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Xinli Wang
- Department of Orthopedics, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Yu Gu
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Longyong Xu
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Jing Ye
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Charlie Degui Chen
- State Key Laboratory of Molecular Biology, Shanghai Key Laboratory of Molecular Andrology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shuangping Guo
- State Key Laboratory of Cancer Biology, Department of Pathology, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Dawei Zhang
- Department of Orthopedics, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Daqing Zhao
- Department of Otolaryngology, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
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20
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Davidovich C, Zhang Q. Allosteric regulation of histone lysine methyltransferases: from context-specific regulation to selective drugs. Biochem Soc Trans 2021; 49:591-607. [PMID: 33769454 PMCID: PMC8106495 DOI: 10.1042/bst20200238] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 02/06/2023]
Abstract
Histone lysine methyltransferases (HKMTs) are key regulators of many cellular processes. By definition, HKMTs catalyse the methylation of lysine residues in histone proteins. The enzymatic activities of HKMTs are under precise control, with their allosteric regulation emerging as a prevalent paradigm. We review the molecular mechanisms of allosteric regulation of HKMTs using well-studied histone H3 (K4, K9, K27 and K36) methyltransferases as examples. We discuss the current advances and future potential in targeting allosteric sites of HKMTs for drug development.
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Affiliation(s)
- Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
- EMBL-Australia and the ARC Centre of Excellence in Advanced Molecular Imaging, Clayton, Victoria, Australia
| | - Qi Zhang
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
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21
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Khan MHF, Akhtar J, Umer Z, Shaheen N, Shaukat A, Munir MS, Mithani A, Anwar S, Tariq M. Kinome-Wide RNAi Screen Uncovers Role of Ballchen in Maintenance of Gene Activation by Trithorax Group in Drosophila. Front Cell Dev Biol 2021; 9:637873. [PMID: 33748127 PMCID: PMC7973098 DOI: 10.3389/fcell.2021.637873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 02/15/2021] [Indexed: 12/19/2022] Open
Abstract
Polycomb group (PcG) and trithorax group (trxG) proteins are evolutionary conserved factors that contribute to cell fate determination and maintenance of cellular identities during development of multicellular organisms. The PcG maintains heritable patterns of gene silencing while trxG acts as anti-silencing factors by conserving activation of cell type specific genes. Genetic and molecular analysis has revealed extensive details about how different PcG and trxG complexes antagonize each other to maintain cell fates, however, the cellular signaling components that contribute to the preservation of gene expression by PcG/trxG remain elusive. Here, we report an ex vivo kinome-wide RNAi screen in Drosophila aimed at identifying cell signaling genes that facilitate trxG in counteracting PcG mediated repression. From the list of trxG candidates, Ballchen (BALL), a histone kinase known to phosphorylate histone H2A at threonine 119 (H2AT119p), was characterized as a trxG regulator. The ball mutant exhibits strong genetic interactions with Polycomb (Pc) and trithorax (trx) mutants and loss of BALL affects expression of trxG target genes. BALL co-localizes with Trithorax on chromatin and depletion of BALL results in increased H2AK118 ubiquitination, a histone mark central to PcG mediated gene silencing. Moreover, BALL was found to substantially associate with known TRX binding sites across the genome. Genome wide distribution of BALL also overlaps with H3K4me3 and H3K27ac at actively transcribed genes. We propose that BALL mediated signaling positively contributes to the maintenance of gene activation by trxG in counteracting the repressive effect of PcG.
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Affiliation(s)
- Muhammad Haider Farooq Khan
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Jawad Akhtar
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Zain Umer
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Najma Shaheen
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Ammad Shaukat
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Shahbaz Munir
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Aziz Mithani
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Saima Anwar
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Tariq
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, Pakistan
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22
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Grinat J, Heuberger J, Vidal RO, Goveas N, Kosel F, Berenguer-Llergo A, Kranz A, Wulf-Goldenberg A, Behrens D, Melcher B, Sauer S, Vieth M, Batlle E, Stewart AF, Birchmeier W. The epigenetic regulator Mll1 is required for Wnt-driven intestinal tumorigenesis and cancer stemness. Nat Commun 2020; 11:6422. [PMID: 33349639 PMCID: PMC7752919 DOI: 10.1038/s41467-020-20222-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 11/16/2020] [Indexed: 12/30/2022] Open
Abstract
Wnt/β-catenin signaling is crucial for intestinal carcinogenesis and the maintenance of intestinal cancer stem cells. Here we identify the histone methyltransferase Mll1 as a regulator of Wnt-driven intestinal cancer. Mll1 is highly expressed in Lgr5+ stem cells and human colon carcinomas with increased nuclear β-catenin. High levels of MLL1 are associated with poor survival of colon cancer patients. The genetic ablation of Mll1 in mice prevents Wnt/β-catenin-driven adenoma formation from Lgr5+ intestinal stem cells. Ablation of Mll1 decreases the self-renewal of human colon cancer spheres and halts tumor growth of xenografts. Mll1 controls the expression of stem cell genes including the Wnt/β-catenin target gene Lgr5. Upon the loss of Mll1, histone methylation at the stem cell promoters switches from activating H3K4 tri-methylation to repressive H3K27 tri-methylation, indicating that Mll1 sustains stem cell gene expression by antagonizing gene silencing through polycomb repressive complex 2 (PRC2)-mediated H3K27 tri-methylation. Transcriptome profiling of Wnt-mutated intestinal tumor-initiating cells reveals that Mll1 regulates Gata4/6 transcription factors, known to sustain cancer stemness and to control goblet cell differentiation. Our results demonstrate that Mll1 is an essential epigenetic regulator of Wnt/β-catenin-induced intestinal tumorigenesis and cancer stemness. Intestinal cancer stem cells (CSC) are associated with colon cancer. Here, the authors show that Wnt/beta-catenin signalling in CSC requires the epigenetic regulator Mll1 to promote stemness and tumourigenesis in murine and human colon cancer models.
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Affiliation(s)
- Johanna Grinat
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125, Berlin, Germany
| | - Julian Heuberger
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125, Berlin, Germany. .,Division of Gastroenterology and Hepatology, Medical Department, Charité University Medicine, 13353, Berlin, Germany.
| | - Ramon Oliveira Vidal
- Laboratory of Functional Genomics, Nutrigenomics and Systems Biology, Scientific Genomics Platforms, Max Delbrück Center for Molecular Medicine (BIMSB/BIH), 13092, Berlin, Germany
| | - Neha Goveas
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307, Dresden, Germany
| | - Frauke Kosel
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125, Berlin, Germany
| | - Antoni Berenguer-Llergo
- Biostatistics and Bioinformatics Unit, Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Andrea Kranz
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307, Dresden, Germany
| | | | - Diana Behrens
- Experimental Pharmacology & Oncology (EPO), 13125, Berlin, Germany
| | - Bálint Melcher
- Institute for Pathology, Klinikum Bayreuth, 95445, Bayreuth, Germany
| | - Sascha Sauer
- Laboratory of Functional Genomics, Nutrigenomics and Systems Biology, Scientific Genomics Platforms, Max Delbrück Center for Molecular Medicine (BIMSB/BIH), 13092, Berlin, Germany
| | - Michael Vieth
- Institute for Pathology, Klinikum Bayreuth, 95445, Bayreuth, Germany
| | - Eduard Batlle
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Barcelona, Spain.,ICREA, Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain
| | - A Francis Stewart
- Biotechnology Center, Center for Molecular and Cellular Bioengineering, Technische Universität Dresden, 01307, Dresden, Germany
| | - Walter Birchmeier
- Cancer Research Program, Max Delbrück Center for Molecular Medicine (MDC) in the Helmholtz Society, 13125, Berlin, Germany.
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23
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Finogenova K, Bonnet J, Poepsel S, Schäfer IB, Finkl K, Schmid K, Litz C, Strauss M, Benda C, Müller J. Structural basis for PRC2 decoding of active histone methylation marks H3K36me2/3. eLife 2020; 9:e61964. [PMID: 33211010 PMCID: PMC7725500 DOI: 10.7554/elife.61964] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/18/2020] [Indexed: 11/13/2022] Open
Abstract
Repression of genes by Polycomb requires that PRC2 modifies their chromatin by trimethylating lysine 27 on histone H3 (H3K27me3). At transcriptionally active genes, di- and tri-methylated H3K36 inhibit PRC2. Here, the cryo-EM structure of PRC2 on dinucleosomes reveals how binding of its catalytic subunit EZH2 to nucleosomal DNA orients the H3 N-terminus via an extended network of interactions to place H3K27 into the active site. Unmodified H3K36 occupies a critical position in the EZH2-DNA interface. Mutation of H3K36 to arginine or alanine inhibits H3K27 methylation by PRC2 on nucleosomes in vitro. Accordingly, Drosophila H3K36A and H3K36R mutants show reduced levels of H3K27me3 and defective Polycomb repression of HOX genes. The relay of interactions between EZH2, the nucleosomal DNA and the H3 N-terminus therefore creates the geometry that permits allosteric inhibition of PRC2 by methylated H3K36 in transcriptionally active chromatin.
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Affiliation(s)
- Ksenia Finogenova
- Max Planck Institute of Biochemistry, Laboratory of Chromatin BiologyMartinsriedGermany
| | - Jacques Bonnet
- Max Planck Institute of Biochemistry, Laboratory of Chromatin BiologyMartinsriedGermany
| | - Simon Poepsel
- California Institute for Quantitative Biology (QB3), University of California, California Institute for Quantitative Biology (QB3), Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital CologneCologneGermany
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of CologneCologneGermany
| | - Ingmar B Schäfer
- Max Planck Institute of Biochemistry, Department of Structural Cell BiologyMartinsriedGermany
| | - Katja Finkl
- Max Planck Institute of Biochemistry, Laboratory of Chromatin BiologyMartinsriedGermany
| | - Katharina Schmid
- Max Planck Institute of Biochemistry, Laboratory of Chromatin BiologyMartinsriedGermany
| | - Claudia Litz
- Max Planck Institute of Biochemistry, Laboratory of Chromatin BiologyMartinsriedGermany
| | - Mike Strauss
- Max Planck Institute of Biochemistry, cryoEM FacilityMartinsriedGermany
| | - Christian Benda
- Max Planck Institute of Biochemistry, Department of Structural Cell BiologyMartinsriedGermany
| | - Jürg Müller
- Max Planck Institute of Biochemistry, Laboratory of Chromatin BiologyMartinsriedGermany
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24
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Cui LX, Tian YQ, Hao HS, Zou HY, Pang YW, Zhao SJ, Zhao XM, Zhu HB, Du WH. Knockdown of ASH1L methyltransferase induced apoptosis inhibiting proliferation and H3K36 methylation in bovine cumulus cells. Theriogenology 2020; 161:65-73. [PMID: 33296745 DOI: 10.1016/j.theriogenology.2020.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/11/2020] [Accepted: 11/14/2020] [Indexed: 12/19/2022]
Abstract
This study aims to investigate the expression and function of absent, small, or homeotic 1-like (ASH1L) methyltransferase in bovine cumulus cells in order to reveal by which mechanisms ASH1L regulates epigenetic modification and apoptosis in cumulus cells. The location of ASH1L and the methylation pattern of H3K36 were detected using immunofluorescence staining in cumulus cells. Quantitative PCR (qPCR) and western blotting were used to screen for effective siRNA targeting the ASH1L gene. Also, the mRNA expression levels of apoptosis-related genes and polycomb inhibitory complex genes were estimated by qPCR after knocking down the ASH1L gene in bovine cumulus cells. Cell proliferation and apoptosis were measured with the CCK-8 method and Annexin V-FITC by flow cytometry, respectively. The results of immunofluorescence analysis showed that ASH1L is located in the nucleus of bovine cumulus cells and is distributed in a dotted pattern. ASH1L knockdown in cumulus cells induced a decrease in the levels of H3K36me1/2/3 methylation (P < 0.05). Additionally, ASH1L knockdown inhibited cell proliferation, increased the apoptosis rate, and upregulated the expression of apoptosis genes CASPASE-3, BAX and BAX/BCL-2 ratio (P < 0.05). Meanwhile, the mRNA expression levels of EZH2 and SUZ12, two subunits of PRC2 protein, were increased in cells with ASH1L knockdown (P < 0.05). Therefore, the expression of ASH1L methyltransferase and its function in on the apoptosis of bovine cumulus cells were first studied. The mechanism by which ASH1L regulates the histone methylation and apoptosis in cumulus cells was also revealed.
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Affiliation(s)
- Li-Xin Cui
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ya-Qing Tian
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hai-Sheng Hao
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hui-Ying Zou
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yun-Wei Pang
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shan-Jiang Zhao
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xue-Ming Zhao
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Hua-Bin Zhu
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wei-Hua Du
- Embryo Biotechnology and Reproduction Laboratory, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
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25
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Ridenour JB, Möller M, Freitag M. Polycomb Repression without Bristles: Facultative Heterochromatin and Genome Stability in Fungi. Genes (Basel) 2020; 11:E638. [PMID: 32527036 PMCID: PMC7348808 DOI: 10.3390/genes11060638] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 05/27/2020] [Accepted: 06/04/2020] [Indexed: 02/06/2023] Open
Abstract
Genome integrity is essential to maintain cellular function and viability. Consequently, genome instability is frequently associated with dysfunction in cells and associated with plant, animal, and human diseases. One consequence of relaxed genome maintenance that may be less appreciated is an increased potential for rapid adaptation to changing environments in all organisms. Here, we discuss evidence for the control and function of facultative heterochromatin, which is delineated by methylation of histone H3 lysine 27 (H3K27me) in many fungi. Aside from its relatively well understood role in transcriptional repression, accumulating evidence suggests that H3K27 methylation has an important role in controlling the balance between maintenance and generation of novelty in fungal genomes. We present a working model for a minimal repressive network mediated by H3K27 methylation in fungi and outline challenges for future research.
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Affiliation(s)
| | | | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis OR 97331, USA; (J.B.R.); (M.M.)
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26
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Gsell C, Richly H, Coin F, Naegeli H. A chromatin scaffold for DNA damage recognition: how histone methyltransferases prime nucleosomes for repair of ultraviolet light-induced lesions. Nucleic Acids Res 2020; 48:1652-1668. [PMID: 31930303 PMCID: PMC7038933 DOI: 10.1093/nar/gkz1229] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/18/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
The excision of mutagenic DNA adducts by the nucleotide excision repair (NER) pathway is essential for genome stability, which is key to avoiding genetic diseases, premature aging, cancer and neurologic disorders. Due to the need to process an extraordinarily high damage density embedded in the nucleosome landscape of chromatin, NER activity provides a unique functional caliper to understand how histone modifiers modulate DNA damage responses. At least three distinct lysine methyltransferases (KMTs) targeting histones have been shown to facilitate the detection of ultraviolet (UV) light-induced DNA lesions in the difficult to access DNA wrapped around histones in nucleosomes. By methylating core histones, these KMTs generate docking sites for DNA damage recognition factors before the chromatin structure is ultimately relaxed and the offending lesions are effectively excised. In view of their function in priming nucleosomes for DNA repair, mutations of genes coding for these KMTs are expected to cause the accumulation of DNA damage promoting cancer and other chronic diseases. Research on the question of how KMTs modulate DNA repair might pave the way to the development of pharmacologic agents for novel therapeutic strategies.
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Affiliation(s)
- Corina Gsell
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Winterthurerstrasse 260, 8057 Zurich, Switzerland
| | - Holger Richly
- Boehringer Ingelheim Pharma, Department of Molecular Biology, Birkendorfer Str. 65, 88397 Biberach an der Riß, Germany
| | - Frédéric Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Winterthurerstrasse 260, 8057 Zurich, Switzerland
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27
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Abstract
Trithorax histone methyltransferase Ash1/ASH1L is tightly regulated because it activates developmental gene transcription and counteracts Polycomb silencing. In this issue of Structure, Lee et al. (2019) and Hou et al. (2019) report the crystal structure of ASH1L bound to its activator MRG15 and suggest a mechanism that releases ASH1L auto-inhibition.
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28
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Bredesen BA, Rehmsmeier M. DNA sequence models of genome-wide Drosophila melanogaster Polycomb binding sites improve generalization to independent Polycomb Response Elements. Nucleic Acids Res 2019; 47:7781-7797. [PMID: 31340029 PMCID: PMC6735708 DOI: 10.1093/nar/gkz617] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 07/01/2019] [Accepted: 07/11/2019] [Indexed: 12/12/2022] Open
Abstract
Polycomb Response Elements (PREs) are cis-regulatory DNA elements that maintain gene transcription states through DNA replication and mitosis. PREs have little sequence similarity, but are enriched in a number of sequence motifs. Previous methods for modelling Drosophila melanogaster PRE sequences (PREdictor and EpiPredictor) have used a set of 7 motifs and a training set of 12 PREs and 16-23 non-PREs. Advances in experimental methods for mapping chromatin binding factors and modifications has led to the publication of several genome-wide sets of Polycomb targets. In addition to the seven motifs previously used, PREs are enriched in the GTGT motif, recently associated with the sequence-specific DNA binding protein Combgap. We investigated whether models trained on genome-wide Polycomb sites generalize to independent PREs when trained with control sequences generated by naive PRE models and including the GTGT motif. We also developed a new PRE predictor: SVM-MOCCA. Training PRE predictors with genome-wide experimental data improves generalization to independent data, and SVM-MOCCA predicts the majority of PREs in three independent experimental sets. We present 2908 candidate PREs enriched in sequence and chromatin signatures. 2412 of these are also enriched in H3K4me1, a mark of Trithorax activated chromatin, suggesting that PREs/TREs have a common sequence code.
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Affiliation(s)
- Bjørn André Bredesen
- Computational Biology Unit, Department of Informatics, University of Bergen, P.O. Box 7803, N-5020 Bergen, Norway
| | - Marc Rehmsmeier
- Computational Biology Unit, Department of Informatics, University of Bergen, P.O. Box 7803, N-5020 Bergen, Norway.,Integrated Research Institute (IRI) for the Life Sciences and Department of Biology, Humboldt-Universität zu Berlin, Unter den Linden 6, 10099 Berlin, Germany
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29
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Wissink EM, Vihervaara A, Tippens ND, Lis JT. Nascent RNA analyses: tracking transcription and its regulation. Nat Rev Genet 2019; 20:705-723. [PMID: 31399713 PMCID: PMC6858503 DOI: 10.1038/s41576-019-0159-6] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/04/2019] [Indexed: 12/19/2022]
Abstract
The programmes that direct an organism's development and maintenance are encoded in its genome. Decoding of this information begins with regulated transcription of genomic DNA into RNA. Although transcription and its control can be tracked indirectly by measuring stable RNAs, it is only by directly measuring nascent RNAs that the immediate regulatory changes in response to developmental, environmental, disease and metabolic signals are revealed. Multiple complementary methods have been developed to quantitatively track nascent transcription genome-wide at nucleotide resolution, all of which have contributed novel insights into the mechanisms of gene regulation and transcription-coupled RNA processing. Here we critically evaluate the array of strategies used for investigating nascent transcription and discuss the recent conceptual advances they have provided.
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Affiliation(s)
- Erin M Wissink
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Anniina Vihervaara
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
| | - Nathaniel D Tippens
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA
- Tri-Institutional Training Program in Computational Biology and Medicine, New York, NY, USA
| | - John T Lis
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
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30
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Genetic Dissection Reveals the Role of Ash1 Domains in Counteracting Polycomb Repression. G3-GENES GENOMES GENETICS 2019; 9:3801-3812. [PMID: 31540973 PMCID: PMC6829142 DOI: 10.1534/g3.119.400579] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Antagonistic functions of Polycomb and Trithorax proteins are essential for proper development of all metazoans. While the Polycomb proteins maintain the repressed state of many key developmental genes, the Trithorax proteins ensure that these genes stay active in cells where they have to be expressed. Ash1 is the Trithorax protein that was proposed to counteract Polycomb repression by methylating lysine 36 of histone H3. However, it was recently shown that genetic replacement of Drosophila histone H3 with the variant that carried Arginine instead of Lysine at position 36 did not impair the ability of Ash1 to counteract Polycomb repression. This argues that Ash1 counteracts Polycomb repression by methylating yet unknown substrate(s) and that it is time to look beyond Ash1 methyltransferase SET domain, at other evolutionary conserved parts of the protein that received little attention. Here we used Drosophila genetics to demonstrate that Ash1 requires each of the BAH, PHD and SET domains to counteract Polycomb repression, while AT hooks are dispensable. Our findings argue that, in vivo, Ash1 acts as a multimer. Thereby it can combine the input of the SET domain and PHD-BAH cassette residing in different peptides. Finally, using new loss of function alleles, we show that zygotic Ash1 is required to prevent erroneous repression of homeotic genes of the bithorax complex in the embryo.
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31
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Rougeot J, Chrispijn ND, Aben M, Elurbe DM, Andralojc KM, Murphy PJ, Jansen PWTC, Vermeulen M, Cairns BR, Kamminga LM. Maintenance of spatial gene expression by Polycomb-mediated repression after formation of a vertebrate body plan. Development 2019; 146:dev.178590. [PMID: 31488564 PMCID: PMC6803366 DOI: 10.1242/dev.178590] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 08/26/2019] [Indexed: 12/22/2022]
Abstract
Polycomb group (PcG) proteins are transcriptional repressors that are important regulators of cell fate during embryonic development. Among them, Ezh2 is responsible for catalyzing the epigenetic repressive mark H3K27me3 and is essential for animal development. The ability of zebrafish embryos lacking both maternal and zygotic ezh2 to form a normal body plan provides a unique model for comprehensively studying Ezh2 function during early development in vertebrates. By using a multi-omics approach, we found that Ezh2 is required for the deposition of H3K27me3 and is essential for proper recruitment of Polycomb group protein Rnf2. However, despite the complete absence of PcG-associated epigenetic mark and proteins, only minor changes in H3K4me3 deposition and gene and protein expression occur. These changes were mainly due to local dysregulation of transcription factors outside their normal expression boundaries. Altogether, our results in zebrafish show that Polycomb-mediated gene repression is important immediately after the body plan is formed to maintain spatially restricted expression profiles of transcription factors, and we highlight the differences that exist in the timing of PcG protein action between vertebrate species. Summary: Our unique zebrafish model of a maternal and zygotic mutant for the Polycomb group gene ezh2 reveals major conserved and divergent mechanisms in epigenetic gene repression during vertebrate development.
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Affiliation(s)
- Julien Rougeot
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Nijmegen 6525 GA, The Netherlands .,Radboud University Medical Center, Department of Molecular Biology, Nijmegen 6525 GA, The Netherlands
| | - Naomi D Chrispijn
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Nijmegen 6525 GA, The Netherlands
| | - Marco Aben
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Nijmegen 6525 GA, The Netherlands.,Radboud University Medical Center, Department of Molecular Biology, Nijmegen 6525 GA, The Netherlands
| | - Dei M Elurbe
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Nijmegen 6525 GA, The Netherlands.,Radboud University Medical Center, Department of Molecular Biology, Nijmegen 6525 GA, The Netherlands
| | - Karolina M Andralojc
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Nijmegen 6525 GA, The Netherlands
| | - Patrick J Murphy
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.,Wilmot Cancer Institute, Rochester Center for Biomedical Informatics, University of Rochester Medical Center, Rochester, NY 14642, USA
| | - Pascal W T C Jansen
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Oncode Institute, Nijmegen 6525 GA, The Netherlands
| | - Michiel Vermeulen
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Oncode Institute, Nijmegen 6525 GA, The Netherlands
| | - Bradley R Cairns
- Howard Hughes Medical Institute, Department of Oncological Sciences and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Leonie M Kamminga
- Radboud University, Faculty of Science, Department of Molecular Biology, Radboud Institute for Molecular Life Sciences, Nijmegen 6525 GA, The Netherlands .,Radboud University Medical Center, Department of Molecular Biology, Nijmegen 6525 GA, The Netherlands
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32
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Umer Z, Akhtar J, Khan MHF, Shaheen N, Haseeb MA, Mazhar K, Mithani A, Anwar S, Tariq M. Genome-wide RNAi screen in Drosophila reveals Enok as a novel trithorax group regulator. Epigenetics Chromatin 2019; 12:55. [PMID: 31547845 PMCID: PMC6757429 DOI: 10.1186/s13072-019-0301-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 09/03/2019] [Indexed: 12/17/2022] Open
Abstract
Background Polycomb group (PcG) and trithorax group (trxG) proteins contribute to the specialization of cell types by maintaining differential gene expression patterns. Initially discovered as positive regulators of HOX genes in forward genetic screens, trxG counteracts PcG-mediated repression of cell type-specific genes. Despite decades of extensive analysis, molecular understanding of trxG action and regulation are still punctuated by many unknowns. This study aimed at discovering novel factors that elicit an anti-silencing effect to facilitate trxG-mediated gene activation. Results We have developed a cell-based reporter system and performed a genome-wide RNAi screen to discover novel factors involved in trxG-mediated gene regulation in Drosophila. We identified more than 200 genes affecting the reporter in a manner similar to trxG genes. From the list of top candidates, we have characterized Enoki mushroom (Enok), a known histone acetyltransferase, as an important regulator of trxG in Drosophila. Mutants of enok strongly suppressed extra sex comb phenotype of Pc mutants and enhanced homeotic transformations associated with trx mutations. Enok colocalizes with both TRX and PC at chromatin. Moreover, depletion of Enok specifically resulted in an increased enrichment of PC and consequently silencing of trxG targets. This downregulation of trxG targets was also accompanied by a decreased occupancy of RNA-Pol-II in the gene body, correlating with an increased stalling at the transcription start sites of these genes. We propose that Enok facilitates trxG-mediated maintenance of gene activation by specifically counteracting PcG-mediated repression. Conclusion Our ex vivo approach led to identification of new trxG candidate genes that warrant further investigation. Presence of chromatin modifiers as well as known members of trxG and their interactors in the genome-wide RNAi screen validated our reverse genetics approach. Genetic and molecular characterization of Enok revealed a hitherto unknown interplay between Enok and PcG/trxG system. We conclude that histone acetylation by Enok positively impacts the maintenance of trxG-regulated gene activation by inhibiting PRC1-mediated transcriptional repression.
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Affiliation(s)
- Zain Umer
- Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan
| | - Jawad Akhtar
- Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan
| | - Muhammad Haider Farooq Khan
- Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan
| | - Najma Shaheen
- Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan
| | - Muhammad Abdul Haseeb
- Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan
| | - Khalida Mazhar
- Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan
| | - Aziz Mithani
- Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan
| | - Saima Anwar
- Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan.,Biomedical Engineering Centre, University of Engineering and Technology Lahore, KSK Campus, Lahore, Pakistan
| | - Muhammad Tariq
- Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan.
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33
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Roles and regulation of histone methylation in animal development. Nat Rev Mol Cell Biol 2019; 20:625-641. [PMID: 31267065 DOI: 10.1038/s41580-019-0151-1] [Citation(s) in RCA: 302] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2019] [Indexed: 12/26/2022]
Abstract
Histone methylation can occur at various sites in histone proteins, primarily on lysine and arginine residues, and it can be governed by multiple positive and negative regulators, even at a single site, to either activate or repress transcription. It is now apparent that histone methylation is critical for almost all stages of development, and its proper regulation is essential for ensuring the coordinated expression of gene networks that govern pluripotency, body patterning and differentiation along appropriate lineages and organogenesis. Notably, developmental histone methylation is highly dynamic. Early embryonic systems display unique histone methylation patterns, prominently including the presence of bivalent (both gene-activating and gene-repressive) marks at lineage-specific genes that resolve to monovalent marks during differentiation, which ensures that appropriate genes are expressed in each tissue type. Studies of the effects of methylation on embryonic stem cell pluripotency and differentiation have helped to elucidate the developmental roles of histone methylation. It has been revealed that methylation and demethylation of both activating and repressive marks are essential for establishing embryonic and extra-embryonic lineages, for ensuring gene dosage compensation via genomic imprinting and for establishing body patterning via HOX gene regulation. Not surprisingly, aberrant methylation during embryogenesis can lead to defects in body patterning and in the development of specific organs. Human genetic disorders arising from mutations in histone methylation regulators have revealed their important roles in the developing skeletal and nervous systems, and they highlight the overlapping and unique roles of different patterns of methylation in ensuring proper development.
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34
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Asada S, Fujino T, Goyama S, Kitamura T. The role of ASXL1 in hematopoiesis and myeloid malignancies. Cell Mol Life Sci 2019; 76:2511-2523. [PMID: 30927018 PMCID: PMC11105736 DOI: 10.1007/s00018-019-03084-7] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Revised: 03/18/2019] [Accepted: 03/25/2019] [Indexed: 12/19/2022]
Abstract
Recent high-throughput genome-wide sequencing studies have identified recurrent somatic mutations in myeloid neoplasms. An epigenetic regulator, Additional sex combs-like 1 (ASXL1), is one of the most frequently mutated genes in all subtypes of myeloid malignancies. ASXL1 mutations are also frequently detected in clonal hematopoiesis, which is associated with an increased risk of mortality. Therefore, it is important to understand how ASXL1 mutations contribute to clonal expansion and myeloid transformation in hematopoietic cells. Studies using ASXL1-depleted human hematopoietic cells and Asxl1 knockout mice have shown that deletion of wild-type ASXL1 protein leads to impaired hematopoiesis and accelerates myeloid malignancies via loss of interaction with polycomb repressive complex 2 proteins. On the other hand, ASXL1 mutations in myeloid neoplasms typically occur near the last exon and result in the expression of C-terminally truncated mutant ASXL1 protein. Biological studies and biochemical analyses of this variant have shed light on its dominant-negative and gain-of-function features in myeloid transformation via a variety of epigenetic changes. Based on these results, it would be possible to establish novel promising therapeutic strategies for myeloid malignancies harboring ASXL1 mutations by blocking interactions between ASXL1 and associating epigenetic regulators. Here, we summarize the clinical implications of ASXL1 mutations, the role of wild-type ASXL1 in normal hematopoiesis, and oncogenic functions of mutant ASXL1 in myeloid neoplasms.
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Affiliation(s)
- Shuhei Asada
- Division of Cellular Therapy, Advanced Clinical Research Center, and Division of Stem Cell Signaling, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 1088639, Japan
| | - Takeshi Fujino
- Division of Cellular Therapy, Advanced Clinical Research Center, and Division of Stem Cell Signaling, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 1088639, Japan
| | - Susumu Goyama
- Division of Cellular Therapy, Advanced Clinical Research Center, and Division of Stem Cell Signaling, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 1088639, Japan
| | - Toshio Kitamura
- Division of Cellular Therapy, Advanced Clinical Research Center, and Division of Stem Cell Signaling, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo, 1088639, Japan.
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35
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Cabianca DS, Muñoz-Jiménez C, Kalck V, Gaidatzis D, Padeken J, Seeber A, Askjaer P, Gasser SM. Active chromatin marks drive spatial sequestration of heterochromatin in C. elegans nuclei. Nature 2019; 569:734-739. [PMID: 31118512 DOI: 10.1038/s41586-019-1243-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 04/29/2019] [Indexed: 12/22/2022]
Abstract
The execution of developmental programs of gene expression requires an accurate partitioning of the genome into subnuclear compartments, with active euchromatin enriched centrally and silent heterochromatin at the nuclear periphery1. The existence of degenerative diseases linked to lamin A mutations suggests that perinuclear binding of chromatin contributes to cell-type integrity2,3. The methylation of lysine 9 of histone H3 (H3K9me) characterizes heterochromatin and mediates both transcriptional repression and chromatin anchoring at the inner nuclear membrane4. In Caenorhabditis elegans embryos, chromodomain protein CEC-4 bound to the inner nuclear membrane tethers heterochromatin through H3K9me3,5, whereas in differentiated tissues, a second heterochromatin-sequestering pathway is induced. Here we use an RNA interference screen in the cec-4 background and identify MRG-1 as a broadly expressed factor that is necessary for this second chromatin anchor in intestinal cells. However, MRG-1 is exclusively bound to euchromatin, suggesting that it acts indirectly. Heterochromatin detachment in double mrg-1; cec-4 mutants is rescued by depleting the histone acetyltransferase CBP-1/p300 or the transcription factor ATF-8, a member of the bZIP family (which is known to recruit CBP/p300). Overexpression of CBP-1 in cec-4 mutants is sufficient to delocalize heterochromatin in an ATF-8-dependent manner. CBP-1 and H3K27ac levels increase in heterochromatin upon mrg-1 knockdown, coincident with delocalization. This suggests that the spatial organization of chromatin in C. elegans is regulated both by the direct perinuclear attachment of silent chromatin, and by an active retention of CBP-1/p300 in euchromatin. The two pathways contribute differentially in embryos and larval tissues, with CBP-1 sequestration by MRG-1 having a major role in differentiated cells.
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Affiliation(s)
- Daphne S Cabianca
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Celia Muñoz-Jiménez
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Seville, Spain
| | - Véronique Kalck
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Dimos Gaidatzis
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Jan Padeken
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Andrew Seeber
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.,Faculty of Natural Sciences, University of Basel, Basel, Switzerland.,Center for Advanced Imaging, Harvard University, Cambridge, MA, USA
| | - Peter Askjaer
- Andalusian Center for Developmental Biology (CABD), Consejo Superior de Investigaciones Científicas, Universidad Pablo de Olavide, Seville, Spain
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland. .,Faculty of Natural Sciences, University of Basel, Basel, Switzerland.
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36
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Brand M, Nakka K, Zhu J, Dilworth FJ. Polycomb/Trithorax Antagonism: Cellular Memory in Stem Cell Fate and Function. Cell Stem Cell 2019; 24:518-533. [PMID: 30951661 PMCID: PMC6866673 DOI: 10.1016/j.stem.2019.03.005] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Stem cells are continuously challenged with the decision to either self-renew or adopt a new fate. Self-renewal is regulated by a system of cellular memory, which must be bypassed for differentiation. Previous studies have identified Polycomb group (PcG) and Trithorax group (TrxG) proteins as key modulators of cellular memory. In this Perspective, we draw from embryonic and adult stem cell studies to discuss the complex roles played by PcG and TrxG in maintaining cell identity while allowing for microenvironment-mediated alterations in cell fate. Finally, we discuss the potential for targeting these proteins as a therapeutic approach in cancer.
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Affiliation(s)
- Marjorie Brand
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada K1H 8L6; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada K1H 8L6.
| | - Kiran Nakka
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada K1H 8L6; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada K1H 8L6
| | - Jiayu Zhu
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada K1H 8L6; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada K1H 8L6
| | - F Jeffrey Dilworth
- Sprott Center for Stem Cell Research, Ottawa Hospital Research Institute, Ottawa, ON, Canada K1H 8L6; Department of Cellular and Molecular Medicine, University of Ottawa, Ottawa, ON, Canada K1H 8L6.
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37
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Dorafshan E, Kahn TG, Glotov A, Savitsky M, Walther M, Reuter G, Schwartz YB. Ash1 counteracts Polycomb repression independent of histone H3 lysine 36 methylation. EMBO Rep 2019; 20:embr.201846762. [PMID: 30833342 DOI: 10.15252/embr.201846762] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 01/31/2019] [Accepted: 02/05/2019] [Indexed: 12/11/2022] Open
Abstract
Polycomb repression is critical for metazoan development. Equally important but less studied is the Trithorax system, which safeguards Polycomb target genes from the repression in cells where they have to remain active. It was proposed that the Trithorax system acts via methylation of histone H3 at lysine 4 and lysine 36 (H3K36), thereby inhibiting histone methyltransferase activity of the Polycomb complexes. Here we test this hypothesis by asking whether the Trithorax group protein Ash1 requires H3K36 methylation to counteract Polycomb repression. We show that Ash1 is the only Drosophila H3K36-specific methyltransferase necessary to prevent excessive Polycomb repression of homeotic genes. Unexpectedly, our experiments reveal no correlation between the extent of H3K36 methylation and the resistance to Polycomb repression. Furthermore, we find that complete substitution of the zygotic histone H3 with a variant in which lysine 36 is replaced by arginine does not cause excessive repression of homeotic genes. Our results suggest that the model, where the Trithorax group proteins methylate histone H3 to inhibit the histone methyltransferase activity of the Polycomb complexes, needs revision.
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Affiliation(s)
| | - Tatyana G Kahn
- Department of Molecular Biology, Umeå University, Umeå, Sweden
| | | | | | - Matthias Walther
- Institute of Developmental Genetics, Martin-Luther University of Halle-Wittenberg, Halle, Germany.,Max Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Gunter Reuter
- Institute of Developmental Genetics, Martin-Luther University of Halle-Wittenberg, Halle, Germany
| | - Yuri B Schwartz
- Department of Molecular Biology, Umeå University, Umeå, Sweden
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Hou P, Huang C, Liu CP, Yang N, Yu T, Yin Y, Zhu B, Xu RM. Structural Insights into Stimulation of Ash1L's H3K36 Methyltransferase Activity through Mrg15 Binding. Structure 2019; 27:837-845.e3. [PMID: 30827843 DOI: 10.1016/j.str.2019.01.015] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/01/2019] [Accepted: 01/28/2019] [Indexed: 12/18/2022]
Abstract
The evolutionarily conserved Trithorax group protein Ash1 is a SET domain histone methyltransferase that mono- and dimethylates lysine 36 of histone H3 (H3K36). Ash1 forms a complex with Mrg15 and Nurf55, and the binding of Mrg15 greatly stimulates the catalytic activity of Ash1, yet the underlying molecular mechanisms remain unknown. Here we report the crystal structure of the tandem Mrg15-interacting and SET domains of human Ash1L in complex with Mrg15. Ash1L interacts with Mrg15 principally via a segment located N-terminal to the catalytic SET domain. Surprisingly, an autoinhibitory loop in the post-SET region of Ash1L is destabilized on Mrg15 binding despite no direct contact. Dynamics of the autoinhibitory loop can be attributed to subtle structural changes of the S-adenosylmethionine (SAM) binding pocket induced by Mrg15 binding, implicating a mechanism of conformational coupling between SAM and substrate binding sites. The findings broaden the understanding of regulation of H3K36 methyltransferases.
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Affiliation(s)
- Peini Hou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 10049, China
| | - Chang Huang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chao-Pei Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Na Yang
- State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy and Tianjin Key Laboratory of Molecular Drug Research, Nankai University, Tianjin 300353, China
| | - Tianshu Yu
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Yuxin Yin
- Institute of Systems Biomedicine, Department of Pathology, School of Basic Medical Sciences, Peking-Tsinghua Center for Life Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Bing Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 10049, China.
| | - Rui-Ming Xu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 10049, China.
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39
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Castiglioni I, Caccia R, Garcia-Manteiga JM, Ferri G, Caretti G, Molineris I, Nishioka K, Gabellini D. The Trithorax protein Ash1L promotes myoblast fusion by activating Cdon expression. Nat Commun 2018; 9:5026. [PMID: 30487570 PMCID: PMC6262021 DOI: 10.1038/s41467-018-07313-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Accepted: 10/24/2018] [Indexed: 12/17/2022] Open
Abstract
Myoblast fusion (MF) is required for muscle growth and repair, and its alteration contributes to muscle diseases. The mechanisms governing this process are incompletely understood, and no epigenetic regulator has been previously described. Ash1L is an epigenetic activator belonging to the Trithorax group of proteins and is involved in FSHD muscular dystrophy, autism and cancer. Its physiological role in skeletal muscle is unknown. Here we report that Ash1L expression is positively correlated with MF and reduced in Duchenne muscular dystrophy. In vivo, ex vivo and in vitro experiments support a selective and evolutionary conserved requirement for Ash1L in MF. RNA- and ChIP-sequencing indicate that Ash1L is required to counteract Polycomb repressive activity to allow activation of selected myogenesis genes, in particular the key MF gene Cdon. Our results promote Ash1L as an important epigenetic regulator of MF and suggest that its activity could be targeted to improve cell therapy for muscle diseases. Myoblast fusion in skeletal muscle is a complex process but how this is regulated is unclear. Here, the authors identify Ash1L, a histone methyltransferase, as modulating myoblast fusion via activation of the myogenesis gene Cdon, and observe decreased Ash1L expression in Duchenne muscular dystrophy.
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Affiliation(s)
- Ilaria Castiglioni
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milano, 20132, Italy
| | - Roberta Caccia
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milano, 20132, Italy
| | - Jose Manuel Garcia-Manteiga
- Center for Translational Genomics and BioInformatics, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milano, 20132, Italy
| | - Giulia Ferri
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milano, 20132, Italy
| | - Giuseppina Caretti
- Department of Biosciences, University of Milan, via Celoria 26, Milano, 20133, Italy
| | - Ivan Molineris
- Center for Translational Genomics and BioInformatics, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milano, 20132, Italy
| | - Kenichi Nishioka
- Department of Biomolecular Sciences, Division of Molecular Genetics and Epigenetics, Faculty of Medicine, Saga University, Saga, Japan.,Laboratory for Developmental Genetics, RIKEN IMS, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa, 230-0045, Japan
| | - Davide Gabellini
- Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, via Olgettina 60, Milano, 20132, Italy.
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40
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Bicocca VT, Ormsby T, Adhvaryu KK, Honda S, Selker EU. ASH1-catalyzed H3K36 methylation drives gene repression and marks H3K27me2/3-competent chromatin. eLife 2018; 7:41497. [PMID: 30468429 PMCID: PMC6251624 DOI: 10.7554/elife.41497] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 10/31/2018] [Indexed: 12/31/2022] Open
Abstract
Methylation of histone H3 at lysine 36 (H3K36me), a widely-distributed chromatin mark, largely results from association of the lysine methyltransferase (KMT) SET-2 with RNA polymerase II (RNAPII), but most eukaryotes also have additional H3K36me KMTs that act independently of RNAPII. These include the orthologs of ASH1, which are conserved in animals, plants, and fungi but whose function and control are poorly understood. We found that Neurospora crassa has just two H3K36 KMTs, ASH1 and SET-2, and were able to explore the function and distribution of each enzyme independently. While H3K36me deposited by SET-2 marks active genes, inactive genes are modified by ASH1 and its activity is critical for their repression. ASH1-marked chromatin can be further modified by methylation of H3K27, and ASH1 catalytic activity modulates the accumulation of H3K27me2/3 both positively and negatively. These findings provide new insight into ASH1 function, H3K27me2/3 establishment, and repression in facultative heterochromatin. Not all genes in a cell’s DNA are active all the time. There are several ways to control this activity. One is by altering how the DNA is packaged into cells. DNA strands are wrapped around proteins called histones to form nucleosomes. Nucleosomes can then be packed together tightly, to restrict access to the DNA at genes that are not active, or loosely to allow access to the DNA of active genes. Chemical marks, such as methyl groups, can be attached to particular sites on histones to influence how they pack together. One important site for such marks is known as position 36 on histone H3, or H3K36 for short. Correctly adding methyl groups to this site is critical for normal development, and when this process goes wrong it can lead to diseases like cancer. An enzyme called SET-2 oversees the methylation of H3K36 in fungi, plants and animals. However, many species have several other enzymes that can also add methyl groups to H3K36, and their roles are less clear. A type of fungus called Neurospora crassa contains just two enzymes that can add methyl groups to H3K36: SET-2, and another enzyme called ASH1. By performing experiments that inactivated SET-2 and ASH1 in this fungus, Bicocca et al. found that each enzyme works on a different set of genes. Genes in regions marked by SET-2 were accessible for the cell to use, while genes marked by ASH1 were inaccessible. ASH1 also affects whether a methyl group is added to another site on histone H3. This mark is important for controlling the activity of genes that are critical for development. ASH1 is found in many other organisms, including humans. The results presented by Bicocca et al. could therefore be built upon to understand the more complicated systems for regulating H3K36 methylation in other species. From there, we can investigate how to intervene when things go wrong during developmental disorders and cancer.
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Affiliation(s)
- Vincent T Bicocca
- Institute of Molecular Biology, University of Oregon, Eugene, United States
| | - Tereza Ormsby
- Department of Biochemistry Faculty of Science, Charles University, Prague, Czech Republic
| | | | - Shinji Honda
- Faculty of Medical Sciences, University of Fukui, Fukui, Japan
| | - Eric U Selker
- Institute of Molecular Biology, University of Oregon, Eugene, United States
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41
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Kreher J, Takasaki T, Cockrum C, Sidoli S, Garcia BA, Jensen ON, Strome S. Distinct Roles of Two Histone Methyltransferases in Transmitting H3K36me3-Based Epigenetic Memory Across Generations in Caenorhabditis elegans. Genetics 2018; 210:969-982. [PMID: 30217796 PMCID: PMC6218224 DOI: 10.1534/genetics.118.301353] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 09/04/2018] [Indexed: 02/07/2023] Open
Abstract
Epigenetic information contributes to proper gene expression and development, and can be transmitted not only through mitotic divisions but also from parents to progeny. We investigated the roles in epigenetic inheritance of MES-4 and MET-1, the two Caenorhabditis elegans enzymes that methylate H3K36 (histone H3 Lys 36). Mass spectrometry analysis confirmed immunostaining results showing that both MES-4 and MET-1 catalyze H3K36me3. In the adult germline, MES-4 is enriched in the distal mitotic zone and MET-1 is enriched in the meiotic pachytene zone. Embryos inherit H3K36me3-marked chromosomes from both the oocyte and sperm, and a maternal load of MES-4 and MET-1 Maternal MES-4 quickly associates with sperm chromosomes; that association requires that the sperm chromosomes bear H3K36me3, suggesting that MES-4 is recruited to chromosomes by preexisting H3K36me3. In embryos that inherit H3K36me3-positive oocyte chromosomes and H3K36me3-negative sperm chromosomes, MES-4 and H3K36me3 are maintained on only a subset of chromosomes until at least the 32-cell stage, likely because MES-4 propagates H3K36me3 on regions of the genome with preexisting H3K36me3. In embryos lacking MES-4, H3K36me3 levels on chromosomes drop precipitously postfertilization. In contrast to the relatively high levels of MES-4 in early-stage embryos, MET-1 levels are low at early stages and start increasing by the ∼26-cell stage, consistent with expression from the zygotic genome. Our findings support the model that MET-1 mediates transcription-coupled H3K36me3 in the parental germline and transcriptionally active embryos, and that MES-4 transmits an epigenetic memory of H3K36me3 across generations and through early embryo cell divisions by maintaining inherited patterns of H3K36me3.
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Affiliation(s)
- Jeremy Kreher
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064
| | - Teruaki Takasaki
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064
| | - Chad Cockrum
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064
| | - Simone Sidoli
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Benjamin A Garcia
- Epigenetics Institute, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark 5230
| | - Susan Strome
- Department of Molecular, Cell and Developmental Biology, University of California Santa Cruz, Santa Cruz, California 95064
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42
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Rosales-Vega M, Hernández-Becerril A, Murillo-Maldonado JM, Zurita M, Vázquez M. The role of the trithorax group TnaA isoforms in Hox gene expression, and in Drosophila late development. PLoS One 2018; 13:e0206587. [PMID: 30372466 PMCID: PMC6205608 DOI: 10.1371/journal.pone.0206587] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/16/2018] [Indexed: 11/18/2022] Open
Abstract
Regulation of developmental gene expression in eukaryotes involves several levels. One of them is the maintenance of gene expression along the life of the animal once it is started by different triggers early in development. One of the questions in the field is when in developmental time, the animal start to use the different maintenance mechanisms. The trithorax group (TrxG) of genes was first characterized as essential for maintaining homeotic gene expression. The TrxG gene tonalli interacts genetically and physically with genes and subunits of the BRAHMA BAP chromatin remodeling complex and encodes TnaA proteins with putative E3 SUMO-ligase activity. In contrast to the phenocritic lethal phase of animals with mutations in other TrxG genes, tna mutant individuals die late in development. In this study we determined the requirements of TnaA for survival at pupal and adult stages, in different tna mutant genotypes where we corroborate the lack of TnaA proteins, and the presence of adult homeotic loss-of-function phenotypes. We also investigated whether the absence of TnaA in haltere and leg larval imaginal discs affects the presence of the homeotic proteins Ultrabithorax and Sex combs reduced respectively by using some of the characterized genotypes and more finely by generating TnaA defective clones induced at different stages of development. We found that, tna is not required for growth or survival of imaginal disc cells and that it is a fine modulator of homeotic gene expression.
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Affiliation(s)
- Marco Rosales-Vega
- Departamento de Fisiología Molecular y Genética del Desarrollo, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Adriana Hernández-Becerril
- Departamento de Fisiología Molecular y Genética del Desarrollo, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Juan Manuel Murillo-Maldonado
- Departamento de Fisiología Molecular y Genética del Desarrollo, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
- Departamento de Neurobiología del Desarrollo y Neurofisiología, Instituto de Neurobiología, Universidad Nacional Autónoma de México, Querétaro, Querétaro, México
| | - Mario Zurita
- Departamento de Fisiología Molecular y Genética del Desarrollo, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Martha Vázquez
- Departamento de Fisiología Molecular y Genética del Desarrollo, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
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43
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Abstract
Gametogenesis represents the most dramatic cellular differentiation pathways in both female and male flies. At the genome level, meiosis ensures that diploid germ cells become haploid gametes. At the epigenome level, extensive changes are required to turn on and shut off gene expression in a precise spatiotemporally controlled manner. Research applying conventional molecular genetics and cell biology, in combination with rapidly advancing genomic tools have helped us to investigate (1) how germ cells maintain lineage specificity throughout their adult reproductive lifetime; (2) what molecular mechanisms ensure proper oogenesis and spermatogenesis, as well as protect genome integrity of the germline; (3) how signaling pathways contribute to germline-soma communication; and (4) if such communication is important. In this chapter, we highlight recent discoveries that have improved our understanding of these questions. On the other hand, restarting a new life cycle upon fertilization is a unique challenge faced by gametes, raising questions that involve intergenerational and transgenerational epigenetic inheritance. Therefore, we also discuss new developments that link changes during gametogenesis to early embryonic development-a rapidly growing field that promises to bring more understanding to some fundamental questions regarding metazoan development.
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44
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Shastrula PK, Lund PJ, Garcia BA, Janicki SM. Rpp29 regulates histone H3.3 chromatin assembly through transcriptional mechanisms. J Biol Chem 2018; 293:12360-12377. [PMID: 29921582 DOI: 10.1074/jbc.ra118.001845] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 05/30/2018] [Indexed: 01/26/2023] Open
Abstract
The histone H3 variant H3.3 is a highly conserved and dynamic regulator of chromatin organization. Therefore, fully elucidating its nucleosome incorporation mechanisms is essential to understanding its functions in epigenetic inheritance. We previously identified the RNase P protein subunit, Rpp29, as a repressor of H3.3 chromatin assembly. Here, we use a biochemical assay to show that Rpp29 interacts with H3.3 through a sequence element in its own N terminus, and we identify a novel interaction with histone H2B at an adjacent site. The fact that archaeal Rpp29 does not include this N-terminal region suggests that it evolved to regulate eukaryote-specific functions. Oncogenic H3.3 mutations alter the H3.3-Rpp29 interaction, which suggests that they could dysregulate Rpp29 function in chromatin assembly. We also used KNS42 cells, an H3.3(G34V) pediatric high-grade glioma cell line, to show that Rpp29 1) represses H3.3 incorporation into transcriptionally active protein-coding, rRNA, and tRNA genes; 2) represses mRNA, protein expression, and antisense RNA; and 3) represses euchromatic post-translational modifications (PTMs) and promotes heterochromatic PTM deposition (i.e. histone H3 Lys-9 trimethylation (H3K9me3) and H3.1/2/3K27me3). Notably, we also found that K27me2 is increased and K36me1 decreased on H3.3(G34V), which suggests that Gly-34 mutations dysregulate Lys-27 and Lys-36 methylation in cis The fact that Rpp29 represses H3.3 chromatin assembly and sense and antisense RNA and promotes H3K9me3 and H3K27me3 suggests that Rpp29 regulates H3.3-mediated epigenetic mechanisms by processing a transcribed signal that recruits H3.3 to its incorporation sites.
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Affiliation(s)
- Prashanth Krishna Shastrula
- From the Wistar Institute, Philadelphia, Pennsylvania 19104.,the Department of Biological Sciences, University of the Sciences in Philadelphia, Philadelphia, Pennsylvania 19104, and
| | - Peder J Lund
- the Epigenetics Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Benjamin A Garcia
- the Epigenetics Institute, Department of Biochemistry and Biophysics, University of Pennsylvania School of Medicine, Philadelphia, Pennsylvania 19104
| | - Susan M Janicki
- From the Wistar Institute, Philadelphia, Pennsylvania 19104,
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45
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Schmähling S, Meiler A, Lee Y, Mohammed A, Finkl K, Tauscher K, Israel L, Wirth M, Philippou-Massier J, Blum H, Habermann B, Imhof A, Song JJ, Müller J. Regulation and function of H3K36 di-methylation by the trithorax-group protein complex AMC. Development 2018. [PMID: 29540501 PMCID: PMC5963871 DOI: 10.1242/dev.163808] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The Drosophila Ash1 protein is a trithorax-group (trxG) regulator that antagonizes Polycomb repression at HOX genes. Ash1 di-methylates lysine 36 in histone H3 (H3K36me2) but how this activity is controlled and at which genes it functions is not well understood. We show that Ash1 protein purified from Drosophila exists in a complex with MRG15 and Caf1 that we named AMC. In Drosophila and human AMC, MRG15 binds a conserved FxLP motif near the Ash1 SET domain and stimulates H3K36 di-methylation on nucleosomes. Drosophila MRG15-null and ash1 catalytic mutants show remarkably specific trxG phenotypes: stochastic loss of HOX gene expression and homeotic transformations in adults. In mutants lacking AMC, H3K36me2 bulk levels appear undiminished but H3K36me2 is reduced in the chromatin of HOX and other AMC-regulated genes. AMC therefore appears to act on top of the H3K36me2/me3 landscape generated by the major H3K36 methyltransferases NSD and Set2. Our analyses suggest that H3K36 di-methylation at HOX genes is the crucial physiological function of AMC and the mechanism by which the complex antagonizes Polycomb repression at these genes. Highlighted Article: The trithorax group protein Ash1 and its regulator MRG15 form a multiprotein complex that maintains expression of HOX and other target genes by methylating histone H3 in their chromatin.
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Affiliation(s)
- Sigrun Schmähling
- Max-Planck Institute of Biochemistry, Laboratory of Chromatin Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Arno Meiler
- Max-Planck Institute of Biochemistry, Computational Biology, Am Klopferspitz 18 82152 Martinsried, Germany
| | - Yoonjung Lee
- Korea Advanced Institute of Science and Technology (KAIST), Department of Biological Sciences, Daejeon 34141, Korea
| | - Arif Mohammed
- Max-Planck Institute of Biochemistry, Laboratory of Chromatin Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Katja Finkl
- Max-Planck Institute of Biochemistry, Laboratory of Chromatin Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Katharina Tauscher
- Max-Planck Institute of Biochemistry, Laboratory of Chromatin Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Lars Israel
- Zentrallabor für Proteinanalytik, BioMedical Center, Ludwig-Maximilians-University Munich, Großhadernerstr. 9, 82152 Martinsried, Germany
| | - Marc Wirth
- Zentrallabor für Proteinanalytik, BioMedical Center, Ludwig-Maximilians-University Munich, Großhadernerstr. 9, 82152 Martinsried, Germany
| | - Julia Philippou-Massier
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, Ludwig-Maximilians-Universität München, Feodor-Lynen-Strasse 25, 81377 Munich, Germany
| | - Bianca Habermann
- Max-Planck Institute of Biochemistry, Computational Biology, Am Klopferspitz 18 82152 Martinsried, Germany
| | - Axel Imhof
- Zentrallabor für Proteinanalytik, BioMedical Center, Ludwig-Maximilians-University Munich, Großhadernerstr. 9, 82152 Martinsried, Germany
| | - Ji-Joon Song
- Korea Advanced Institute of Science and Technology (KAIST), Department of Biological Sciences, Daejeon 34141, Korea
| | - Jürg Müller
- Max-Planck Institute of Biochemistry, Laboratory of Chromatin Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
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Histone Demethylase Activity of Utx Is Essential for Viability and Regulation of HOX Gene Expression in Drosophila. Genetics 2017; 208:633-637. [PMID: 29247011 PMCID: PMC5788527 DOI: 10.1534/genetics.117.300421] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 12/12/2017] [Indexed: 12/12/2022] Open
Abstract
The trimethylation of histone H3 at lysine 27 (H3K27me3) by Polycomb Repressive Complex 2 (PRC2) is essential for the repression of Polycomb target genes. However, the role of enzymatic demethylation of H3K27me3 by the KDM6-family demethylases Utx, Uty, and JmjD3 is less clear. Studies in both mice and worms led to the proposal that KDM6 proteins, but not their H3K27me3 demethylase activity, is critical for normal development. Here, we investigated the requirement of the demethylase activity of the single KDM6 family member Utx in Drosophila. We generated Drosophila expressing a full-length but catalytically inactive Utx protein and found that these mutants show the same phenotypes as animals lacking the Utx protein. Specifically, animals lacking maternally deposited active Utx demethylase in the early embryo show stochastic loss of HOX gene expression that appears to be propagated in a clonal fashion. This suggests that Utx demethylase activity is critical for the removal of ectopic H3K27 trimethylation from active HOX genes during the onset of zygotic gene transcription, and thereby prevents the inappropriate installment of long-term repression by Polycomb. Conversely, maternally deposited catalytically active Utx protein suffices to permit animals that lack zygotic expression of enzymatically active Utx to develop into morphologically normal adults, which eclose from the pupal case but die shortly thereafter. Utx demethylase activity is therefore also essential to sustain viability in adult flies. Together, these analyses identify the earliest embryonic stages and the adult stage as two phases during the Drosophila life cycle that critically require H3K27me3 demethylase activity.
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Huang C, Yang F, Zhang Z, Zhang J, Cai G, Li L, Zheng Y, Chen S, Xi R, Zhu B. Mrg15 stimulates Ash1 H3K36 methyltransferase activity and facilitates Ash1 Trithorax group protein function in Drosophila. Nat Commun 2017; 8:1649. [PMID: 29158494 PMCID: PMC5696344 DOI: 10.1038/s41467-017-01897-3] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 10/23/2017] [Indexed: 12/28/2022] Open
Abstract
Ash1 is a Trithorax group protein that possesses H3K36-specific histone methyltransferase activity, which antagonizes Polycomb silencing. Here we report the identification of two Ash1 complex subunits, Mrg15 and Nurf55. In vitro, Mrg15 stimulates the enzymatic activity of Ash1. In vivo, Mrg15 is recruited by Ash1 to their common targets, and Mrg15 reinforces Ash1 chromatin association and facilitates the proper deposition of H3K36me2. To dissect the functional role of Mrg15 in the context of the Ash1 complex, we identify an Ash1 point mutation (Ash1-R1288A) that displays a greatly attenuated interaction with Mrg15. Knock-in flies bearing this mutation display multiple homeotic transformation phenotypes, and these phenotypes are partially rescued by overexpressing the Mrg15-Nurf55 fusion protein, which stabilizes the association of Mrg15 with Ash1. In summary, Mrg15 is a subunit of the Ash1 complex, a stimulator of Ash1 enzymatic activity and a critical regulator of the TrxG protein function of Ash1 in Drosophila.
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Affiliation(s)
- Chang Huang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Fu Yang
- National institute of Biological Sciences, Beijing, 102206, China
| | - Zhuqiang Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Jing Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Gaihong Cai
- National institute of Biological Sciences, Beijing, 102206, China
| | - Lin Li
- National institute of Biological Sciences, Beijing, 102206, China
| | - Yong Zheng
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - She Chen
- National institute of Biological Sciences, Beijing, 102206, China
| | - Rongwen Xi
- National institute of Biological Sciences, Beijing, 102206, China.
| | - Bing Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China. .,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Gupta RP, Bajpai A, Sinha P. Selector genes display tumor cooperation and inhibition in Drosophila epithelium in a developmental context-dependent manner. Biol Open 2017; 6:1581-1591. [PMID: 29141951 PMCID: PMC5703612 DOI: 10.1242/bio.027821] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
During animal development, selector genes determine identities of body segments and those of individual organs. Selector genes are also misexpressed in cancers, although their contributions to tumor progression per se remain poorly understood. Using a model of cooperative tumorigenesis, we show that gain of selector genes results in tumor cooperation, but in only select developmental domains of the wing, haltere and eye-antennal imaginal discs of Drosophila larva. Thus, the field selector, Eyeless (Ey), and the segment selector, Ultrabithorax (Ubx), readily cooperate to bring about neoplastic transformation of cells displaying somatic loss of the tumor suppressor, Lgl, but in only those developmental domains that express the homeo-box protein, Homothorax (Hth), and/or the Zinc-finger protein, Teashirt (Tsh). In non-Hth/Tsh-expressing domains of these imaginal discs, however, gain of Ey in lgl- somatic clones induces neoplastic transformation in the distal wing disc and haltere, but not in the eye imaginal disc. Likewise, gain of Ubx in lgl- somatic clones induces transformation in the eye imaginal disc but not in its endogenous domain, namely, the haltere imaginal disc. Our results reveal that selector genes could behave as tumor drivers or inhibitors depending on the tissue contexts of their gains.
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Affiliation(s)
- Ram Prakash Gupta
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Anjali Bajpai
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Pradip Sinha
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur 208016, India
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49
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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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50
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Schuettengruber B, Bourbon HM, Di Croce L, Cavalli G. Genome Regulation by Polycomb and Trithorax: 70 Years and Counting. Cell 2017; 171:34-57. [DOI: 10.1016/j.cell.2017.08.002] [Citation(s) in RCA: 611] [Impact Index Per Article: 87.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 07/17/2017] [Accepted: 08/01/2017] [Indexed: 01/05/2023]
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