1
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Estell C, West S. ZC3H4/Restrictor Exerts a Stranglehold on Pervasive Transcription. J Mol Biol 2024:168707. [PMID: 39002716 DOI: 10.1016/j.jmb.2024.168707] [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: 05/14/2024] [Revised: 07/06/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024]
Abstract
The regulation of transcription by RNA polymerase II (RNAPII) underpins all cellular processes and is perturbed in thousands of diseases. In humans, RNAPII transcribes ∼20000 protein-coding genes and engages in apparently futile non-coding transcription at thousands of other sites. Despite being so ubiquitous, this transcription is usually attenuated soon after initiation and the resulting products are immediately degraded by the nuclear exosome. We and others have recently described a new complex, "Restrictor", which appears to control such unproductive transcription. Underpinned by the RNA binding protein, ZC3H4, Restrictor curtails unproductive/pervasive transcription genome-wide. Here, we discuss these recent discoveries and speculate on some of the many unknowns regarding Restrictor function and mechanism.
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Affiliation(s)
- Chris Estell
- The Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.
| | - Steven West
- The Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.
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2
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Hoshii T, Kikuchi S, Kujirai T, Masuda T, Ito T, Yasuda S, Matsumoto M, Rahmutulla B, Fukuyo M, Murata T, Kurumizaka H, Kaneda A. BOD1L mediates chromatin binding and non-canonical function of H3K4 methyltransferase SETD1A. Nucleic Acids Res 2024:gkae605. [PMID: 38989615 DOI: 10.1093/nar/gkae605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/04/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
The H3K4 methyltransferase SETD1A plays an essential role in both development and cancer. However, essential components involved in SETD1A chromatin binding remain unclear. Here, we discovered that BOD1L exhibits the highest correlated SETD1A co-dependency in human cancer cell lines. BOD1L knockout reduces leukemia cells in vitro and in vivo, and mimics the transcriptional profiles observed in SETD1A knockout cells. The loss of BOD1L immediately reduced SETD1A distribution at transcriptional start sites (TSS), induced transcriptional elongation defect, and increased the RNA polymerase II content at TSS; however, it did not reduce H3K4me3. The Shg1 domain of BOD1L has a DNA binding ability, and a tryptophan residue (W104) in the domain recruits SETD1A to chromatin through the association with SETD1A FLOS domain. In addition, the BOD1L-SETD1A complex associates with transcriptional regulators, including E2Fs. These results reveal that BOD1L mediates chromatin and SETD1A, and regulates the non-canonical function of SETD1A in transcription.
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Affiliation(s)
- Takayuki Hoshii
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Sota Kikuchi
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takeshi Masuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
| | - Tomoko Ito
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Satoshi Yasuda
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba-shi, Chiba 263-8522, Japan
| | - Makoto Matsumoto
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba-shi, Chiba 263-8522, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
- Health and Disease Omics Center, Chiba University, Chiba-shi, Chiba 260-8670, Japan
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3
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Sigafoos AN, Tolosa EJ, Carr RM, Fernandez-Barrena MG, Almada LL, Pease DR, Hogenson TL, Raja Arul GL, Mousavi F, Sen S, Vera RE, Marks DL, Flores LF, LaRue-Nolan KC, Wu C, Bamlet WR, Vrabel AM, Sicotte H, Schenk EL, Smyrk TC, Zhang L, Rabe KG, Oberg AL, Zaphiropoulos PG, Chevet E, Graham RP, Hagen CE, di Magliano MP, Elsawa SF, Pin CL, Mao J, McWilliams RR, Fernandez-Zapico ME. KRAS Promotes GLI2-Dependent Transcription during Pancreatic Carcinogenesis. CANCER RESEARCH COMMUNICATIONS 2024; 4:1677-1689. [PMID: 38896052 PMCID: PMC11232480 DOI: 10.1158/2767-9764.crc-23-0464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 04/19/2024] [Accepted: 06/14/2024] [Indexed: 06/21/2024]
Abstract
Aberrant activation of GLI transcription factors has been implicated in the pathogenesis of different tumor types including pancreatic ductal adenocarcinoma. However, the mechanistic link with established drivers of this disease remains in part elusive. In this study, using a new genetically engineered mouse model overexpressing constitutively active mouse form of GLI2 and a combination of genome-wide assays, we provide evidence of a novel mechanism underlying the interplay between KRAS, a major driver of pancreatic ductal adenocarcinoma development, and GLI2 to control oncogenic gene expression. These mice, also expressing KrasG12D, show significantly reduced median survival rate and accelerated tumorigenesis compared with the KrasG12D only expressing mice. Analysis of the mechanism using RNA sequencing demonstrate higher levels of GLI2 targets, particularly tumor growth-promoting genes, including Ccnd1, N-Myc, and Bcl2, in KrasG12D mutant cells. Furthermore, chromatin immunoprecipitation sequencing studies showed that in these cells KrasG12D increases the levels of trimethylation of lysine 4 of the histone 3 (H3K4me3) at the promoter of GLI2 targets without affecting significantly the levels of other major active chromatin marks. Importantly, Gli2 knockdown reduces H3K4me3 enrichment and gene expression induced by mutant Kras. In summary, we demonstrate that Gli2 plays a significant role in pancreatic carcinogenesis by acting as a downstream effector of KrasG12D to control gene expression.
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Affiliation(s)
- Ashley N. Sigafoos
- Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota.
| | - Ezequiel J. Tolosa
- Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota.
| | - Ryan M. Carr
- Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota.
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota.
| | - Maite G. Fernandez-Barrena
- Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota.
| | - Luciana L. Almada
- Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota.
| | - David R. Pease
- Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota.
| | - Tara L. Hogenson
- Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota.
| | - Glancis L. Raja Arul
- Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota.
| | - Fatemeh Mousavi
- Department of Physiology and Pharmacology, University of Western Ontario, London, Canada.
- Department of Oncology, University of Western Ontario, London, Canada.
| | - Sandhya Sen
- Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota.
| | - Renzo E. Vera
- Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota.
| | - David L. Marks
- Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota.
| | - Luis F. Flores
- Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota.
| | - Kayla C. LaRue-Nolan
- Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota.
| | - Chen Wu
- Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota.
| | - William R. Bamlet
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.
| | - Anne M. Vrabel
- Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota.
| | - Hugues Sicotte
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.
| | - Erin L. Schenk
- Division of Medical Oncology, Mayo Clinic, Rochester, Minnesota.
| | - Thomas C. Smyrk
- Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota.
| | - Lizhi Zhang
- Division of Anatomic Pathology, Mayo Clinic, Rochester, Minnesota.
| | - Kari G. Rabe
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.
| | - Ann L. Oberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota.
| | | | - Eric Chevet
- Université de Rennes, CEDEX, Rennes, France.
| | | | | | - Marina P. di Magliano
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan.
| | - Sherine F. Elsawa
- Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota.
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire.
| | - Christopher L. Pin
- Department of Physiology and Pharmacology, University of Western Ontario, London, Canada.
- Department of Oncology, University of Western Ontario, London, Canada.
| | - Junhao Mao
- University of Massachusetts Medical School, Worcester, Massachusetts.
| | | | - Martin E. Fernandez-Zapico
- Division of Oncology Research, Schulze Center for Novel Therapeutics, Mayo Clinic, Rochester, Minnesota.
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Van HT, Xie G, Dong P, Liu Z, Ge K. KMT2 Family of H3K4 Methyltransferases: Enzymatic Activity-dependent and -independent Functions. J Mol Biol 2024; 436:168453. [PMID: 38266981 PMCID: PMC10957308 DOI: 10.1016/j.jmb.2024.168453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 01/26/2024]
Abstract
Histone-lysine N-methyltransferase 2 (KMT2) methyltransferases are critical for gene regulation, cell differentiation, animal development, and human diseases. KMT2 biological roles are often attributed to their methyltransferase activities on lysine 4 of histone H3 (H3K4). However, recent data indicate that KMT2 proteins also possess non-enzymatic functions. In this review, we discuss the current understanding of KMT2 family, with a focus on their enzymatic activity-dependent and -independent functions. Six mammalian KMT2 proteins of three subgroups, KMT2A/B (MLL1/2), KMT2C/D (MLL3/4), and KMT2F/G (SETD1A/B or SET1A/B), have shared and distinct protein domains, catalytic substrates, genomic localizations, and associated complex subunits. Recent studies have revealed the importance of KMT2C/D in enhancer regulation, differentiation, development, tumor suppression and highlighted KMT2C/D enzymatic activity-dependent and -independent roles in mouse embryonic development and cell differentiation. Catalytic dependent and independent functions for KMT2A/B and KMT2F/G in gene regulation, differentiation, and development are less understood. Finally, we provide our perspectives and lay out future research directions that may help advance the investigation on enzymatic activity-dependent and -independent biological roles and working mechanisms of KMT2 methyltransferases.
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Affiliation(s)
- Hieu T Van
- Adipocyte Biology and Gene Regulation Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 50, Room 4149, 50 South Dr, Bethesda, MD 20892, USA.
| | - Guojia Xie
- Adipocyte Biology and Gene Regulation Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 50, Room 4149, 50 South Dr, Bethesda, MD 20892, USA.
| | - Peng Dong
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
| | - Zhe Liu
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, VA 20147, USA.
| | - Kai Ge
- Adipocyte Biology and Gene Regulation Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Building 50, Room 4149, 50 South Dr, Bethesda, MD 20892, USA.
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5
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Russo M, Piccolo V, Polizzese D, Prosperini E, Borriero C, Polletti S, Bedin F, Marenda M, Michieletto D, Mandana GM, Rodighiero S, Cuomo A, Natoli G. Restrictor synergizes with Symplekin and PNUTS to terminate extragenic transcription. Genes Dev 2023; 37:1017-1040. [PMID: 38092518 PMCID: PMC10760643 DOI: 10.1101/gad.351057.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023]
Abstract
Transcription termination pathways mitigate the detrimental consequences of unscheduled promiscuous initiation occurring at hundreds of thousands of genomic cis-regulatory elements. The Restrictor complex, composed of the Pol II-interacting protein WDR82 and the RNA-binding protein ZC3H4, suppresses processive transcription at thousands of extragenic sites in mammalian genomes. Restrictor-driven termination does not involve nascent RNA cleavage, and its interplay with other termination machineries is unclear. Here we show that efficient termination at Restrictor-controlled extragenic transcription units involves the recruitment of the protein phosphatase 1 (PP1) regulatory subunit PNUTS, a negative regulator of the SPT5 elongation factor, and Symplekin, a protein associated with RNA cleavage complexes but also involved in cleavage-independent and phosphatase-dependent termination of noncoding RNAs in yeast. PNUTS and Symplekin act synergistically with, but independently from, Restrictor to dampen processive extragenic transcription. Moreover, the presence of limiting nuclear levels of Symplekin imposes a competition for its recruitment among multiple transcription termination machineries, resulting in mutual regulatory interactions. Hence, by synergizing with Restrictor, Symplekin and PNUTS enable efficient termination of processive, long-range extragenic transcription.
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Affiliation(s)
- Marta Russo
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Viviana Piccolo
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Danilo Polizzese
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Elena Prosperini
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Carolina Borriero
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Sara Polletti
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Fabio Bedin
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Mattia Marenda
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Davide Michieletto
- School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Gaurav Madappa Mandana
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Simona Rodighiero
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Alessandro Cuomo
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy
| | - Gioacchino Natoli
- Department of Experimental Oncology, European Institute of Oncology (IEO), Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS), Milan I-20139, Italy;
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6
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Barsoum M, Sayadi-Boroujeni R, Stenzel AT, Bussmann P, Lüscher-Firzlaff J, Lüscher B. Sequential deregulation of histone marks, chromatin accessibility and gene expression in response to PROTAC-induced degradation of ASH2L. Sci Rep 2023; 13:22565. [PMID: 38114530 PMCID: PMC10730889 DOI: 10.1038/s41598-023-49284-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/06/2023] [Indexed: 12/21/2023] Open
Abstract
The trithorax protein ASH2L is essential for organismal and tissue development. As a subunit of COMPASS/KMT2 complexes, ASH2L is necessary for methylation of histone H3 lysine 4 (H3K4). Mono- and tri-methylation at this site mark active enhancers and promoters, respectively, although the functional relevance of H3K4 methylation is only partially understood. ASH2L has a long half-life, which results in a slow decrease upon knockout. This has made it difficult to define direct consequences. To overcome this limitation, we employed a PROTAC system to rapidly degrade ASH2L and address direct effects. ASH2L loss resulted in inhibition of proliferation of mouse embryo fibroblasts. Shortly after ASH2L degradation H3K4me3 decreased with its half-life varying between promoters. Subsequently, H3K4me1 increased at promoters and decreased at some enhancers. H3K27ac and H3K27me3, histone marks closely linked to H3K4 methylation, were affected with considerable delay. In parallel, chromatin compaction increased at promoters. Of note, nascent gene transcription was not affected early but overall RNA expression was deregulated late after ASH2L loss. Together, these findings suggest that downstream effects are ordered but relatively slow, despite the rapid loss of ASH2L and inactivation of KMT2 complexes. It appears that the systems that control gene transcription are well buffered and strong effects are only beginning to unfold after considerable delay.
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Affiliation(s)
- Mirna Barsoum
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany.
| | - Roksaneh Sayadi-Boroujeni
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany
- Bayer AG, Crop Science Division, R&D, Pest Control, 40789, Monheim am Rhein, Germany
| | - Alexander T Stenzel
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany
- Institute of Human Genetics, Faculty of Medicine, University of Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Philip Bussmann
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany
| | - Juliane Lüscher-Firzlaff
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany.
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7
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Ait Said M, Bejjani F, Abdouni A, Ségéral E, Emiliani S. Premature transcription termination complex proteins PCF11 and WDR82 silence HIV-1 expression in latently infected cells. Proc Natl Acad Sci U S A 2023; 120:e2313356120. [PMID: 38015843 PMCID: PMC10710072 DOI: 10.1073/pnas.2313356120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/30/2023] [Indexed: 11/30/2023] Open
Abstract
Postintegration transcriptional silencing of HIV-1 leads to the establishment of a pool of latently infected cells. In these cells, mechanisms controlling RNA Polymerase II (RNAPII) pausing and premature transcription termination (PTT) remain to be explored. Here, we found that the cleavage and polyadenylation (CPA) factor PCF11 represses HIV-1 expression independently of the other subunits of the CPA complex or the polyadenylation signal located at the 5' LTR. We show that PCF11 interacts with the RNAPII-binding protein WDR82. Knock-down of PCF11 or WDR82 reactivated HIV-1 expression in latently infected cells. To silence HIV-1 transcription, PCF11 and WDR82 are specifically recruited at the promoter-proximal region of the provirus in an interdependent manner. Codepletion of PCF11 and WDR82 indicated that they act on the same pathway to repress HIV expression. These findings reveal PCF11/WDR82 as a PTT complex silencing HIV-1 expression in latently infected cells.
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Affiliation(s)
- Melissa Ait Said
- Université Paris Cité, Institut Cochin, INSERM, CNRS, ParisF-75014, France
| | - Fabienne Bejjani
- Université Paris Cité, Institut Cochin, INSERM, CNRS, ParisF-75014, France
| | - Ahmed Abdouni
- Université Paris Cité, Institut Cochin, INSERM, CNRS, ParisF-75014, France
| | - Emmanuel Ségéral
- Université Paris Cité, Institut Cochin, INSERM, CNRS, ParisF-75014, France
| | - Stéphane Emiliani
- Université Paris Cité, Institut Cochin, INSERM, CNRS, ParisF-75014, France
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8
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Amin HM, Szabo B, Abukhairan R, Zeke A, Kardos J, Schad E, Tantos A. In Vivo and In Vitro Characterization of the RNA Binding Capacity of SETD1A (KMT2F). Int J Mol Sci 2023; 24:16032. [PMID: 38003223 PMCID: PMC10671326 DOI: 10.3390/ijms242216032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 11/03/2023] [Accepted: 11/05/2023] [Indexed: 11/26/2023] Open
Abstract
For several histone lysine methyltransferases (HKMTs), RNA binding has been already shown to be a functionally relevant feature, but detailed information on the RNA interactome of these proteins is not always known. Of the six human KMT2 proteins responsible for the methylation of the H3K4 residue, two-SETD1A and SETD1B-contain RNA recognition domains (RRMs). Here we investigated the RNA binding capacity of SETD1A and identified a broad range of interacting RNAs within HEK293T cells. Our analysis revealed that similar to yeast Set1, SETD1A is also capable of binding several coding and non-coding RNAs, including RNA species related to RNA processing. We also show direct RNA binding activity of the individual RRM domain in vitro, which is in contrast with the RRM domain found in yeast Set1. Structural modeling revealed important details on the possible RNA recognition mode of SETD1A and highlighted some fundamental differences between SETD1A and Set1, explaining the differences in the RNA binding capacity of their respective RRMs.
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Affiliation(s)
- Harem Muhamad Amin
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (H.M.A.); (B.S.); (R.A.); (E.S.)
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
- Department of Biology, College of Science, University of Sulaimani, Sulaymaniyah 46001, Kurdistan Region, Iraq
| | - Beata Szabo
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (H.M.A.); (B.S.); (R.A.); (E.S.)
| | - Rawan Abukhairan
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (H.M.A.); (B.S.); (R.A.); (E.S.)
| | - Andras Zeke
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (H.M.A.); (B.S.); (R.A.); (E.S.)
| | - József Kardos
- ELTE NAP Neuroimmunology Research Group, Department of Biochemistry, Institute of Biology, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary;
| | - Eva Schad
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (H.M.A.); (B.S.); (R.A.); (E.S.)
| | - Agnes Tantos
- Institute of Enzymology, HUN-REN Research Centre for Natural Sciences, H-1117 Budapest, Hungary; (H.M.A.); (B.S.); (R.A.); (E.S.)
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9
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Chen Y, Craven GB, Kamber RA, Cuesta A, Zhersh S, Moroz YS, Bassik MC, Taunton J. Direct mapping of ligandable tyrosines and lysines in cells with chiral sulfonyl fluoride probes. Nat Chem 2023; 15:1616-1625. [PMID: 37460812 DOI: 10.1038/s41557-023-01281-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 06/23/2023] [Indexed: 11/05/2023]
Abstract
Advances in chemoproteomic technology have revealed covalent interactions between small molecules and protein nucleophiles, primarily cysteine, on a proteome-wide scale. Most chemoproteomic screening approaches are indirect, relying on competition between electrophilic fragments and a minimalist electrophilic probe with inherently limited proteome coverage. Here we develop a chemoproteomic platform for direct electrophile-site identification based on enantiomeric pairs of clickable arylsulfonyl fluoride probes. Using stereoselective site modification as a proxy for ligandability in intact cells, we identify 634 tyrosines and lysines within functionally diverse protein sites, liganded by structurally diverse probes. Among multiple validated sites, we discover a chiral probe that modifies Y228 in the MYC binding site of the epigenetic regulator WDR5, as revealed by a high-resolution crystal structure. A distinct chiral probe stimulates tumour cell phagocytosis by covalently modifying Y387 in the recently discovered immuno-oncology target APMAP. Our work provides a deep resource of ligandable tyrosines and lysines for the development of covalent chemical probes.
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Affiliation(s)
- Ying Chen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Gregory B Craven
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | - Roarke A Kamber
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Adolfo Cuesta
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA
| | | | - Yurii S Moroz
- National Taras Shevchenko University of Kyiv, Kyiv, Ukraine
- Chemspace LLC, Kyiv, Ukraine
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, USA
- Program in Chemistry, Engineering, and Medicine for Human Health (ChEM-H), Stanford University, Stanford, CA, USA
| | - Jack Taunton
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA, USA.
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10
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Perlee S, Kikuchi S, Nakadai T, Masuda T, Ohtsuki S, Matsumoto M, Rahmutulla B, Fukuyo M, Cifani P, Kentsis A, Roeder RG, Kaneda A, Hoshii T. SETD1A function in leukemia is mediated through interaction with mitotic regulators BuGZ/BUB3. EMBO Rep 2023; 24:e57108. [PMID: 37535603 PMCID: PMC10561176 DOI: 10.15252/embr.202357108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/11/2023] [Accepted: 07/18/2023] [Indexed: 08/05/2023] Open
Abstract
The H3K4 methyltransferase SETD1A plays a crucial role in leukemia cell survival through its noncatalytic FLOS domain-mediated recruitment of cyclin K and regulation of DNA damage response genes. In this study, we identify a functional nuclear localization signal in and interaction partners of the FLOS domain. Our screen for FLOS domain-binding partners reveals that the SETD1A FLOS domain binds mitosis-associated proteins BuGZ/BUB3. Inhibition of both cyclin K and BuGZ/BUB3-binding motifs in SETD1A shows synergistic antileukemic effects. BuGZ/BUB3 localize to SETD1A-bound promoter-TSS regions and SETD1A-negative H3K4me1-positive enhancer regions adjacent to SETD1A target genes. The GLEBS motif and intrinsically disordered region of BuGZ are required for both SETD1A-binding and leukemia cell proliferation. Cell-cycle-specific SETD1A restoration assays indicate that SETD1A expression at the G1/S phase of the cell cycle promotes both the expression of DNA damage response genes and cell cycle progression in leukemia cells.
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Affiliation(s)
- Sarah Perlee
- Department of Cancer Biology and GeneticsMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
- Gerstner Graduate School of Biomedical SciencesMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Sota Kikuchi
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityChibaJapan
| | - Tomoyoshi Nakadai
- Laboratory of Biochemistry and Molecular BiologyThe Rockefeller UniversityNew YorkNYUSA
| | - Takeshi Masuda
- Laboratory of Pharmaceutical Microbiology, Faculty of Life SciencesKumamoto UniversityKumamotoJapan
- Institute for Advanced BiosciencesKeio UniversityTsuruokaJapan
| | - Sumio Ohtsuki
- Laboratory of Pharmaceutical Microbiology, Faculty of Life SciencesKumamoto UniversityKumamotoJapan
| | - Makoto Matsumoto
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityChibaJapan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityChibaJapan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityChibaJapan
| | - Paolo Cifani
- Molecular Pharmacology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Alex Kentsis
- Molecular Pharmacology ProgramMemorial Sloan Kettering Cancer CenterNew YorkNYUSA
| | - Robert G Roeder
- Laboratory of Biochemistry and Molecular BiologyThe Rockefeller UniversityNew YorkNYUSA
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityChibaJapan
| | - Takayuki Hoshii
- Department of Molecular Oncology, Graduate School of MedicineChiba UniversityChibaJapan
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11
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Gilan O, Talarmain L, Bell CC, Neville D, Knezevic K, Ferguson DT, Boudes M, Chan YC, Davidovich C, Lam EYN, Dawson MA. CRISPR-ChIP reveals selective regulation of H3K79me2 by Menin in MLL leukemia. Nat Struct Mol Biol 2023; 30:1592-1606. [PMID: 37679565 DOI: 10.1038/s41594-023-01087-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 08/03/2023] [Indexed: 09/09/2023]
Abstract
Chromatin regulation involves the selective recruitment of chromatin factors to facilitate DNA repair, replication and transcription. Here we demonstrate the utility of coupling unbiased functional genomics with chromatin immunoprecipitation (CRISPR-ChIP) to identify the factors associated with active chromatin modifications in mammalian cells. Specifically, an integrated reporter containing a cis-regulatory element of interest and a single guide RNA provide a chromatinized template for a direct readout for regulators of histone modifications associated with actively transcribed genes such as H3K4me3 and H3K79me2. With CRISPR-ChIP, we identify all the nonredundant COMPASS complex members required for H3K4me3 and demonstrate that RNA polymerase II is dispensable for the maintenance of H3K4me3. As H3K79me2 has a putative oncogenic function in leukemia cells driven by MLL translocations, using CRISPR-ChIP we reveal a functional partitioning of H3K79 methylation into two distinct regulatory units: an oncogenic DOT1L complex directed by the MLL fusion protein in a Menin-dependent manner and a separate endogenous DOT1L complex, where catalytic activity is directed by MLLT10. Overall, CRISPR-ChIP provides a powerful tool for the unbiased interrogation of the mechanisms underpinning chromatin regulation.
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Affiliation(s)
- Omer Gilan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia.
| | - Laure Talarmain
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Charles C Bell
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Daniel Neville
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
| | - Kathy Knezevic
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Daniel T Ferguson
- Australian Centre for Blood Diseases, Monash University, Melbourne, Victoria, Australia
| | - Marion Boudes
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Yih-Chih Chan
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- EMBL-Australia, Clayton, Victoria, Australia
| | - Enid Y N Lam
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- Department of Clinical Haematology, Peter MacCallum Cancer Centre & Royal Melbourne Hospital, Melbourne, Victoria, Australia.
- Centre for Cancer Research, University of Melbourne, Melbourne, Victoria, Australia.
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12
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Graham-Paquin AL, Saini D, Sirois J, Hossain I, Katz MS, Zhuang QKW, Kwon SY, Yamanaka Y, Bourque G, Bouchard M, Pastor WA. ZMYM2 is essential for methylation of germline genes and active transposons in embryonic development. Nucleic Acids Res 2023; 51:7314-7329. [PMID: 37395395 PMCID: PMC10415128 DOI: 10.1093/nar/gkad540] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 05/24/2023] [Accepted: 06/09/2023] [Indexed: 07/04/2023] Open
Abstract
ZMYM2 is a transcriptional repressor whose role in development is largely unexplored. We found that Zmym2-/- mice show embryonic lethality by E10.5. Molecular characterization of Zmym2-/- embryos revealed two distinct defects. First, they fail to undergo DNA methylation and silencing of germline gene promoters, resulting in widespread upregulation of germline genes. Second, they fail to methylate and silence the evolutionarily youngest and most active LINE element subclasses in mice. Zmym2-/- embryos show ubiquitous overexpression of LINE-1 protein as well as aberrant expression of transposon-gene fusion transcripts. ZMYM2 homes to sites of PRC1.6 and TRIM28 complex binding, mediating repression of germline genes and transposons respectively. In the absence of ZMYM2, hypermethylation of histone 3 lysine 4 occurs at target sites, creating a chromatin landscape unfavourable for establishment of DNA methylation. ZMYM2-/- human embryonic stem cells also show aberrant upregulation and demethylation of young LINE elements, indicating a conserved role in repression of active transposons. ZMYM2 is thus an important new factor in DNA methylation patterning in early embryonic development.
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Affiliation(s)
- Adda-Lee Graham-Paquin
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- The Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Deepak Saini
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jacinthe Sirois
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- The Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Ishtiaque Hossain
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Megan S Katz
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- The Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - Qinwei Kim-Wee Zhuang
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto, Japan
| | - Sin Young Kwon
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Yojiro Yamanaka
- The Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- Institute for the Advanced Study of Human Biology (WPI-ASHBi), Kyoto, Japan
- Canadian Center for Computational Genomics,McGill University, Montreal, Quebec, Canada
| | - Maxime Bouchard
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- The Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
| | - William A Pastor
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
- The Rosalind & Morris Goodman Cancer Institute, McGill University, Montreal, Quebec, Canada
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13
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Zhao Y, Tabet D, Rubio Contreras D, Lao L, Kousholt AN, Weile J, Melo H, Hoeg L, Feng S, Coté AG, Lin ZY, Setiaputra D, Jonkers J, Gingras AC, Gómez Herreros F, Roth FP, Durocher D. Genome-scale mapping of DNA damage suppressors through phenotypic CRISPR-Cas9 screens. Mol Cell 2023; 83:2792-2809.e9. [PMID: 37478847 PMCID: PMC10530064 DOI: 10.1016/j.molcel.2023.06.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 04/18/2023] [Accepted: 06/21/2023] [Indexed: 07/23/2023]
Abstract
To maintain genome integrity, cells must accurately duplicate their genome and repair DNA lesions when they occur. To uncover genes that suppress DNA damage in human cells, we undertook flow-cytometry-based CRISPR-Cas9 screens that monitored DNA damage. We identified 160 genes whose mutation caused spontaneous DNA damage, a list enriched in essential genes, highlighting the importance of genomic integrity for cellular fitness. We also identified 227 genes whose mutation caused DNA damage in replication-perturbed cells. Among the genes characterized, we discovered that deoxyribose-phosphate aldolase DERA suppresses DNA damage caused by cytarabine (Ara-C) and that GNB1L, a gene implicated in 22q11.2 syndrome, promotes biogenesis of ATR and related phosphatidylinositol 3-kinase-related kinases (PIKKs). These results implicate defective PIKK biogenesis as a cause of some phenotypes associated with 22q11.2 syndrome. The phenotypic mapping of genes that suppress DNA damage therefore provides a rich resource to probe the cellular pathways that influence genome maintenance.
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Affiliation(s)
- Yichao Zhao
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | - Daniel Tabet
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | | | - Linjiang Lao
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Arne Nedergaard Kousholt
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Jochen Weile
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Donnelly Centre and Department of Computer Science, University of Toronto, 160 College Street, Toronto M5S 3E1, Canada
| | - Henrique Melo
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Lisa Hoeg
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Sumin Feng
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Atina G Coté
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Dheva Setiaputra
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Jos Jonkers
- Division of Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada
| | | | - Frederick P Roth
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada; Donnelly Centre and Department of Computer Science, University of Toronto, 160 College Street, Toronto M5S 3E1, Canada
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada.
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14
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Cui G, Zhou J, Sun J, Kou X, Su Z, Xu Y, Liu T, Sun L, Li W, Wu X, Wei Q, Gao S, Shi K. WD repeat domain 82 (Wdr82) facilitates mouse iPSCs generation by interfering mitochondrial oxidative phosphorylation and glycolysis. Cell Mol Life Sci 2023; 80:218. [PMID: 37470863 PMCID: PMC10359378 DOI: 10.1007/s00018-023-04871-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 07/01/2023] [Accepted: 07/10/2023] [Indexed: 07/21/2023]
Abstract
BACKGROUND Abundantly expressed factors in the oocyte cytoplasm can remarkably reprogram terminally differentiated germ cells or somatic cells into totipotent state within a short time. However, the mechanism of the different factors underlying the reprogramming process remains uncertain. METHODS On the basis of Yamanaka factors OSKM induction method, MEF cells were induced and reprogrammed into iPSCs under conditions of the oocyte-derived factor Wdr82 overexpression and/or knockdown, so as to assess the reprogramming efficiency. Meanwhile, the cellular metabolism was monitored and evaluated during the reprogramming process. The plurpotency of the generated iPSCs was confirmed via pluripotent gene expression detection, embryoid body differentiation and chimeric mouse experiment. RESULTS Here, we show that the oocyte-derived factor Wdr82 promotes the efficiency of MEF reprogramming into iPSCs to a greater degree than the Yamanaka factors OSKM. The Wdr82-expressing iPSC line showed pluripotency to differentiate and transmit genetic material to chimeric offsprings. In contrast, the knocking down of Wdr82 can significantly reduce the efficiency of somatic cell reprogramming. We further demonstrate that the significant suppression of oxidative phosphorylation in mitochondria underlies the molecular mechanism by which Wdr82 promotes the efficiency of somatic cell reprogramming. Our study suggests a link between mitochondrial energy metabolism remodeling and cell fate transition or stem cell function maintenance, which might shed light on the embryonic development and stem cell biology.
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Affiliation(s)
- Guina Cui
- Key Laboratory of Animal Bioengineering and Disease Prevention of Shandong Province, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, 271018, China
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Jingxuan Zhou
- Key Laboratory of Animal Bioengineering and Disease Prevention of Shandong Province, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, 271018, China
| | - Jiatong Sun
- Key Laboratory of Animal Bioengineering and Disease Prevention of Shandong Province, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, 271018, China
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Xiaochen Kou
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Zhongqu Su
- Key Laboratory of Animal Bioengineering and Disease Prevention of Shandong Province, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, 271018, China
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Yiliang Xu
- Key Laboratory of Animal Bioengineering and Disease Prevention of Shandong Province, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, 271018, China
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China
| | - Tingjun Liu
- Key Laboratory of Animal Bioengineering and Disease Prevention of Shandong Province, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, 271018, China
| | - Lili Sun
- Key Laboratory of Animal Bioengineering and Disease Prevention of Shandong Province, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, 271018, China
| | - Wenhui Li
- Key Laboratory of Animal Bioengineering and Disease Prevention of Shandong Province, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, 271018, China
| | - Xuanning Wu
- Key Laboratory of Animal Bioengineering and Disease Prevention of Shandong Province, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, 271018, China
| | - Qingqing Wei
- Key Laboratory of Animal Bioengineering and Disease Prevention of Shandong Province, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, 271018, China
| | - Shaorong Gao
- Clinical and Translational Research Center of Shanghai First Maternity and Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, 200092, China.
| | - Kerong Shi
- Key Laboratory of Animal Bioengineering and Disease Prevention of Shandong Province, College of Animal Science and Technology, Shandong Agricultural University, No. 61 Daizong Street, Taian, 271018, China.
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15
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Wadhwani N, Nayak S, Wang Y, Hashizume R, Jie C, Mania-Farnell B, James CD, Xi G, Tomita T. WDR82-Mediated H3K4me3 Is Associated with Tumor Proliferation and Therapeutic Efficacy in Pediatric High-Grade Gliomas. Cancers (Basel) 2023; 15:3429. [PMID: 37444539 PMCID: PMC10340597 DOI: 10.3390/cancers15133429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/29/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Pediatric high-grade gliomas (pHGGs) are common malignant brain tumors without effective treatment and poor patient survival. Abnormal posttranslational modification at the histone H3 tail plays critical roles in tumor cell malignancy. We have previously shown that the trimethylation of lysine 4 at histone H3 (H3K4me3) plays a significant role in pediatric ependymoma malignancy and is associated with tumor therapeutic sensitivity. Here, we show that H3K4me3 and its methyltransferase WDR82 are elevated in pHGGs. A reduction in H3K4me3 by downregulating WDR82 decreases H3K4me3 promoter occupancy and the expression of genes associated with stem cell features, cell proliferation, the cell cycle, and DNA damage repair. A reduction in WDR82-mediated H3K4me3 increases the response of pediatric glioma cells to chemotherapy. These findings suggest that WDR82-mediated H3K4me3 is an important determinant of pediatric glioma malignancy and therapeutic response. This highlights the need for a more thorough understanding of the potential of WDR82 as an epigenetic target to increase therapeutic efficacy and improve the prognosis for children with malignant gliomas.
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Affiliation(s)
- Nitin Wadhwani
- Department of Pathology, Ann & Robert H. Lurie Children’s Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Sonali Nayak
- Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children’s Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Yufen Wang
- Department of Radio-oncology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Rintaro Hashizume
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Chunfa Jie
- Department of Biochemistry and Nutrition, Des Moines University Medicine and Health Sciences, Des Moines, IA 50312, USA
| | - Barbara Mania-Farnell
- Department of Biological Sciences, Purdue University Northwest, Hammond, IN 46323, USA
| | - Charles David James
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Guifa Xi
- Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children’s Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Tadanori Tomita
- Division of Pediatric Neurosurgery, Ann & Robert H. Lurie Children’s Hospital of Chicago, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
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16
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Estell C, Davidson L, Eaton JD, Kimura H, Gold VAM, West S. A restrictor complex of ZC3H4, WDR82, and ARS2 integrates with PNUTS to control unproductive transcription. Mol Cell 2023:S1097-2765(23)00385-4. [PMID: 37329883 DOI: 10.1016/j.molcel.2023.05.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/29/2023] [Accepted: 05/18/2023] [Indexed: 06/19/2023]
Abstract
The transcriptional termination of unstable non-coding RNAs (ncRNAs) is poorly understood compared to coding transcripts. We recently identified ZC3H4-WDR82 ("restrictor") as restricting human ncRNA transcription, but how it does this is unknown. Here, we show that ZC3H4 additionally associates with ARS2 and the nuclear exosome targeting complex. The domains of ZC3H4 that contact ARS2 and WDR82 are required for ncRNA restriction, suggesting their presence in a functional complex. Consistently, ZC3H4, WDR82, and ARS2 co-transcriptionally control an overlapping population of ncRNAs. ZC3H4 is proximal to the negative elongation factor, PNUTS, which we show enables restrictor function and is required to terminate the transcription of all major RNA polymerase II transcript classes. In contrast to short ncRNAs, longer protein-coding transcription is supported by U1 snRNA, which shields transcripts from restrictor and PNUTS at hundreds of genes. These data provide important insights into the mechanism and control of transcription by restrictor and PNUTS.
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Affiliation(s)
- Chris Estell
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Lee Davidson
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Joshua D Eaton
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Hiroshi Kimura
- Cell Biology Centre, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Steven West
- Living Systems Institute, University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom.
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17
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Rouvière JO, Salerno-Kochan A, Lykke-Andersen S, Garland W, Dou Y, Rathore O, Molska EŠ, Wu G, Schmid M, Bugai A, Jakobsen L, Žumer K, Cramer P, Andersen JS, Conti E, Jensen TH. ARS2 instructs early transcription termination-coupled RNA decay by recruiting ZC3H4 to nascent transcripts. Mol Cell 2023:S1097-2765(23)00384-2. [PMID: 37329882 DOI: 10.1016/j.molcel.2023.05.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 03/29/2023] [Accepted: 05/18/2023] [Indexed: 06/19/2023]
Abstract
The RNA-binding ARS2 protein is centrally involved in both early RNA polymerase II (RNAPII) transcription termination and transcript decay. Despite its essential nature, the mechanisms by which ARS2 enacts these functions have remained unclear. Here, we show that a conserved basic domain of ARS2 binds a corresponding acidic-rich, short linear motif (SLiM) in the transcription restriction factor ZC3H4. This interaction recruits ZC3H4 to chromatin to elicit RNAPII termination, independent of other early termination pathways defined by the cleavage and polyadenylation (CPA) and Integrator (INT) complexes. We find that ZC3H4, in turn, forms a direct connection to the nuclear exosome targeting (NEXT) complex, hereby facilitating rapid degradation of the nascent RNA. Hence, ARS2 instructs the coupled transcription termination and degradation of the transcript onto which it is bound. This contrasts with ARS2 function at CPA-instructed termination sites where the protein exclusively partakes in RNA suppression via post-transcriptional decay.
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Affiliation(s)
- Jérôme O Rouvière
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Anna Salerno-Kochan
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Munich, Germany
| | - Søren Lykke-Andersen
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - William Garland
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Yuhui Dou
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Om Rathore
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Ewa Šmidová Molska
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Guifen Wu
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Manfred Schmid
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Andrii Bugai
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark
| | - Lis Jakobsen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Kristina Žumer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Am Fassberg 11, 37077 Göttingen, Germany
| | - Jens S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Elena Conti
- Department of Structural Cell Biology, Max Planck Institute of Biochemistry, Martinsried, Munich, Germany
| | - Torben Heick Jensen
- Department of Molecular Biology and Genetics, Universitetsbyen 81, Aarhus University, Aarhus, Denmark.
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18
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Malik KK, Sridhara SC, Lone KA, Katariya PD, Pulimamidi D, Tyagi S. MLL methyltransferases regulate H3K4 methylation to ensure CENP-A assembly at human centromeres. PLoS Biol 2023; 21:e3002161. [PMID: 37379335 PMCID: PMC10335677 DOI: 10.1371/journal.pbio.3002161] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 07/11/2023] [Accepted: 05/12/2023] [Indexed: 06/30/2023] Open
Abstract
The active state of centromeres is epigenetically defined by the presence of CENP-A interspersed with histone H3 nucleosomes. While the importance of dimethylation of H3K4 for centromeric transcription has been highlighted in various studies, the identity of the enzyme(s) depositing these marks on the centromere is still unknown. The MLL (KMT2) family plays a crucial role in RNA polymerase II (Pol II)-mediated gene regulation by methylating H3K4. Here, we report that MLL methyltransferases regulate transcription of human centromeres. CRISPR-mediated down-regulation of MLL causes loss of H3K4me2, resulting in an altered epigenetic chromatin state of the centromeres. Intriguingly, our results reveal that loss of MLL, but not SETD1A, increases co-transcriptional R-loop formation, and Pol II accumulation at the centromeres. Finally, we report that the presence of MLL and SETD1A is crucial for kinetochore maintenance. Altogether, our data reveal a novel molecular framework where both the H3K4 methylation mark and the methyltransferases regulate stability and identity of the centromere.
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Affiliation(s)
- Kausika Kumar Malik
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | - Sreerama Chaitanya Sridhara
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
| | - Kaisar Ahmad Lone
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
- Graduate Studies, Regional Centre for Biotechnology, Faridabad, India
| | - Payal Deepakbhai Katariya
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | - Deepshika Pulimamidi
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
| | - Shweta Tyagi
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
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19
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Deshpande N, Bryk M. Diverse and dynamic forms of gene regulation by the S. cerevisiae histone methyltransferase Set1. Curr Genet 2023; 69:91-114. [PMID: 37000206 DOI: 10.1007/s00294-023-01265-3] [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: 03/11/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 04/01/2023]
Abstract
Gene transcription is an essential and highly regulated process. In eukaryotic cells, the structural organization of nucleosomes with DNA wrapped around histone proteins impedes transcription. Chromatin remodelers, transcription factors, co-activators, and histone-modifying enzymes work together to make DNA accessible to RNA polymerase. Histone lysine methylation can positively or negatively regulate gene transcription. Methylation of histone 3 lysine 4 by SET-domain-containing proteins is evolutionarily conserved from yeast to humans. In higher eukaryotes, mutations in SET-domain proteins are associated with defects in the development and segmentation of embryos, skeletal and muscle development, and diseases, including several leukemias. Since histone methyltransferases are evolutionarily conserved, the mechanisms of gene regulation mediated by these enzymes are also conserved. Budding yeast Saccharomyces cerevisiae is an excellent model system to study the impact of histone 3 lysine 4 (H3K4) methylation on eukaryotic gene regulation. Unlike larger eukaryotes, yeast cells have only one enzyme that catalyzes H3K4 methylation, Set1. In this review, we summarize current knowledge about the impact of Set1-catalyzed H3K4 methylation on gene transcription in S. cerevisiae. We describe the COMPASS complex, factors that influence H3K4 methylation, and the roles of Set1 in gene silencing at telomeres and heterochromatin, as well as repression and activation at euchromatic loci. We also discuss proteins that "read" H3K4 methyl marks to regulate transcription and summarize alternate functions for Set1 beyond H3K4 methylation.
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Affiliation(s)
- Neha Deshpande
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Mary Bryk
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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20
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Spencley AL, Bar S, Swigut T, Flynn RA, Lee CH, Chen LF, Bassik MC, Wysocka J. Co-transcriptional genome surveillance by HUSH is coupled to termination machinery. Mol Cell 2023; 83:1623-1639.e8. [PMID: 37164018 PMCID: PMC10915761 DOI: 10.1016/j.molcel.2023.04.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/12/2023] [Accepted: 04/12/2023] [Indexed: 05/12/2023]
Abstract
The HUSH complex recognizes and silences foreign DNA such as viruses, transposons, and transgenes without prior exposure to its targets. Here, we show that endogenous targets of the HUSH complex fall into two distinct classes based on the presence or absence of H3K9me3. These classes are further distinguished by their transposon content and differential response to the loss of HUSH. A de novo genomic rearrangement at the Sox2 locus induces a switch from H3K9me3-independent to H3K9me3-associated HUSH targeting, resulting in silencing. We further demonstrate that HUSH interacts with the termination factor WDR82 and-via its component MPP8-with nascent RNA. HUSH accumulates at sites of high RNAPII occupancy including long exons and transcription termination sites in a manner dependent on WDR82 and CPSF. Together, our results uncover the functional diversity of HUSH targets and show that this vertebrate-specific complex exploits evolutionarily ancient transcription termination machinery for co-transcriptional chromatin targeting and genome surveillance.
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Affiliation(s)
- Andrew L Spencley
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA; Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, USA
| | - Shiran Bar
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Ryan A Flynn
- Stem Cell Program, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Cameron H Lee
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Liang-Fu Chen
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael C Bassik
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA.
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21
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Bao S, Xu C. Molecular insight into the SETD1A/B N-terminal region and its interaction with WDR82. Biochem Biophys Res Commun 2023; 658:136-140. [PMID: 37030068 DOI: 10.1016/j.bbrc.2023.03.064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023]
Abstract
SETD1A and SETD1B originate from Set1, the sole H3K4 methyltransferase in yeast, and they play important roles in active gene transcription. Here, we present the crystal structures of the RRM domains of human SETD1A and SETD1B. Although both RRM domains adopt a canonical RRM fold, their structural features are different from that of the yeast Set1 RRM domain, their yeast homolog. By using an ITC binding assay, we found an intrinsically disordered region in SETD1A/B binds WDR82. The structural analysis implies that the positively charged regions within human RRM domains might be involved in binding to RNA. Our work provides structural insight into the assembly of WDR82 with the catalytic subunits SETD1A/B in the context of the whole complex.
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22
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Ritchie FD, Lizarraga SB. The role of histone methyltransferases in neurocognitive disorders associated with brain size abnormalities. Front Neurosci 2023; 17:989109. [PMID: 36845425 PMCID: PMC9950662 DOI: 10.3389/fnins.2023.989109] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 01/17/2023] [Indexed: 02/12/2023] Open
Abstract
Brain size is controlled by several factors during neuronal development, including neural progenitor proliferation, neuronal arborization, gliogenesis, cell death, and synaptogenesis. Multiple neurodevelopmental disorders have co-morbid brain size abnormalities, such as microcephaly and macrocephaly. Mutations in histone methyltransferases that modify histone H3 on Lysine 36 and Lysine 4 (H3K36 and H3K4) have been identified in neurodevelopmental disorders involving both microcephaly and macrocephaly. H3K36 and H3K4 methylation are both associated with transcriptional activation and are proposed to sterically hinder the repressive activity of the Polycomb Repressor Complex 2 (PRC2). During neuronal development, tri-methylation of H3K27 (H3K27me3) by PRC2 leads to genome wide transcriptional repression of genes that regulate cell fate transitions and neuronal arborization. Here we provide a review of neurodevelopmental processes and disorders associated with H3K36 and H3K4 histone methyltransferases, with emphasis on processes that contribute to brain size abnormalities. Additionally, we discuss how the counteracting activities of H3K36 and H3K4 modifying enzymes vs. PRC2 could contribute to brain size abnormalities which is an underexplored mechanism in relation to brain size control.
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23
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Hughes AL, Szczurek AT, Kelley JR, Lastuvkova A, Turberfield AH, Dimitrova E, Blackledge NP, Klose RJ. A CpG island-encoded mechanism protects genes from premature transcription termination. Nat Commun 2023; 14:726. [PMID: 36759609 PMCID: PMC9911701 DOI: 10.1038/s41467-023-36236-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 01/23/2023] [Indexed: 02/11/2023] Open
Abstract
Transcription must be tightly controlled to regulate gene expression and development. However, our understanding of the molecular mechanisms that influence transcription and how these are coordinated in cells to ensure normal gene expression remains rudimentary. Here, by dissecting the function of the SET1 chromatin-modifying complexes that bind to CpG island-associated gene promoters, we discover that they play a specific and essential role in enabling the expression of low to moderately transcribed genes. Counterintuitively, this effect can occur independently of SET1 complex histone-modifying activity and instead relies on an interaction with the RNA Polymerase II-binding protein WDR82. Unexpectedly, we discover that SET1 complexes enable gene expression by antagonising premature transcription termination by the ZC3H4/WDR82 complex at CpG island-associated genes. In contrast, at extragenic sites of transcription, which typically lack CpG islands and SET1 complex occupancy, we show that the activity of ZC3H4/WDR82 is unopposed. Therefore, we reveal a gene regulatory mechanism whereby CpG islands are bound by a protein complex that specifically protects genic transcripts from premature termination, effectively distinguishing genic from extragenic transcription and enabling normal gene expression.
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Affiliation(s)
- Amy L Hughes
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | | | - Anna Lastuvkova
- Department of Biochemistry, University of Oxford, Oxford, UK
| | | | | | | | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK.
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24
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Morelli E, Fulciniti M, Samur MK, Ribeiro CF, Wert-Lamas L, Henninger JE, Gullà A, Aktas-Samur A, Todoerti K, Talluri S, Park WD, Federico C, Scionti F, Amodio N, Bianchi G, Johnstone M, Liu N, Gramegna D, Maisano D, Russo NA, Lin C, Tai YT, Neri A, Chauhan D, Hideshima T, Shammas MA, Tassone P, Gryaznov S, Young RA, Anderson KC, Novina CD, Loda M, Munshi NC. A MIR17HG-derived long noncoding RNA provides an essential chromatin scaffold for protein interaction and myeloma growth. Blood 2023; 141:391-405. [PMID: 36126301 PMCID: PMC10082365 DOI: 10.1182/blood.2022016892] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 09/08/2022] [Accepted: 09/13/2022] [Indexed: 01/31/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) can drive tumorigenesis and are susceptible to therapeutic intervention. Here, we used a large-scale CRISPR interference viability screen to interrogate cell-growth dependency to lncRNA genes in multiple myeloma (MM) and identified a prominent role for the miR-17-92 cluster host gene (MIR17HG). We show that an MIR17HG-derived lncRNA, named lnc-17-92, is the main mediator of cell-growth dependency acting in a microRNA- and DROSHA-independent manner. Lnc-17-92 provides a chromatin scaffold for the functional interaction between c-MYC and WDR82, thus promoting the expression of ACACA, which encodes the rate-limiting enzyme of de novo lipogenesis acetyl-coA carboxylase 1. Targeting MIR17HG pre-RNA with clinically applicable antisense molecules disrupts the transcriptional and functional activities of lnc-17-92, causing potent antitumor effects both in vitro and in vivo in 3 preclinical animal models, including a clinically relevant patient-derived xenograft NSG mouse model. This study establishes a novel oncogenic function of MIR17HG and provides potent inhibitors for translation to clinical trials.
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Affiliation(s)
- Eugenio Morelli
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Mariateresa Fulciniti
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Mehmet K. Samur
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Caroline F. Ribeiro
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Leon Wert-Lamas
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA
| | - Jon E. Henninger
- Whitehead Institute of Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA
| | - Annamaria Gullà
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Anil Aktas-Samur
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Katia Todoerti
- Department of Hematology, Fondazione Cà Granda IRCCS Policlinico, Milan, Italy
| | - Srikanth Talluri
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- VA Boston Healthcare System, Boston, MA
| | - Woojun D. Park
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Cinzia Federico
- Department of Clinical and Experimental Medicine, Magna Graecia University, Catanzaro, Italy
| | - Francesca Scionti
- Department of Clinical and Experimental Medicine, Magna Graecia University, Catanzaro, Italy
- Clinical Research Development and Phase I Unit, ASST Spedali Civili di Brescia, Brescia, Italy
| | - Nicola Amodio
- Department of Clinical and Experimental Medicine, Magna Graecia University, Catanzaro, Italy
| | - Giada Bianchi
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Megan Johnstone
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
| | - Na Liu
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
| | - Doriana Gramegna
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Domenico Maisano
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Nicola A. Russo
- Istituto di Ricerche Genetiche “G. Salvatore,” Biogem s.c.ar.l., Avellino, Italy
| | - Charles Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Yu-Tzu Tai
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Antonino Neri
- Department of Hematology, Fondazione Cà Granda IRCCS Policlinico, Milan, Italy
- Department of Oncology and Hemato-oncology, University of Milan, Milan, Italy
- Scientific Directorate, Azienda USL-IRCCS Reggio Emilia, Reggio Emilia, Italy
| | - Dharminder Chauhan
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Teru Hideshima
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Masood A. Shammas
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- VA Boston Healthcare System, Boston, MA
| | - Pierfrancesco Tassone
- Department of Clinical and Experimental Medicine, Magna Graecia University, Catanzaro, Italy
| | | | - Richard A. Young
- Whitehead Institute of Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA
| | - Kenneth C. Anderson
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
| | - Carl D. Novina
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA
| | - Massimo Loda
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Nikhil C. Munshi
- Department of Medical Oncology, Jerome Lipper Multiple Myeloma Center, Dana-Farber Cancer Institute, Boston, MA
- Harvard Medical School, Boston, MA
- VA Boston Healthcare System, Boston, MA
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25
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Barsoum M, Stenzel AT, Bochyńska A, Kuo CC, Tsompanidis A, Sayadi-Boroujeni R, Bussmann P, Lüscher-Firzlaff J, Costa IG, Lüscher B. Loss of the Ash2l subunit of histone H3K4 methyltransferase complexes reduces chromatin accessibility at promoters. Sci Rep 2022; 12:21506. [PMID: 36513698 PMCID: PMC9747801 DOI: 10.1038/s41598-022-25881-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Changes in gene expression programs are intimately linked to cell fate decisions. Post-translational modifications of core histones contribute to control gene expression. Methylation of lysine 4 of histone H3 (H3K4) correlates with active promoters and gene transcription. This modification is catalyzed by KMT2 methyltransferases, which require interaction with 4 core subunits, WDR5, RBBP5, ASH2L and DPY30, for catalytic activity. Ash2l is necessary for organismal development and for tissue homeostasis. In mouse embryo fibroblasts (MEFs), Ash2l loss results in gene repression, provoking a senescence phenotype. We now find that upon knockout of Ash2l both H3K4 mono- and tri-methylation (H3K4me1 and me3, respectively) were deregulated. In particular, loss of H3K4me3 at promoters correlated with gene repression, especially at CpG island promoters. Ash2l loss resulted in increased loading of histone H3 and reduced chromatin accessibility at promoters, accompanied by an increase of repressing and a decrease of activating histone marks. Moreover, we observed altered binding of CTCF upon Ash2l loss. Lost and gained binding was noticed at promoter-associated and intergenic sites, respectively. Thus, Ash2l loss and reduction of H3K4me3 correlate with altered chromatin accessibility and transcription factor binding. These findings contribute to a more detailed understanding of mechanistic consequences of H3K4me3 loss and associated repression of gene transcription and thus of the observed cellular consequences.
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Affiliation(s)
- Mirna Barsoum
- grid.1957.a0000 0001 0728 696XInstitute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Alexander T. Stenzel
- grid.1957.a0000 0001 0728 696XInstitute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Agnieszka Bochyńska
- grid.1957.a0000 0001 0728 696XInstitute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Chao-Chung Kuo
- grid.1957.a0000 0001 0728 696XInstitute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany ,grid.1957.a0000 0001 0728 696XInterdisciplinary Center for Clinical Research (IZKF), Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Alexander Tsompanidis
- grid.1957.a0000 0001 0728 696XInstitute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Roksaneh Sayadi-Boroujeni
- grid.1957.a0000 0001 0728 696XInstitute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Philip Bussmann
- grid.1957.a0000 0001 0728 696XInstitute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Juliane Lüscher-Firzlaff
- grid.1957.a0000 0001 0728 696XInstitute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Ivan G. Costa
- grid.1957.a0000 0001 0728 696XInstitute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany.
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26
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The PNUTS-PP1 complex acts as an intrinsic barrier to herpesvirus KSHV gene expression and replication. Nat Commun 2022; 13:7447. [PMID: 36460671 PMCID: PMC9718767 DOI: 10.1038/s41467-022-35268-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 11/24/2022] [Indexed: 12/03/2022] Open
Abstract
Control of RNA Polymerase II (pol II) elongation is a critical component of gene expression in mammalian cells. The PNUTS-PP1 complex controls elongation rates, slowing pol II after polyadenylation sites to promote termination. The Kaposi's sarcoma-associated herpesvirus (KSHV) co-opts pol II to express its genes, but little is known about its regulation of pol II elongation. We identified PNUTS as a suppressor of a KSHV reporter gene in a genome-wide CRISPR screen. PNUTS depletion enhances global KSHV gene expression and overall viral replication. Mechanistically, PNUTS requires PP1 interaction, binds viral RNAs downstream of polyadenylation sites, and restricts transcription readthrough of viral genes. Surprisingly, PNUTS also represses productive elongation at the 5´ ends of the KSHV reporter and the KSHV T1.4 RNA. From these data, we conclude that PNUTS' activity constitutes an intrinsic barrier to KSHV replication likely by suppressing pol II elongation at promoter-proximal regions.
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27
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Poreba E, Lesniewicz K, Durzynska J. Histone-lysine N-methyltransferase 2 (KMT2) complexes - a new perspective. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2022; 790:108443. [PMID: 36154872 DOI: 10.1016/j.mrrev.2022.108443] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 06/25/2022] [Accepted: 09/19/2022] [Indexed: 01/01/2023]
Abstract
Histone H3 Lys4 (H3K4) methylation is catalyzed by the Histone-Lysine N-Methyltransferase 2 (KMT2) protein family, and its members are required for gene expression control. In vertebrates, the KMT2s function in large multisubunit complexes known as COMPASS or COMPASS-like complexes (COMplex of Proteins ASsociated with Set1). The activity of these complexes is critical for proper development, and mutation-induced defects in their functioning have frequently been found in human cancers. Moreover, inherited or de novo mutations in KMT2 genes are among the etiological factors in neurodevelopmental disorders such as Kabuki and Kleefstra syndromes. The canonical role of KMT2s is to catalyze H3K4 methylation, which results in a permissive chromatin environment that drives gene expression. However, current findings described in this review demonstrate that these enzymes can regulate processes that are not dependent on methylation: noncatalytic functions of KMT2s include DNA damage response, cell division, and metabolic activities. Moreover, these enzymes may also methylate non-histone substrates and play a methylation-dependent function in the DNA damage response. In this review, we present an overview of the new, noncanonical activities of KMT2 complexes in a variety of cellular processes. These discoveries may have crucial implications for understanding the functions of these methyltransferases in developmental processes, disease, and epigenome-targeting therapeutic strategies in the future.
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Affiliation(s)
- Elzbieta Poreba
- Department of Genetics, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
| | - Krzysztof Lesniewicz
- Department of Molecular and Cellular Biology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland
| | - Julia Durzynska
- Department of Genetics, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland.
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Kusuyama J, Makarewicz NS, Albertson BG, Alves-Wagner AB, Conlin RH, Prince NB, Alves CR, Ramachandran K, Kozuka C, Xiudong Y, Xia Y, Hirshman MF, Hatta T, Nagatomi R, Nozik ES, Goodyear LJ. Maternal Exercise-Induced SOD3 Reverses the Deleterious Effects of Maternal High-Fat Diet on Offspring Metabolism Through Stabilization of H3K4me3 and Protection Against WDR82 Carbonylation. Diabetes 2022; 71:1170-1181. [PMID: 35290440 PMCID: PMC9163554 DOI: 10.2337/db21-0706] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 03/09/2022] [Indexed: 01/19/2023]
Abstract
Preclinical studies reveal maternal exercise as a promising intervention to reduce the transmission of multigenerational metabolic dysfunction caused by maternal obesity. The benefits of maternal exercise on offspring health may arise from multiple factors and have recently been shown to involve DNA demethylation of critical hepatic genes leading to enhanced glucose metabolism in offspring. Histone modification is another epigenetic regulator, yet the effects of maternal obesity and exercise on histone methylation in offspring are not known. Here, we find that maternal high-fat diet (HFD; 60% kcal from fat) induced dysregulation of offspring liver glucose metabolism in C57BL/6 mice through a mechanism involving increased reactive oxygen species, WD repeat-containing 82 (WDR82) carbonylation, and inactivation of histone H3 lysine 4 (H3K4) methyltransferase leading to decreased H3K4me3 at the promoters of glucose metabolic genes. Remarkably, the entire signal was restored if the HFD-fed dams had exercised during pregnancy. WDR82 overexpression in hepatoblasts mimicked the effects of maternal exercise on H3K4me3 levels. Placental superoxide dismutase 3 (SOD3), but not antioxidant treatment with N-acetylcysteine was necessary for the regulation of H3K4me3, gene expression, and glucose metabolism. Maternal exercise regulates a multicomponent epigenetic system in the fetal liver resulting in the transmission of the benefits of exercise to offspring.
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Affiliation(s)
- Joji Kusuyama
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA
- Frontier Research Institute for Interdisciplinary Sciences, Tohoku University, Sendai, Japan
- Division of Biomedical Engineering for Health and Welfare, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Corresponding authors: Laurie J. Goodyear, , and Joji Kusuyama,
| | - Nathan S. Makarewicz
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA
| | - Brent G. Albertson
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA
| | - Ana Barbara Alves-Wagner
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA
| | - Royce H. Conlin
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA
| | - Noah B. Prince
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA
| | - Christiano R.R. Alves
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA
| | - Krithika Ramachandran
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA
| | - Chisayo Kozuka
- YCI Laboratory for Metabolic Epigenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yang Xiudong
- Graduate School of Biomedical Sciences, University of Texas at Houston, Houston, TX
| | - Yang Xia
- Graduate School of Biomedical Sciences, University of Texas at Houston, Houston, TX
| | - Michael F. Hirshman
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA
| | - Toshihisa Hatta
- Department of Anatomy, Kanazawa Medical University, Kanazawa, Japan
| | - Ryoichi Nagatomi
- Division of Biomedical Engineering for Health and Welfare, Graduate School of Biomedical Engineering, Tohoku University, Sendai, Japan
- Department of Medicine and Science in Sports and Exercise, Tohoku University School of Medicine, Sendai, Japan
| | - Eva S. Nozik
- Cardiovascular Pulmonary Research Laboratories and Pediatric Critical Care, Department of Pediatrics, University of Colorado Anschutz Medical Center, Aurora, CO
| | - Laurie J. Goodyear
- Section on Integrative Physiology and Metabolism, Joslin Diabetes Center, Harvard Medical School, Boston, MA
- Corresponding authors: Laurie J. Goodyear, , and Joji Kusuyama,
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Chan J, Kumar A, Kono H. RNAPII driven post-translational modifications of nucleosomal histones. Trends Genet 2022; 38:1076-1095. [PMID: 35618507 DOI: 10.1016/j.tig.2022.04.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 04/08/2022] [Accepted: 04/22/2022] [Indexed: 12/12/2022]
Abstract
The current understanding of how specific distributions of histone post-translational modifications (PTMs) are achieved throughout the chromatin remains incomplete. This review focuses on the role of RNA polymerase II (RNAPII) in establishing H2BK120/K123 ubiquitination and H3K4/K36 methylation distribution. The rate of RNAPII transcription is mainly a function of the RNAPII elongation and recruitment rates. Two major mechanisms link RNAPII's transcription rate to the distribution of PTMs. First, the phosphorylation patterns of Ser2P/Ser5P in the C-terminal domain of RNAPII change as a function of time, since the start of elongation, linking them to the elongation rate. Ser2P/Ser5P recruits specific histone PTM enzymes/activators to the nucleosome. Second, multiple rounds of binding and catalysis by the enzymes are required to establish higher methylations (H3K4/36me3). Thus, methylation states are determined by the transcription rate. In summary, the first mechanism determines the location of methylations in the gene, while the second mechanism determines the methylation state.
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Affiliation(s)
- Justin Chan
- Molecular Modelling and Simulation (MMS) Team, Institute for Quantum Life Science (iQLS), National Institutes for Quantum Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
| | - Amarjeet Kumar
- Molecular Modelling and Simulation (MMS) Team, Institute for Quantum Life Science (iQLS), National Institutes for Quantum Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan
| | - Hidetoshi Kono
- Molecular Modelling and Simulation (MMS) Team, Institute for Quantum Life Science (iQLS), National Institutes for Quantum Science and Technology (QST), 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215, Japan.
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Cenik BK, Sze CC, Ryan CA, Das S, Cao K, Douillet D, Rendleman EJ, Zha D, Khan NH, Bartom E, Shilatifard A. A synthetic lethality screen reveals ING5 as a genetic dependency of catalytically dead Set1A/COMPASS in mouse embryonic stem cells. Proc Natl Acad Sci U S A 2022; 119:e2118385119. [PMID: 35500115 PMCID: PMC9171609 DOI: 10.1073/pnas.2118385119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/21/2022] [Indexed: 11/18/2022] Open
Abstract
Embryonic stem cells (ESCs) are defined by their ability to self-renew and the potential to differentiate into all tissues of the developing organism. We previously demonstrated that deleting the catalytic SET domain of the Set1A/complex of proteins associated with SET1 histone methyltransferase (Set1A/COMPASS) in mouse ESCs does not impair their viability or ability to self-renew; however, it leads to defects in differentiation. The precise mechanisms by which Set1A executes these functions remain to be elucidated. In this study, we demonstrate that mice lacking the SET domain of Set1A are embryonic lethal at a stage that is unique from null alleles. To gain insight into Set1A function in regulating pluripotency, we conducted a CRISPR/Cas9-mediated dropout screen and identified the MOZ/MORF (monocytic leukaemia zinc finger protein/monocytic leukaemia zinc finger protein-related factor) and HBO1 (HAT bound to ORC1) acetyltransferase complex member ING5 as a synthetic perturbation to Set1A. The loss of Ing5 in Set1AΔSET mouse ESCs decreases the fitness of these cells, and the simultaneous loss of ING5 and in Set1AΔSET leads to up-regulation of differentiation-associated genes. Taken together, our results point toward Set1A/COMPASS and ING5 as potential coregulators of the self-renewal and differentiation status of ESCs.
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Affiliation(s)
- Bercin K. Cenik
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Christie C. Sze
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Caila A. Ryan
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Siddhartha Das
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Kaixiang Cao
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Delphine Douillet
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Emily J. Rendleman
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Didi Zha
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Nabiha Haleema Khan
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Elizabeth Bartom
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Robert H. Lurie NCI Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Robert H. Lurie NCI Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
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Park K, Zhong J, Jang JS, Kim J, Kim HJ, Lee JH, Kim J. ZWC complex-mediated SPT5 phosphorylation suppresses divergent antisense RNA transcription at active gene promoters. Nucleic Acids Res 2022; 50:3835-3851. [PMID: 35325203 PMCID: PMC9023261 DOI: 10.1093/nar/gkac193] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/08/2022] [Accepted: 03/13/2022] [Indexed: 11/14/2022] Open
Abstract
The human genome encodes large numbers of non-coding RNAs, including divergent antisense transcripts at transcription start sites (TSSs). However, molecular mechanisms by which divergent antisense transcription is regulated have not been detailed. Here, we report a novel ZWC complex composed of ZC3H4, WDR82 and CK2 that suppresses divergent antisense transcription. The ZWC complex preferentially localizes at TSSs of active genes through direct interactions of ZC3H4 and WDR82 subunits with the S5p RNAPII C-terminal domain. ZC3H4 depletion leads to increased divergent antisense transcription, especially at genes that naturally produce divergent antisense transcripts. We further demonstrate that the ZWC complex phosphorylates the previously uncharacterized N-terminal acidic domain of SPT5, a subunit of the transcription-elongation factor DSIF, and that this phosphorylation is responsible for suppressing divergent antisense transcription. Our study provides evidence that the newly identified ZWC-DSIF axis regulates the direction of transcription during the transition from early to productive elongation.
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Affiliation(s)
- Kihyun Park
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Jian Zhong
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
| | - Jin Sung Jang
- Medical Genome Facility, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jihyun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
| | - Hye-Jung Kim
- New Drug Development Center, OSONG Medical Innovation Foundation, Cheongju 28160, South Korea
| | - Jeong-Heon Lee
- Epigenomics Program, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905, USA
- Division of Experimental Pathology and Laboratory Medicine, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Jaehoon Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, South Korea
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Liu Z, Wu A, Wu Z, Wang T, Pan Y, Li B, Zhang X, Yu M. TOX4 facilitates promoter-proximal pausing and C-terminal domain dephosphorylation of RNA polymerase II in human cells. Commun Biol 2022; 5:300. [PMID: 35365735 PMCID: PMC8975821 DOI: 10.1038/s42003-022-03214-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/02/2022] [Indexed: 11/24/2022] Open
Abstract
TOX4 is one of the regulatory factors of PP1 phosphatases with poorly understood functions. Here we show that chromatin occupancy pattern of TOX4 resembles that of RNA polymerase II (Pol II), and its loss increases cellular level of C-terminal domain (CTD) phosphorylated Pol II but mainly decreases Pol II occupancy on promoters. In addition, elongation rate analyses by 4sUDRB-seq suggest that TOX4 restricts pause release and early elongation but promotes late elongation. Moreover, TT-seq analyses indicate that TOX4 loss mainly decreases transcriptional output. Mechanistically, TOX4 may restrict pause release through facilitating CTD serine 2 and DSIF dephosphorylation, and promote Pol II recycling and reinitiation through facilitating CTD serines 2 and 5 dephosphorylation. Furthermore, among the PP1 phosphatases, TOX4 preferentially binds PP1α and is capable of facilitating Pol II CTD dephosphorylation in vitro. These results lay the foundation for a better understanding of the role of TOX4 in transcriptional regulation. As a role of TOX4, one of the regulatory proteins of PP1 phosphatases, in transcriptional regulation, authors here show that TOX4 restricts pause release and early productive elongation, and promotes Pol II recycling and transcriptional reinitiation.
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Affiliation(s)
- Ziling Liu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Aiwei Wu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Zhen Wu
- State key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Talang Wang
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China
| | - Yixuan Pan
- Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Bing Li
- Department of Biochemistry and Molecular Cell Biology, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
| | - Xumin Zhang
- State key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, 200438, Shanghai, China
| | - Ming Yu
- Sheng Yushou Center of Cell Biology and Immunology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 200240, Shanghai, China. .,Ministry of Education Key Laboratory of Systems Biomedicine, Shanghai Jiao Tong University, 200240, Shanghai, China.
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Control of non-productive RNA polymerase II transcription via its early termination in metazoans. Biochem Soc Trans 2022; 50:283-295. [PMID: 35166324 DOI: 10.1042/bst20201140] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 01/11/2022] [Accepted: 01/24/2022] [Indexed: 11/17/2022]
Abstract
Transcription establishes the universal first step of gene expression where RNA is produced by a DNA-dependent RNA polymerase. The most versatile of eukaryotic RNA polymerases, RNA polymerase II (Pol II), transcribes a broad range of DNA including protein-coding and a variety of non-coding transcription units. Although Pol II can be configured as a durable enzyme capable of transcribing hundreds of kilobases, there is reliable evidence of widespread abortive Pol II transcription termination shortly after initiation, which is often followed by rapid degradation of the associated RNA. The molecular details underlying this phenomenon are still vague but likely reflect the action of quality control mechanisms on the early Pol II complex. Here, we summarize current knowledge of how and when such promoter-proximal quality control is asserted on metazoan Pol II.
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Wilson KD, Porter EG, Garcia BA. Reprogramming of the epigenome in neurodevelopmental disorders. Crit Rev Biochem Mol Biol 2022; 57:73-112. [PMID: 34601997 PMCID: PMC9462920 DOI: 10.1080/10409238.2021.1979457] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The etiology of neurodevelopmental disorders (NDDs) remains a challenge for researchers. Human brain development is tightly regulated and sensitive to cellular alterations caused by endogenous or exogenous factors. Intriguingly, the surge of clinical sequencing studies has revealed that many of these disorders are monogenic and monoallelic. Notably, chromatin regulation has emerged as highly dysregulated in NDDs, with many syndromes demonstrating phenotypic overlap, such as intellectual disabilities, with one another. Here we discuss epigenetic writers, erasers, readers, remodelers, and even histones mutated in NDD patients, predicted to affect gene regulation. Moreover, this review focuses on disorders associated with mutations in enzymes involved in histone acetylation and methylation, and it highlights syndromes involving chromatin remodeling complexes. Finally, we explore recently discovered histone germline mutations and their pathogenic outcome on neurological function. Epigenetic regulators are mutated at every level of chromatin organization. Throughout this review, we discuss mechanistic investigations, as well as various animal and iPSC models of these disorders and their usefulness in determining pathomechanism and potential therapeutics. Understanding the mechanism of these mutations will illuminate common pathways between disorders. Ultimately, classifying these disorders based on their effects on the epigenome will not only aid in prognosis in patients but will aid in understanding the role of epigenetic machinery throughout neurodevelopment.
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Affiliation(s)
- Khadija D. Wilson
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Elizabeth G. Porter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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microRNA-155-3p delivered by M2 macrophages-derived exosomes enhances the progression of medulloblastoma through regulation of WDR82. J Transl Med 2022; 20:13. [PMID: 34983581 PMCID: PMC8728908 DOI: 10.1186/s12967-021-03156-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 11/19/2021] [Indexed: 01/12/2023] Open
Abstract
Objective Exosomes, membranous nanovesicles, naturally bringing proteins, mRNAs, and microRNAs (miRNAs), play crucial roles in tumor pathogenesis. This study was to investigate the role of miR-155-3p from M2 macrophages-derived exosomes (M2-Exo) in promoting medulloblastoma (MB) progression by mediating WD repeat domain 82 (WDR82). Methods miR-155-3p expression was detected by RT-qPCR. The relationship of miR-155-3p with clinicopathological features of MB patients was analyzed. M2-Exo were isolated and identified by TEM, NTA and Western blot. CCK-8 assay, colony formation assay, flow cytometry, wound healing assay, and Transwell assay were performed to explore the role of miR-155-3p-enriched M2-Exo on the progression of MB cells. Luciferase assay were used to identify the relationship between miR-155-3p and WDR82. The effect of miR-155-3p-enriched M2-Exo on tumorigenesis of MB was confirmed by the xenograft nude mice model. Results miR-155-3p was up-regulated in MB tissues of patients and MB cell lines. High miR-155-3p expression was correlated with the pathological type and molecular subtype classification of MB patients. WDR82 was a direct target of miR-155-3p. miR-155-3p was packaged into M2-Exo. miR-155-3p-enriched M2-Exo promoted the progression of Daoy cells. miR-155-3p-enriched M2-Exo promoted in vivo tumorigenesis. Conclusion The study highlights that miR-155-3p-loaded M2-Exo enhances the growth of MB cells via down-regulating WDR82, which might provide a deep insight into MB mechanism. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-03156-y.
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Michurina A, Sakib MS, Kerimoglu C, Krüger DM, Kaurani L, Islam MR, Joshi PD, Schröder S, Centeno TP, Zhou J, Pradhan R, Cha J, Xu X, Eichele G, Zeisberg EM, Kranz A, Stewart AF, Fischer A. Postnatal expression of the lysine methyltransferase SETD1B is essential for learning and the regulation of neuron-enriched genes. EMBO J 2022; 41:e106459. [PMID: 34806773 PMCID: PMC8724770 DOI: 10.15252/embj.2020106459] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/04/2021] [Accepted: 10/15/2021] [Indexed: 01/04/2023] Open
Abstract
In mammals, histone 3 lysine 4 methylation (H3K4me) is mediated by six different lysine methyltransferases. Among these enzymes, SETD1B (SET domain containing 1b) has been linked to syndromic intellectual disability in human subjects, but its role in the mammalian postnatal brain has not been studied yet. Here, we employ mice deficient for Setd1b in excitatory neurons of the postnatal forebrain, and combine neuron-specific ChIP-seq and RNA-seq approaches to elucidate its role in neuronal gene expression. We observe that Setd1b controls the expression of a set of genes with a broad H3K4me3 peak at their promoters, enriched for neuron-specific genes linked to learning and memory function. Comparative analyses in mice with conditional deletion of Kmt2a and Kmt2b histone methyltransferases show that SETD1B plays a more pronounced and potent role in regulating such genes. Moreover, postnatal loss of Setd1b leads to severe learning impairment, suggesting that SETD1B-dependent regulation of H3K4me levels in postnatal neurons is critical for cognitive function.
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Affiliation(s)
- Alexandra Michurina
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - M Sadman Sakib
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Cemil Kerimoglu
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Dennis Manfred Krüger
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Lalit Kaurani
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Md Rezaul Islam
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Parth Devesh Joshi
- Department for Gene and BehaviorMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Sophie Schröder
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Tonatiuh Pena Centeno
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Jiayin Zhou
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Ranjit Pradhan
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Julia Cha
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
| | - Xingbo Xu
- Department of Cardiology and PneumologyUniversity Medical Center of GöttingenGeorg‐August UniversityGöttingenGermany
- German Centre for Cardiovascular Research (DZHK)Partner Site GöttingenGöttingenGermany
| | - Gregor Eichele
- Department for Gene and BehaviorMax Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Elisabeth M Zeisberg
- Department of Cardiology and PneumologyUniversity Medical Center of GöttingenGeorg‐August UniversityGöttingenGermany
- German Centre for Cardiovascular Research (DZHK)Partner Site GöttingenGöttingenGermany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC)University of GöttingenGermany
| | - Andrea Kranz
- Biotechnology CenterCenter for Molecular and Cellular BioengineeringDresden University of TechnologyDresdenGermany
| | - A Francis Stewart
- Biotechnology CenterCenter for Molecular and Cellular BioengineeringDresden University of TechnologyDresdenGermany
- Max‐Planck‐Institute for Cell Biology and GeneticsDresdenGermany
| | - André Fischer
- Department for Systems Medicine and EpigeneticsGerman Center for Neurodegenerative Diseases (DZNE)GöttingenGermany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC)University of GöttingenGermany
- Department of Psychiatry and PsychotherapyUniversity Medical Center GöttingenGöttingenGermany
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Blackledge NP, Klose RJ. The molecular principles of gene regulation by Polycomb repressive complexes. Nat Rev Mol Cell Biol 2021; 22:815-833. [PMID: 34400841 PMCID: PMC7612013 DOI: 10.1038/s41580-021-00398-y] [Citation(s) in RCA: 178] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/01/2021] [Indexed: 12/12/2022]
Abstract
Precise control of gene expression is fundamental to cell function and development. Although ultimately gene expression relies on DNA-binding transcription factors to guide the activity of the transcription machinery to genes, it has also become clear that chromatin and histone post-translational modification have fundamental roles in gene regulation. Polycomb repressive complexes represent a paradigm of chromatin-based gene regulation in animals. The Polycomb repressive system comprises two central protein complexes, Polycomb repressive complex 1 (PRC1) and PRC2, which are essential for normal gene regulation and development. Our early understanding of Polycomb function relied on studies in simple model organisms, but more recently it has become apparent that this system has expanded and diverged in mammals. Detailed studies are now uncovering the molecular mechanisms that enable mammalian PRC1 and PRC2 to identify their target sites in the genome, communicate through feedback mechanisms to create Polycomb chromatin domains and control transcription to regulate gene expression. In this Review, we discuss and contextualize the emerging principles that define how this fascinating chromatin-based system regulates gene expression in mammals.
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Affiliation(s)
| | - Robert J Klose
- Department of Biochemistry, University of Oxford, Oxford, UK.
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38
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Wang S, Bleeck A, Nadif Kasri N, Kleefstra T, van Rhijn JR, Schubert D. SETD1A Mediated H3K4 Methylation and Its Role in Neurodevelopmental and Neuropsychiatric Disorders. Front Mol Neurosci 2021; 14:772000. [PMID: 34803610 PMCID: PMC8595121 DOI: 10.3389/fnmol.2021.772000] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 10/12/2021] [Indexed: 01/07/2023] Open
Abstract
Posttranslational modification of histones and related gene regulation are shown to be affected in an increasing number of neurological disorders. SETD1A is a chromatin remodeler that influences gene expression through the modulation of mono- di- and trimethylation marks on Histone-H3-Lysine-4 (H3K4me1/2/3). H3K4 methylation is predominantly described to result in transcriptional activation, with its mono- di- and trimethylated forms differentially enriched at promoters or enhancers. Recently, dominant mostly de novo variants in SETD1A have clinically been linked to developmental delay, intellectual disability (DD/ID), and schizophrenia (SCZ). Affected individuals often display both developmental and neuropsychiatric abnormalities. The primary diagnoses are mainly dependent on the age at which the individual is assessed. Investigations in mouse models of SETD1A dysfunction have been able to recapitulate key behavioral features associated with ID and SCZ. Furthermore, functional investigations suggest disrupted synaptic and neuronal network function in these mouse models. In this review, we provide an overview of pre-clinical studies on the role of SETD1A in neuronal development. A better understanding of the pathobiology underlying these disorders may provide novel opportunities for therapeutic intervention. As such, we will discuss possible strategies to move forward in elucidating the genotype-phenotype correlation in SETD1A associated disorders.
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Affiliation(s)
- Shan Wang
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, Netherlands
| | - Anna Bleeck
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, Netherlands
| | - Nael Nadif Kasri
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, Netherlands.,Department of Human Genetics, Radboudumc, Nijmegen, Netherlands
| | - Tjitske Kleefstra
- Department of Human Genetics, Radboudumc, Nijmegen, Netherlands.,Centre of Excellence for Neuropsychiatry, Vincent van Gogh Institute for Psychiatry, Venray, Netherlands
| | - Jon-Ruben van Rhijn
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, Netherlands
| | - Dirk Schubert
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboudumc, Nijmegen, Netherlands
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39
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Zhang Z, Liu T, Dong H, Li J, Sun H, Qian X, Qin W. An RNA tagging approach for system-wide RNA-binding proteome profiling and dynamics investigation upon transcription inhibition. Nucleic Acids Res 2021; 49:e65. [PMID: 33693821 PMCID: PMC8216453 DOI: 10.1093/nar/gkab156] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 02/17/2021] [Accepted: 03/08/2021] [Indexed: 12/20/2022] Open
Abstract
RNA-protein interactions play key roles in epigenetic, transcriptional and posttranscriptional regulation. To reveal the regulatory mechanisms of these interactions, global investigation of RNA-binding proteins (RBPs) and monitor their changes under various physiological conditions are needed. Herein, we developed a psoralen probe (PP)-based method for RNA tagging and ribonucleic-protein complex (RNP) enrichment. Isolation of both coding and noncoding RNAs and mapping of 2986 RBPs including 782 unknown candidate RBPs from HeLa cells was achieved by PP enrichment, RNA-sequencing and mass spectrometry analysis. The dynamics study of RNPs by PP enrichment after the inhibition of RNA synthesis provides the first large-scale distribution profile of RBPs bound to RNAs with different decay rates. Furthermore, the remarkably greater decreases in the abundance of the RBPs obtained by PP-enrichment than by global proteome profiling suggest that PP enrichment after transcription inhibition offers a valuable way for large-scale evaluation of the candidate RBPs.
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Affiliation(s)
- Zheng Zhang
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Tong Liu
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Hangyan Dong
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jian Li
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Haofan Sun
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Xiaohong Qian
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China
| | - Weijie Qin
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing 102206, China.,College of Basic Medicine, Anhui Medical University, Hefei 230032, China
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40
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Hsu CL, Lo YC, Kao CF. H3K4 Methylation in Aging and Metabolism. EPIGENOMES 2021; 5:14. [PMID: 34968301 PMCID: PMC8594702 DOI: 10.3390/epigenomes5020014] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/02/2021] [Accepted: 06/15/2021] [Indexed: 02/03/2023] Open
Abstract
During the process of aging, extensive epigenetic alterations are made in response to both exogenous and endogenous stimuli. Here, we summarize the current state of knowledge regarding one such alteration, H3K4 methylation (H3K4me), as it relates to aging in different species. We especially highlight emerging evidence that links this modification with metabolic pathways, which may provide a mechanistic link to explain its role in aging. H3K4me is a widely recognized marker of active transcription, and it appears to play an evolutionarily conserved role in determining organism longevity, though its influence is context specific and requires further clarification. Interestingly, the modulation of H3K4me dynamics may occur as a result of nutritional status, such as methionine restriction. Methionine status appears to influence H3K4me via changes in the level of S-adenosyl methionine (SAM, the universal methyl donor) or the regulation of H3K4-modifying enzyme activities. Since methionine restriction is widely known to extend lifespan, the mechanistic link between methionine metabolic flux, the sensing of methionine concentrations and H3K4me status may provide a cogent explanation for several seemingly disparate observations in aging organisms, including age-dependent H3K4me dynamics, gene expression changes, and physiological aberrations. These connections are not yet entirely understood, especially at a molecular level, and will require further elucidation. To conclude, we discuss some potential H3K4me-mediated molecular mechanisms that may link metabolic status to the aging process.
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Affiliation(s)
- Chia-Ling Hsu
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan;
| | - Yi-Chen Lo
- Graduate Institute of Food Science and Technology, National Taiwan University, Taipei 10617, Taiwan;
| | - Cheng-Fu Kao
- Institute of Cellular and Organismic Biology, Academia Sinica, Taipei 11529, Taiwan;
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41
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Kummeling J, Stremmelaar DE, Raun N, Reijnders MRF, Willemsen MH, Ruiterkamp-Versteeg M, Schepens M, Man CCO, Gilissen C, Cho MT, McWalter K, Sinnema M, Wheless JW, Simon MEH, Genetti CA, Casey AM, Terhal PA, van der Smagt JJ, van Gassen KLI, Joset P, Bahr A, Steindl K, Rauch A, Keller E, Raas-Rothschild A, Koolen DA, Agrawal PB, Hoffman TL, Powell-Hamilton NN, Thiffault I, Engleman K, Zhou D, Bodamer O, Hoefele J, Riedhammer KM, Schwaibold EMC, Tasic V, Schubert D, Top D, Pfundt R, Higgs MR, Kramer JM, Kleefstra T. Characterization of SETD1A haploinsufficiency in humans and Drosophila defines a novel neurodevelopmental syndrome. Mol Psychiatry 2021; 26:2013-2024. [PMID: 32346159 DOI: 10.1038/s41380-020-0725-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 04/01/2020] [Accepted: 04/01/2020] [Indexed: 12/18/2022]
Abstract
Defects in histone methyltransferases (HMTs) are major contributing factors in neurodevelopmental disorders (NDDs). Heterozygous variants of SETD1A involved in histone H3 lysine 4 (H3K4) methylation were previously identified in individuals with schizophrenia. Here, we define the clinical features of the Mendelian syndrome associated with haploinsufficiency of SETD1A by investigating 15 predominantly pediatric individuals who all have de novo SETD1A variants. These individuals present with a core set of symptoms comprising global developmental delay and/or intellectual disability, subtle facial dysmorphisms, behavioral and psychiatric problems. We examined cellular phenotypes in three patient-derived lymphoblastoid cell lines with three variants: p.Gly535Alafs*12, c.4582-2_4582delAG, and p.Tyr1499Asp. These patient cell lines displayed DNA damage repair defects that were comparable to previously observed RNAi-mediated depletion of SETD1A. This suggested that these variants, including the p.Tyr1499Asp in the catalytic SET domain, behave as loss-of-function (LoF) alleles. Previous studies demonstrated a role for SETD1A in cell cycle control and differentiation. However, individuals with SETD1A variants do not show major structural brain defects or severe microcephaly, suggesting that defective proliferation and differentiation of neural progenitors is unlikely the single underlying cause of the disorder. We show here that the Drosophila melanogaster SETD1A orthologue is required in postmitotic neurons of the fly brain for normal memory, suggesting a role in post development neuronal function. Together, this study defines a neurodevelopmental disorder caused by dominant de novo LoF variants in SETD1A and further supports a role for H3K4 methyltransferases in the regulation of neuronal processes underlying normal cognitive functioning.
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Affiliation(s)
- Joost Kummeling
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Diante E Stremmelaar
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Nicholas Raun
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada.,Department of Physiology and Pharmacology, The University of Western Ontario, London, ON, Canada
| | - Margot R F Reijnders
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6229 ER, Maastricht, The Netherlands
| | - Marjolein H Willemsen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Martina Ruiterkamp-Versteeg
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Marga Schepens
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Calvin C O Man
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Christian Gilissen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | | | | | - Margje Sinnema
- Department of Clinical Genetics and School for Oncology & Developmental Biology (GROW), Maastricht University Medical Center, 6229 ER, Maastricht, The Netherlands
| | - James W Wheless
- Division of Pediatric Neurology, University of Tennessee Health Science Center, Memphis, TN, USA.,Neuroscience Institute & Le Bonheur Comprehensive Epilepsy Program, Le Bonheur Children's Hospital, Memphis, TN, USA
| | - Marleen E H Simon
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Casie A Genetti
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital/Harvard Medical School, Boston, MA, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Alicia M Casey
- Division of Pulmonary and Respiratory Diseases, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Paulien A Terhal
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Jasper J van der Smagt
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Koen L I van Gassen
- Department of Genetics, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Pascal Joset
- Institute of Medical Genetics, University of Zurich, Schlieren, 8952, Zurich, Switzerland
| | - Angela Bahr
- Institute of Medical Genetics, University of Zurich, Schlieren, 8952, Zurich, Switzerland
| | - Katharina Steindl
- Institute of Medical Genetics, University of Zurich, Schlieren, 8952, Zurich, Switzerland
| | - Anita Rauch
- Institute of Medical Genetics, University of Zurich, Schlieren, 8952, Zurich, Switzerland
| | - Elmar Keller
- Division of Neuropediatrics, Cantonal Hospital Graubuenden, Chur, Switzerland
| | - Annick Raas-Rothschild
- Institute of Rare Disease, Danek Gertner Institute of Human Genetics, Sheba Medical Center, Tel Hashomer, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Israel
| | - David A Koolen
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Pankaj B Agrawal
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital/Harvard Medical School, Boston, MA, USA.,The Manton Center for Orphan Disease Research, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.,Division of Newborn Medicine, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Trevor L Hoffman
- Regional Department of Genetics, Southern California Kaiser Permanente Medical Group, 1188N. Euclid Street, Anaheim, CA, 92801, USA
| | - Nina N Powell-Hamilton
- Division of Medical Genetics, Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA.,Department of Pathology and Laboratory Medicine, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Isabelle Thiffault
- Center for Pediatric Genomic Medicine, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA.,Division of Clinical Genetics, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Kendra Engleman
- Department of Pediatrics, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Dihong Zhou
- Department of Pediatrics, Children's Mercy Hospital, University of Missouri-Kansas City School of Medicine, Kansas City, MO, USA
| | - Olaf Bodamer
- Division of Genetics and Genomics, Department of Medicine, Boston Children's Hospital/Harvard Medical School, Boston, MA, USA
| | - Julia Hoefele
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | - Korbinian M Riedhammer
- Institute of Human Genetics, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany.,Department of Nephrology, Klinikum rechts der Isar, Technical University of Munich, Munich, Germany
| | | | - Velibor Tasic
- Medical School Skopje, University Children's Hospital, Skopje, North Macedonia
| | - Dirk Schubert
- Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Deniz Top
- Department of Pediatrics, Dalhousie University, Halifax, NS, Canada
| | - Rolph Pfundt
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands
| | - Martin R Higgs
- Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Jamie M Kramer
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS, Canada.,Department of Physiology and Pharmacology, The University of Western Ontario, London, ON, Canada
| | - Tjitske Kleefstra
- Department of Human Genetics, Donders Institute for Brain, Cognition and Behavior, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, The Netherlands.
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42
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Estell C, Davidson L, Steketee PC, Monier A, West S. ZC3H4 restricts non-coding transcription in human cells. eLife 2021; 10:67305. [PMID: 33913806 PMCID: PMC8137146 DOI: 10.7554/elife.67305] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/27/2021] [Indexed: 02/06/2023] Open
Abstract
The human genome encodes thousands of non-coding RNAs. Many of these terminate early and are then rapidly degraded, but how their transcription is restricted is poorly understood. In a screen for protein-coding gene transcriptional termination factors, we identified ZC3H4. Its depletion causes upregulation and extension of hundreds of unstable transcripts, particularly antisense RNAs and those transcribed from so-called super-enhancers. These loci are occupied by ZC3H4, suggesting that it directly functions in their transcription. Consistently, engineered tethering of ZC3H4 to reporter RNA promotes its degradation by the exosome. ZC3H4 is predominantly metazoan –interesting when considering its impact on enhancer RNAs that are less prominent in single-celled organisms. Finally, ZC3H4 loss causes a substantial reduction in cell proliferation, highlighting its overall importance. In summary, we identify ZC3H4 as playing an important role in restricting non-coding transcription in multicellular organisms.
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Affiliation(s)
- Chris Estell
- The Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Lee Davidson
- The Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Pieter C Steketee
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Adam Monier
- The Living Systems Institute, University of Exeter, Exeter, United Kingdom
| | - Steven West
- The Living Systems Institute, University of Exeter, Exeter, United Kingdom
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43
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A first exon termination checkpoint preferentially suppresses extragenic transcription. Nat Struct Mol Biol 2021; 28:337-346. [PMID: 33767452 PMCID: PMC7610630 DOI: 10.1038/s41594-021-00572-y] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/12/2021] [Indexed: 01/31/2023]
Abstract
Interactions between the splicing machinery and RNA polymerase II increase protein-coding gene transcription. Similarly, exons and splicing signals of enhancer-generated long noncoding RNAs (elncRNAs) augment enhancer activity. However, elncRNAs are inefficiently spliced, suggesting that, compared with protein-coding genes, they contain qualitatively different exons with a limited ability to drive splicing. We show here that the inefficiently spliced first exons of elncRNAs as well as promoter-antisense long noncoding RNAs (pa-lncRNAs) in human and mouse cells trigger a transcription termination checkpoint that requires WDR82, an RNA polymerase II-binding protein, and its RNA-binding partner of previously unknown function, ZC3H4. We propose that the first exons of elncRNAs and pa-lncRNAs are an intrinsic component of a regulatory mechanism that, on the one hand, maximizes the activity of these cis-regulatory elements by recruiting the splicing machinery and, on the other, contains elements that suppress pervasive extragenic transcription.
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44
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Zhou S, Liu X, Sun W, Zhang M, Yin Y, Pan S, He D, Shen M, Yang J, Zheng Q, Wang W. The COMPASS-like complex modulates fungal development and pathogenesis by regulating H3K4me3-mediated targeted gene expression in Magnaporthe oryzae. MOLECULAR PLANT PATHOLOGY 2021; 22:422-439. [PMID: 33559339 PMCID: PMC7938624 DOI: 10.1111/mpp.13035] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 12/01/2020] [Accepted: 01/05/2021] [Indexed: 05/07/2023]
Abstract
Histone-3-lysine-4 (H3K4) methylation is catalysed by the multiprotein complex known as the Set1/COMPASS or MLL/COMPASS-like complex, an element that is highly evolutionarily conserved from yeast to humans. However, the components and mechanisms by which the COMPASS-like complex targets the H3K4 methylation of plant-pathogenic genes in fungi remain elusive. Here we present a comprehensive analysis combining biochemical, molecular, and genome-wide approaches to characterize the roles of the COMPASS-like family in the rice blast fungus Magnaporthe oryzae, a model plant pathogen. We purified and identified six conserved subunits of COMPASS from M. oryzae: MoBre2 (Cps60/ASH2L), MoSpp1 (Cps40/Cfp1), MoSwd2 (Cps35), MoSdc1 (Cps25/DPY30), MoSet1 (MLL/ALL), and MoRbBP5 (Cps50), using an affinity tag on MoBre2. We determined the sequence repeat in dual-specificity kinase splA and ryanodine receptors domain of MoBre2 can interact directly with the DPY30 domain of MoSdc1 in vitro. Furthermore, we found that deletion of the genes encoding COMPASS subunits of MoBre2, MoSPP1, and MoSwd2 caused similar defects regarding invasive hyphal development and pathogenicity. Genome-wide profiling of H3K4me3 revealed that it has remarkable co-occupancy at the transcription start site regions of target genes. Significantly, these target genes are often involved in spore germination and pathogenesis. Decreased gene expression caused by the deletion of MoBre2, MoSwd2, or MoSpp1 was highly correlated with a decrease in H3K4me3. These results suggest that MoBre2, MoSpp1, and MoSwd2 function as a whole COMPASS complex, contributing to fungal development and pathogenesis by regulating H3K4me3-targeted genes in M. oryzae.
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Affiliation(s)
- Sida Zhou
- Beijing Key Laboratory of New Technology in Agricultural ApplicationNational Demonstration Center for Experimental Plant Production EducationBeijing University of AgricultureBeijingChina
| | - Xiuying Liu
- Center for Research and CooperationNovogene Bioinformatics InstituteBeijingChina
| | - Wanyu Sun
- Beijing Key Laboratory of New Technology in Agricultural ApplicationNational Demonstration Center for Experimental Plant Production EducationBeijing University of AgricultureBeijingChina
| | - Mengyu Zhang
- Beijing Key Laboratory of New Technology in Agricultural ApplicationNational Demonstration Center for Experimental Plant Production EducationBeijing University of AgricultureBeijingChina
| | - Yue Yin
- Beijing Key Laboratory of New Technology in Agricultural ApplicationNational Demonstration Center for Experimental Plant Production EducationBeijing University of AgricultureBeijingChina
| | - Song Pan
- Ministry of Agriculture Key Laboratory of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Dan He
- Ministry of Agriculture Key Laboratory of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Mi Shen
- Ministry of Agriculture Key Laboratory of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Jun Yang
- Ministry of Agriculture Key Laboratory of Pest Monitoring and Green ManagementCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Qi Zheng
- Center for Research and CooperationNovogene Bioinformatics InstituteBeijingChina
| | - Weixiang Wang
- Beijing Key Laboratory of New Technology in Agricultural ApplicationNational Demonstration Center for Experimental Plant Production EducationBeijing University of AgricultureBeijingChina
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45
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Greulich F, Wierer M, Mechtidou A, Gonzalez-Garcia O, Uhlenhaut NH. The glucocorticoid receptor recruits the COMPASS complex to regulate inflammatory transcription at macrophage enhancers. Cell Rep 2021; 34:108742. [PMID: 33567280 PMCID: PMC7873837 DOI: 10.1016/j.celrep.2021.108742] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 12/09/2020] [Accepted: 01/20/2021] [Indexed: 12/30/2022] Open
Abstract
Glucocorticoids (GCs) are effective anti-inflammatory drugs; yet, their mechanisms of action are poorly understood. GCs bind to the glucocorticoid receptor (GR), a ligand-gated transcription factor controlling gene expression in numerous cell types. Here, we characterize GR’s protein interactome and find the SETD1A (SET domain containing 1A)/COMPASS (complex of proteins associated with Set1) histone H3 lysine 4 (H3K4) methyltransferase complex highly enriched in activated mouse macrophages. We show that SETD1A/COMPASS is recruited by GR to specific cis-regulatory elements, coinciding with H3K4 methylation dynamics at subsets of sites, upon treatment with lipopolysaccharide (LPS) and GCs. By chromatin immunoprecipitation sequencing (ChIP-seq) and RNA-seq, we identify subsets of GR target loci that display SETD1A occupancy, H3K4 mono-, di-, or tri-methylation patterns, and transcriptional changes. However, our data on methylation status and COMPASS recruitment suggest that SETD1A has additional transcriptional functions. Setd1a loss-of-function studies reveal that SETD1A/COMPASS is required for GR-controlled transcription of subsets of macrophage target genes. We demonstrate that the SETD1A/COMPASS complex cooperates with GR to mediate anti-inflammatory effects. GR’s transcriptional complex in macrophages includes COMPASS proteins GR ligand changes SETD1A chromatin occupancy in activated macrophages Subsets of GR target sites show COMPASS binding and H3K4 methylation dynamics SETD1A is required for some of GR’s anti-inflammatory actions
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Affiliation(s)
- Franziska Greulich
- Institute for Diabetes and Obesity (IDO) & Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), 85764 Neuherberg (Munich), Germany; Metabolic Programming, School of Life Sciences Weihenstephan, ZIEL - Institute for Food & Health, Technische Universitaet Muenchen (TUM), 85354 Freising, Germany
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Aikaterini Mechtidou
- Institute for Diabetes and Obesity (IDO) & Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), 85764 Neuherberg (Munich), Germany
| | - Omar Gonzalez-Garcia
- Institute for Diabetes and Obesity (IDO) & Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), 85764 Neuherberg (Munich), Germany
| | - N Henriette Uhlenhaut
- Institute for Diabetes and Obesity (IDO) & Institute for Diabetes and Cancer (IDC), Helmholtz Center Munich (HMGU) and German Center for Diabetes Research (DZD), 85764 Neuherberg (Munich), Germany; Metabolic Programming, School of Life Sciences Weihenstephan, ZIEL - Institute for Food & Health, Technische Universitaet Muenchen (TUM), 85354 Freising, Germany; Metabolic Biochemistry and Genetics, Gene Center, Ludwig-Maximilians-Universitaet LMU, 81377 Munich, Germany.
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46
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Aberrant Activity of Histone-Lysine N-Methyltransferase 2 (KMT2) Complexes in Oncogenesis. Int J Mol Sci 2020; 21:ijms21249340. [PMID: 33302406 PMCID: PMC7762615 DOI: 10.3390/ijms21249340] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 12/04/2020] [Accepted: 12/06/2020] [Indexed: 02/06/2023] Open
Abstract
KMT2 (histone-lysine N-methyltransferase subclass 2) complexes methylate lysine 4 on the histone H3 tail at gene promoters and gene enhancers and, thus, control the process of gene transcription. These complexes not only play an essential role in normal development but have also been described as involved in the aberrant growth of tissues. KMT2 mutations resulting from the rearrangements of the KMT2A (MLL1) gene at 11q23 are associated with pediatric mixed-lineage leukemias, and recent studies demonstrate that KMT2 genes are frequently mutated in many types of human cancers. Moreover, other components of the KMT2 complexes have been reported to contribute to oncogenesis. This review summarizes the recent advances in our knowledge of the role of KMT2 complexes in cell transformation. In addition, it discusses the therapeutic targeting of different components of the KMT2 complexes.
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WDR82/PNUTS-PP1 Prevents Transcription-Replication Conflicts by Promoting RNA Polymerase II Degradation on Chromatin. Cell Rep 2020; 33:108469. [PMID: 33264625 DOI: 10.1016/j.celrep.2020.108469] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 10/05/2020] [Accepted: 11/10/2020] [Indexed: 02/08/2023] Open
Abstract
Transcription-replication (T-R) conflicts cause replication stress and loss of genome integrity. However, the transcription-related processes that restrain such conflicts are poorly understood. Here, we demonstrate that the RNA polymerase II (RNAPII) C-terminal domain (CTD) phosphatase protein phosphatase 1 (PP1) nuclear targeting subunit (PNUTS)-PP1 inhibits replication stress. Depletion of PNUTS causes lower EdU uptake, S phase accumulation, and slower replication fork rates. In addition, the PNUTS binding partner WDR82 also promotes RNAPII-CTD dephosphorylation and suppresses replication stress. RNAPII has a longer residence time on chromatin after depletion of PNUTS or WDR82. Furthermore, the RNAPII residence time is greatly enhanced by proteasome inhibition in control cells but less so in PNUTS- or WDR82-depleted cells, indicating that PNUTS and WDR82 promote degradation of RNAPII on chromatin. Notably, reduced replication is dependent on transcription and the phospho-CTD binding protein CDC73 after depletion of PNUTS/WDR82. Altogether, our results suggest that RNAPII-CTD dephosphorylation is required for the continuous turnover of RNAPII on chromatin, thereby preventing T-R conflicts.
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Abstract
The Trithorax group (TrxG) of proteins is a large family of epigenetic regulators that form multiprotein complexes to counteract repressive developmental gene expression programmes established by the Polycomb group of proteins and to promote and maintain an active state of gene expression. Recent studies are providing new insights into how two crucial families of the TrxG - the COMPASS family of histone H3 lysine 4 methyltransferases and the SWI/SNF family of chromatin remodelling complexes - regulate gene expression and developmental programmes, and how misregulation of their activities through genetic abnormalities leads to pathologies such as developmental disorders and malignancies.
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Sugeedha J, Gautam J, Tyagi S. SET1/MLL family of proteins: functions beyond histone methylation. Epigenetics 2020; 16:469-487. [PMID: 32795105 PMCID: PMC8078731 DOI: 10.1080/15592294.2020.1809873] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The SET1 family of enzymes are well known for their involvement in the histone 3 lysine 4 (H3K4) methylation, a conserved trait of euchromatin associated with transcriptional activation. These methyltransferases are distinct, and involved in various biological functions in the cell. Impairment in the function of SET1 family members leads to a number of abnormalities such as skeletal and neurological defects, leukaemogenesis and even lethality. Tremendous progress has been made in understanding the unique biological roles and the mechanism of SET1 enzymes in context with H3K4 methylation/canonical functions. However, in recent years, several studies have indicated the novel role of SET1 family proteins, other than H3K4 methylation, which are equally important for cellular functions. In this review, we focus on these non-canonical function of SET1 family members.
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Affiliation(s)
- Jeyapal Sugeedha
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
| | - Jyoti Gautam
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
| | - Shweta Tyagi
- Laboratory of Cell Cycle Regulation, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, India
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Wells D, Bitoun E, Moralli D, Zhang G, Hinch A, Jankowska J, Donnelly P, Green C, Myers SR. ZCWPW1 is recruited to recombination hotspots by PRDM9 and is essential for meiotic double strand break repair. eLife 2020; 9:53392. [PMID: 32744506 PMCID: PMC7494361 DOI: 10.7554/elife.53392] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 07/31/2020] [Indexed: 12/13/2022] Open
Abstract
During meiosis, homologous chromosomes pair and recombine, enabling balanced segregation and generating genetic diversity. In many vertebrates, double-strand breaks (DSBs) initiate recombination within hotspots where PRDM9 binds, and deposits H3K4me3 and H3K36me3. However, no protein(s) recognising this unique combination of histone marks have been identified. We identified Zcwpw1, containing H3K4me3 and H3K36me3 recognition domains, as having highly correlated expression with Prdm9. Here, we show that ZCWPW1 has co-evolved with PRDM9 and, in human cells, is strongly and specifically recruited to PRDM9 binding sites, with higher affinity than sites possessing H3K4me3 alone. Surprisingly, ZCWPW1 also recognises CpG dinucleotides. Male Zcwpw1 knockout mice show completely normal DSB positioning, but persistent DMC1 foci, severe DSB repair and synapsis defects, and downstream sterility. Our findings suggest ZCWPW1 recognition of PRDM9-bound sites at DSB hotspots is critical for synapsis, and hence fertility. Sexual reproduction – that is, the combination of sex cells from two different individuals to produce an embryo – is one of the many mechanisms that have evolved to maintain genetic diversity. Most human cells contain 23 pairs of chromosomes, with each chromosome in a pair carrying either a paternal or maternal copy of the same gene. To form an embryo with the right number of chromosomes, each sex cell (the egg or sperm cell) must only contain one chromosome from each pair. Sex cells are produced from parent cells containing two sets of paternal and maternal chromosomes: these cells then divide twice to form four sex cells which contain only one chromosome from each pair. Before the parent cell divides, a process known as ‘recombination’ takes place, which allows chromosomes in a pair to exchange bits of genetic information. This reshuffling ensures that each chromosome in a sex cell is unique. A protein called PRDM9 helps control which sections of genetic information are recombined by modifying proteins attached to the chromosomes, marking them as locations for exchange. The DNA at each of these sites is then broken and repaired using the genetic sequence of the chromosome it is paired with as a template, thus causing the two chromosomes to swap genes. In 2019, a group of researchers found a set of genes in the testis of mice that are expressed at the same time as the gene for PRDM9. This suggested that another protein called ZCWPW1 is likely involved in recombination, but the precise role of this protein was unclear. To answer this question, Wells, Bitoun et al. – including many of the researchers involved in the 2019 study – examined human cells grown in the laboratory to determine where ZCWPW1 binds to in the chromosome. This revealed that ZCWPW1 can be found at the same sites as PRDM9, which is responsible for bringing it there. Furthermore, cells from male mice lacking the gene for ZCWPW1 cannot complete the exchange of genetic information between chromosomes, meaning that the mice are infertile. As such, ZCWPW1 seems to connect location selection by PRDM9 to the DNA repair mechanisms needed for gene exchange between chromosomes. Infertility is a significant issue for humans affecting as many as one in every six couples. Fertility is complex and many of the biological mechanisms involved are not fully understood. This work suggests that both PRDM9 and ZCWPW1 are key to the production of sex cells and may be worth investigating as factors that affect fertility in humans.
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Affiliation(s)
- Daniel Wells
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom.,Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Emmanuelle Bitoun
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom.,Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Daniela Moralli
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom
| | - Gang Zhang
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom
| | - Anjali Hinch
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom
| | - Julia Jankowska
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom
| | - Peter Donnelly
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom.,Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Catherine Green
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom
| | - Simon R Myers
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom.,Department of Statistics, University of Oxford, Oxford, United Kingdom
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