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Zhang Y, Fan S, He L, Li L. The ZDHHC13/ZDHHC17 subfamily: From biological functions to therapeutic targets of diseases. Pharmacol Res 2024; 209:107418. [PMID: 39306022 DOI: 10.1016/j.phrs.2024.107418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 09/11/2024] [Accepted: 09/11/2024] [Indexed: 10/03/2024]
Abstract
The ZDHHC13/ZDHHC17 subfamily belongs to the zinc finger DHHC-domain containing (ZDHHC) family, including ZDHHC13 and ZDHHC17. Recent studies have shown that the ZDHHC13/ZDHHC17 subfamily is involved in various pathological and physiological processes, including S-palmitoylation, Mg2+ transport, and CALCOCO1-mediated Golgiphagy. Moreover, the ZDHHC13/ZDHHC17 subfamily plays a crucial role in the occurrence and development of many diseases, including Huntington disease (HD), osteoporosis, atopic dermatitis, diabetes, and cancer. In the present review, we describe the distribution, structure, and post-translational modifications (PTMs) of the ZDHHC13/ZDHHC17 subfamily. Moreover, we effectively summarize the biological functions and associated diseases of this subfamily. Given the pleiotropy of the ZDHHC13/ZDHHC17 subfamily, it is imperative to conduct further research on its members to comprehend the pertinent pathophysiological mechanisms and to devise tactics for managing and controlling various diseases.
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Affiliation(s)
- Ying Zhang
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan 421001, China
| | - Sisi Fan
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan 421001, China
| | - Lu He
- The First Affiliated Hospital, Department of Neurosurgery, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.
| | - Lanfang Li
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang, Hunan 421001, China.
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2
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Wang HC, Chen R, Yang W, Li Y, Muthukumar R, Patel RM, Casey EB, Denby E, Magee JA. Kmt2c restricts G-CSF-driven HSC mobilization and granulocyte production in a methyltransferase-independent manner. Cell Rep 2024; 43:114542. [PMID: 39046877 PMCID: PMC11423277 DOI: 10.1016/j.celrep.2024.114542] [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: 11/30/2023] [Revised: 06/10/2024] [Accepted: 07/09/2024] [Indexed: 07/27/2024] Open
Abstract
Granulocyte colony-stimulating factor (G-CSF) is widely used to enhance myeloid recovery after chemotherapy and to mobilize hematopoietic stem cells (HSCs) for transplantation. Unfortunately, through the course of chemotherapy, cancer patients can acquire leukemogenic mutations that cause therapy-related myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML). This raises the question of whether therapeutic G-CSF might potentiate therapy-related MDS/AML by disproportionately stimulating mutant HSCs and other myeloid progenitors. A common mutation in therapy-related MDS/AML involves chromosome 7 deletions that inactivate many tumor suppressor genes, including KMT2C. Here, we show that Kmt2c deletions hypersensitize murine HSCs and myeloid progenitors to G-CSF, as evidenced by increased HSC mobilization and enhanced granulocyte production from granulocyte-monocyte progenitors (GMPs). Furthermore, Kmt2c attenuates the G-CSF response independently from its SET methyltransferase function. Altogether, the data raise concerns that monosomy 7 can hypersensitize progenitors to G-CSF, such that clinical use of G-CSF may amplify the risk of therapy-related MDS/AML.
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Affiliation(s)
- Helen C Wang
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Ran Chen
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Wei Yang
- Department of Genetics, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Yanan Li
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Rohini Muthukumar
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Riddhi M Patel
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Emily B Casey
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Elisabeth Denby
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA
| | - Jeffrey A Magee
- Department of Pediatrics, Division of Hematology and Oncology, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine, 660 S. Euclid Avenue, St. Louis, MO 63110, USA.
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3
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Yu H, Lesch BJ. Functional Roles of H3K4 Methylation in Transcriptional Regulation. Mol Cell Biol 2024:1-11. [PMID: 39155435 DOI: 10.1080/10985549.2024.2388254] [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: 06/12/2024] [Revised: 07/29/2024] [Accepted: 07/30/2024] [Indexed: 08/20/2024] Open
Abstract
Histone 3 lysine 4 methylation (H3K4me) is a highly evolutionary conserved chromatin modification associated with active transcription, and its three methylation states-mono, di, and trimethylation-mark distinct regulatory elements. However, whether H3K4me plays functional roles in transcriptional regulation or is merely a by-product of histone methyltransferases recruited to actively transcribed loci is still under debate. Here, we outline the studies that have addressed this question in yeast, Drosophila, and mammalian systems. We review evidence from histone residue mutation, histone modifier manipulation, and epigenetic editing, focusing on the relative roles of H3K4me1 and H3K4me3. We conclude that H3K4me1 and H3K4me3 may have convergent functions in establishing open chromatin and promoting transcriptional activation during cell differentiation.
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Affiliation(s)
- Haoming Yu
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
| | - Bluma J Lesch
- Department of Genetics, Yale School of Medicine, New Haven, Connecticut, USA
- Department of Obstetrics, Gynecology & Reproductive Sciences, Yale School of Medicine, New Haven, Connecticut, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, Connecticut, USA
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4
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Karayol R, Borroto MC, Haghshenas S, Namasivayam A, Reilly J, Levy MA, Relator R, Kerkhof J, McConkey H, Shvedunova M, Petersen AK, Magnussen K, Zweier C, Vasileiou G, Reis A, Savatt JM, Mulligan MR, Bicknell LS, Poke G, Abu-El-Haija A, Duis J, Hannig V, Srivastava S, Barkoudah E, Hauser NS, van den Born M, Hamiel U, Henig N, Baris Feldman H, McKee S, Krapels IPC, Lei Y, Todorova A, Yordanova R, Atemin S, Rogac M, McConnell V, Chassevent A, Barañano KW, Shashi V, Sullivan JA, Peron A, Iascone M, Canevini MP, Friedman J, Reyes IA, Kierstein J, Shen JJ, Ahmed FN, Mao X, Almoguera B, Blanco-Kelly F, Platzer K, Treu AB, Quilichini J, Bourgois A, Chatron N, Januel L, Rougeot C, Carere DA, Monaghan KG, Rousseau J, Myers KA, Sadikovic B, Akhtar A, Campeau PM. MSL2 variants lead to a neurodevelopmental syndrome with lack of coordination, epilepsy, specific dysmorphisms, and a distinct episignature. Am J Hum Genet 2024; 111:1330-1351. [PMID: 38815585 PMCID: PMC11267526 DOI: 10.1016/j.ajhg.2024.05.001] [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: 09/23/2023] [Revised: 04/30/2024] [Accepted: 05/01/2024] [Indexed: 06/01/2024] Open
Abstract
Epigenetic dysregulation has emerged as an important etiological mechanism of neurodevelopmental disorders (NDDs). Pathogenic variation in epigenetic regulators can impair deposition of histone post-translational modifications leading to aberrant spatiotemporal gene expression during neurodevelopment. The male-specific lethal (MSL) complex is a prominent multi-subunit epigenetic regulator of gene expression and is responsible for histone 4 lysine 16 acetylation (H4K16ac). Using exome sequencing, here we identify a cohort of 25 individuals with heterozygous de novo variants in MSL complex member MSL2. MSL2 variants were associated with NDD phenotypes including global developmental delay, intellectual disability, hypotonia, and motor issues such as coordination problems, feeding difficulties, and gait disturbance. Dysmorphisms and behavioral and/or psychiatric conditions, including autism spectrum disorder, and to a lesser extent, seizures, connective tissue disease signs, sleep disturbance, vision problems, and other organ anomalies, were observed in affected individuals. As a molecular biomarker, a sensitive and specific DNA methylation episignature has been established. Induced pluripotent stem cells (iPSCs) derived from three members of our cohort exhibited reduced MSL2 levels. Remarkably, while NDD-associated variants in two other members of the MSL complex (MOF and MSL3) result in reduced H4K16ac, global H4K16ac levels are unchanged in iPSCs with MSL2 variants. Regardless, MSL2 variants altered the expression of MSL2 targets in iPSCs and upon their differentiation to early germ layers. Our study defines an MSL2-related disorder as an NDD with distinguishable clinical features, a specific blood DNA episignature, and a distinct, MSL2-specific molecular etiology compared to other MSL complex-related disorders.
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Affiliation(s)
- Remzi Karayol
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Maria Carla Borroto
- Centre de recherche Azrieli du CHU Sainte-Justine, Montreal, QC H3T 1C5, Canada
| | - Sadegheh Haghshenas
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Anoja Namasivayam
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Jack Reilly
- Department of Pediatrics, Clinical Neurological Sciences and Epidemiology, Western University, London, ON N6A 3K7, Canada
| | - Michael A Levy
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Raissa Relator
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Jennifer Kerkhof
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada
| | - Haley McConkey
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada
| | - Maria Shvedunova
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany
| | - Andrea K Petersen
- Department of Genetics and Metabolism, Randall Children's and Legacy Emanuel Hospitals, Portland, OR 97227, USA
| | - Kari Magnussen
- Department of Genetics and Metabolism, Randall Children's and Legacy Emanuel Hospitals, Portland, OR 97227, USA
| | - Christiane Zweier
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany; Department of Human Genetics, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland
| | - Georgia Vasileiou
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - André Reis
- Institute of Human Genetics, Friedrich-Alexander-Universität Erlangen-Nürnberg, 91054 Erlangen, Germany
| | - Juliann M Savatt
- Autism & Developmental Medicine Institute, Geisinger, Danville, PA, USA
| | - Meghan R Mulligan
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Louise S Bicknell
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Gemma Poke
- Genetic Health Service New Zealand, Wellington, New Zealand
| | - Aya Abu-El-Haija
- Division of Genetics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, USA
| | - Jessica Duis
- Section of Genetics & Metabolism, Department of Pediatrics, University of Colorado, Children's Hospital Colorado, Aurora, CO, USA
| | - Vickie Hannig
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Siddharth Srivastava
- Translational Neuroscience Center, Department of Neurology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
| | | | - Natalie S Hauser
- Medical Genetics, Inova Fairfax Hospital, Falls Church, VA 22042, USA
| | - Myrthe van den Born
- Department of Clinical Genetics, Erasmus MC, University Medical Center, Rotterdam, the Netherlands
| | - Uri Hamiel
- Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center & Faculty of Medicine, Tel Aviv University, Tel Aviv 6423906, Israel
| | - Noa Henig
- Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center, Tel Aviv 6423906, Israel
| | - Hagit Baris Feldman
- Genetics Institute and Genomics Center, Tel Aviv Sourasky Medical Center & Faculty of Medicine, Tel Aviv University, Tel Aviv 6423906, Israel
| | - Shane McKee
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast Health & Social Care Trust, Belfast BT9 7AB, UK
| | - Ingrid P C Krapels
- Department of Clinical Genetics, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Yunping Lei
- Center for Precision Environmental Health, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Albena Todorova
- Department of Medical Chemistry and Biochemistry, Medical University Sofia, Sofia, Bulgaria; Genetic Medico-Diagnostic Laboratory "Genica", Sofia, Bulgaria
| | - Ralitsa Yordanova
- Department of pediatrics "Prof. Ivan Andreev", Medical university - Plovdiv, Plovdiv, Bulgaria; Department of Pediatrics, University Hospital "St. George", Plovdiv, Bulgaria
| | - Slavena Atemin
- Genetic Medico-Diagnostic Laboratory "Genica", Sofia, Bulgaria
| | - Mihael Rogac
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Vivienne McConnell
- Northern Ireland Regional Genetics Service, Belfast City Hospital, Belfast Health & Social Care Trust, Belfast BT9 7AB, UK
| | - Anna Chassevent
- Department of Neurogenetics, Kennedy Krieger Institute, Baltimore, MD, USA
| | - Kristin W Barañano
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Vandana Shashi
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jennifer A Sullivan
- Department of Pediatrics, Division of Medical Genetics, Duke University School of Medicine, Durham, NC 27710, USA
| | - Angela Peron
- SOC Genetica Medica, Meyer Children's Hospital IRCCS, Florence, Italy; Department of Biomedical, Experimental and Clinical Sciences "Mario Serio", Università degli Studi di Firenze, Florence, Italy
| | - Maria Iascone
- Department of Medical Genetics, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Maria P Canevini
- Epilepsy Center - Sleep Medicine Center, Childhood and Adolescence Neuropsychiatry Unit, ASST Santi Paolo e Carlo, San Paolo Hospital, Milan, Italy; Department of Health Sciences, University of Milan, Milan, Italy
| | - Jennifer Friedman
- Departments of Neurosciences and Pediatrics, University of California, San Diego, La Jolla, CA, USA; Rady Children's Institute for Genomic Medicine and Rady Children's Hospital, San Diego, CA, USA
| | - Iris A Reyes
- Rady Children's Institute for Genomic Medicine and Rady Children's Hospital, San Diego, CA, USA
| | - Janell Kierstein
- Section of Genetics & Metabolism, Department of Pediatrics, University of Colorado, Children's Hospital Colorado, Aurora, CO, USA
| | - Joseph J Shen
- Division of Genomic Medicine, Department of Pediatrics, MIND Institute, UC Davis, Sacramento, CA 95817, USA
| | - Faria N Ahmed
- Division of Genomic Medicine, Department of Pediatrics, UC Davis, Sacramento, CA 95817, USA
| | - Xiao Mao
- National Health Commission Key Laboratory of Birth Defects Research and Prevention, Hunan Provincial Maternal and Child Health Care Hospital, Hunan, China; Nanhua University, Chiayi County, Taiwan
| | - Berta Almoguera
- Department of Genetics and Genomics, Fundacion Jimenez Diaz University Hospital, Health Research Institute-Fundacion Jimenez Diaz, Universidad Autonoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Fiona Blanco-Kelly
- Department of Genetics and Genomics, Fundacion Jimenez Diaz University Hospital, Health Research Institute-Fundacion Jimenez Diaz, Universidad Autonoma de Madrid (IIS-FJD, UAM), Madrid, Spain; Center for Biomedical Network Research on Rare Diseases (CIBERER), Madrid, Spain
| | - Konrad Platzer
- Institute of Human Genetics, University of Leipzig Medical Center, Leipzig, German
| | | | - Juliette Quilichini
- Service de Médecine Génomique des maladies de système et d'organe, APHP, Centre Université Paris Cité, Paris, France
| | - Alexia Bourgois
- Normandy University, UNICAEN, Caen University Hospital, Department of Genetics, UR 7450 BioTARGen, FHU G4 Genomics, Caen, France
| | - Nicolas Chatron
- Department of Genetics, Lyon University Hospital, Lyon, France; Pathophysiology and Genetics of Neuron and Muscle (PGNM, UCBL - CNRS UMR5261 - INSERM U1315), Université Claude Bernard Lyon 1, Lyon, France
| | - Louis Januel
- Department of Genetics, Lyon University Hospital, Lyon, France
| | | | | | | | - Justine Rousseau
- Centre de recherche Azrieli du CHU Sainte-Justine, Montreal, QC H3T 1C5, Canada
| | - Kenneth A Myers
- Child Health and Human Development, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Bekim Sadikovic
- Verspeeten Clinical Genome Centre, London Health Sciences Centre, London, ON N6A 5W9, Canada; Department of Pathology and Laboratory Medicine, Western University, London, ON N6A 3K7, Canada.
| | - Asifa Akhtar
- Max-Planck Institute of Immunobiology and Epigenetics, Freiburg, Germany.
| | - Philippe M Campeau
- Centre de recherche Azrieli du CHU Sainte-Justine, Montreal, QC H3T 1C5, Canada; Department of Pediatrics, University of Montreal, Montreal, QC H3T 1C5, Canada
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5
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Anyetei-Anum CS, Leatham-Jensen MP, Fox GC, Smith BR, Krajewski K, Strahl BD, Dowen JM, Matera AG, Duronio RJ, McKay DJ. Dual roles of histone H3 lysine-4 in antagonizing Polycomb group function and promoting target gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.25.600669. [PMID: 38979215 PMCID: PMC11230394 DOI: 10.1101/2024.06.25.600669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Tight control over cell identity gene expression is necessary for proper adult form and function. The opposing activities of Polycomb and trithorax complexes determine the ON/OFF state of targets like the Hox genes. Trithorax encodes a methyltransferase specific to histone H3 lysine-4 (H3K4). However, there is no direct evidence that H3K4 regulates Polycomb group target genes in vivo . Here, we demonstrate two key roles for replication-dependent histone H3.2K4 in target control. We find that H3.2K4 antagonizes Polycomb group catalytic activity and that it is required for proper target gene activation. We conclude that H3.2K4 directly regulates expression of Polycomb targets.
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Zhang Y, Xie G, Lee JE, Zandian M, Sudarshan D, Estavoyer B, Benz C, Viita T, Asgaritarghi G, Lachance C, Messmer C, Simonetti L, Sinha VK, Lambert JP, Chen YW, Wang SP, Ivarsson Y, Affar EB, Côté J, Ge K, Kutateladze TG. ASXLs binding to the PHD2/3 fingers of MLL4 provides a mechanism for the recruitment of BAP1 to active enhancers. Nat Commun 2024; 15:4883. [PMID: 38849395 PMCID: PMC11161652 DOI: 10.1038/s41467-024-49391-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: 10/09/2022] [Accepted: 05/31/2024] [Indexed: 06/09/2024] Open
Abstract
The human methyltransferase and transcriptional coactivator MLL4 and its paralog MLL3 are frequently mutated in cancer. MLL4 and MLL3 monomethylate histone H3K4 and contain a set of uncharacterized PHD fingers. Here, we report a novel function of the PHD2 and PHD3 (PHD2/3) fingers of MLL4 and MLL3 that bind to ASXL2, a component of the Polycomb repressive H2AK119 deubiquitinase (PR-DUB) complex. The structure of MLL4 PHD2/3 in complex with the MLL-binding helix (MBH) of ASXL2 and mutational analyses reveal the molecular mechanism which is conserved in homologous ASXL1 and ASXL3. The native interaction of the Trithorax MLL3/4 complexes with the PR-DUB complex in vivo depends solely on MBH of ASXL1/2, coupling the two histone modifying activities. ChIP-seq analysis in embryonic stem cells demonstrates that MBH of ASXL1/2 is required for the deubiquitinase BAP1 recruitment to MLL4-bound active enhancers. Our findings suggest an ASXL1/2-dependent functional link between the MLL3/4 and PR-DUB complexes.
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Affiliation(s)
- Yi Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
- Department of Biochemistry, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - Guojia Xie
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, 20892, USA
| | - Ji-Eun Lee
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, 20892, USA
| | - Mohamad Zandian
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Deepthi Sudarshan
- St-Patrick Research Group in Basic Oncology, Oncology Division of CHU de Québec-Université Laval Research, Laval University Cancer Research Center, Quebec City, QC, G1R 3S3, Canada
| | - Benjamin Estavoyer
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC, H1T 2M4, Canada
| | - Caroline Benz
- Department of Chemistry, BMC, Uppsala University, Uppsala, 75237, Sweden
| | - Tiina Viita
- St-Patrick Research Group in Basic Oncology, Oncology Division of CHU de Québec-Université Laval Research, Laval University Cancer Research Center, Quebec City, QC, G1R 3S3, Canada
| | - Golareh Asgaritarghi
- St-Patrick Research Group in Basic Oncology, Oncology Division of CHU de Québec-Université Laval Research, Laval University Cancer Research Center, Quebec City, QC, G1R 3S3, Canada
| | - Catherine Lachance
- St-Patrick Research Group in Basic Oncology, Oncology Division of CHU de Québec-Université Laval Research, Laval University Cancer Research Center, Quebec City, QC, G1R 3S3, Canada
| | - Clémence Messmer
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC, H1T 2M4, Canada
| | - Leandro Simonetti
- Department of Chemistry, BMC, Uppsala University, Uppsala, 75237, Sweden
| | - Vikrant Kumar Sinha
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Jean-Philippe Lambert
- St-Patrick Research Group in Basic Oncology, Oncology Division of CHU de Québec-Université Laval Research, Laval University Cancer Research Center, Quebec City, QC, G1R 3S3, Canada
| | - Yu-Wen Chen
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan, ROC
| | - Shu-Ping Wang
- Institute of Biomedical Sciences, Academia Sinica, Taipei, 11529, Taiwan, ROC
| | - Ylva Ivarsson
- Department of Chemistry, BMC, Uppsala University, Uppsala, 75237, Sweden
| | - El Bachir Affar
- Maisonneuve-Rosemont Hospital Research Center, Montréal, QC, H1T 2M4, Canada
- Department of Medicine, University of Montréal, Montréal, QC, H3C 3J7, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Oncology Division of CHU de Québec-Université Laval Research, Laval University Cancer Research Center, Quebec City, QC, G1R 3S3, Canada.
| | - Kai Ge
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, 20892, USA.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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7
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Becht DC, Mohid SA, Lee JE, Zandian M, Benz C, Biswas S, Sinha VK, Ivarsson Y, Ge K, Zhang Y, Kutateladze TG. MLL4 binds TET3. Structure 2024; 32:706-714.e3. [PMID: 38579707 PMCID: PMC11162309 DOI: 10.1016/j.str.2024.03.005] [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: 09/20/2023] [Revised: 02/01/2024] [Accepted: 03/11/2024] [Indexed: 04/07/2024]
Abstract
Human mixed lineage leukemia 4 (MLL4), also known as KMT2D, regulates cell type specific transcriptional programs through enhancer activation. Along with the catalytic methyltransferase domain, MLL4 contains seven less characterized plant homeodomain (PHD) fingers. Here, we report that the sixth PHD finger of MLL4 (MLL4PHD6) binds to the hydrophobic motif of ten-eleven translocation 3 (TET3), a dioxygenase that converts methylated cytosine into oxidized derivatives. The solution NMR structure of the TET3-MLL4PHD6 complex and binding assays show that, like histone H4 tail, TET3 occupies the hydrophobic site of MLL4PHD6, and that this interaction is conserved in the seventh PHD finger of homologous MLL3 (MLL3PHD7). Analysis of genomic localization of endogenous MLL4 and ectopically expressed TET3 in mouse embryonic stem cells reveals a high degree overlap on active enhancers and suggests a potential functional relationship of MLL4 and TET3.
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Affiliation(s)
- Dustin C Becht
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Sk Abdul Mohid
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Ji-Eun Lee
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Mohamad Zandian
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Caroline Benz
- Department of Chemistry - BMC, Uppsala University, 751 23 Uppsala, Sweden
| | - Soumi Biswas
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Vikrant Kumar Sinha
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Ylva Ivarsson
- Department of Chemistry - BMC, Uppsala University, 751 23 Uppsala, Sweden
| | - Kai Ge
- Laboratory of Endocrinology and Receptor Biology, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Yi Zhang
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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8
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Liu S, Cao Y, Cui K, Ren G, Zhao T, Wang X, Wei D, Chen Z, Gurram RK, Liu C, Wu C, Zhu J, Zhao K. Regulation of T helper cell differentiation by the interplay between histone modification and chromatin interaction. Immunity 2024; 57:987-1004.e5. [PMID: 38614090 PMCID: PMC11096031 DOI: 10.1016/j.immuni.2024.03.018] [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: 08/13/2023] [Revised: 12/30/2023] [Accepted: 03/22/2024] [Indexed: 04/15/2024]
Abstract
The development and function of the immune system are controlled by temporospatial gene expression programs, which are regulated by cis-regulatory elements, chromatin structure, and trans-acting factors. In this study, we cataloged the dynamic histone modifications and chromatin interactions at regulatory regions during T helper (Th) cell differentiation. Our data revealed that the H3K4me1 landscape established by MLL4 in naive CD4+ T cells is critical for restructuring the regulatory interaction network and orchestrating gene expression during the early phase of Th differentiation. GATA3 plays a crucial role in further configuring H3K4me1 modification and the chromatin interaction network during Th2 differentiation. Furthermore, we demonstrated that HSS3-anchored chromatin loops function to restrict the activity of the Th2 locus control region (LCR), thus coordinating the expression of Th2 cytokines. Our results provide insights into the mechanisms of how the interplay between histone modifications, chromatin looping, and trans-acting factors contributes to the differentiation of Th cells.
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Affiliation(s)
- Shuai Liu
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yaqiang Cao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kairong Cui
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gang Ren
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tingting Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xuezheng Wang
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Danping Wei
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zuojia Chen
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rama Krishna Gurram
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chengyu Liu
- Transgenic Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Chuan Wu
- Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jinfang Zhu
- Molecular and Cellular Immunoregulation Section, Laboratory of Immune System Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Keji Zhao
- Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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9
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Kubo N, Chen PB, Hu R, Ye Z, Sasaki H, Ren B. H3K4me1 facilitates promoter-enhancer interactions and gene activation during embryonic stem cell differentiation. Mol Cell 2024; 84:1742-1752.e5. [PMID: 38513661 PMCID: PMC11069443 DOI: 10.1016/j.molcel.2024.02.030] [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: 12/24/2023] [Revised: 02/17/2024] [Accepted: 02/26/2024] [Indexed: 03/23/2024]
Abstract
Histone H3 lysine 4 mono-methylation (H3K4me1) marks poised or active enhancers. KMT2C (MLL3) and KMT2D (MLL4) catalyze H3K4me1, but their histone methyltransferase activities are largely dispensable for transcription during early embryogenesis in mammals. To better understand the role of H3K4me1 in enhancer function, we analyze dynamic enhancer-promoter (E-P) interactions and gene expression during neural differentiation of the mouse embryonic stem cells. We found that KMT2C/D catalytic activities were only required for H3K4me1 and E-P contacts at a subset of candidate enhancers, induced upon neural differentiation. By contrast, a majority of enhancers retained H3K4me1 in KMT2C/D catalytic mutant cells. Surprisingly, H3K4me1 signals at these KMT2C/D-independent sites were reduced after acute depletion of KMT2B, resulting in aggravated transcriptional defects. Our observations therefore implicate KMT2B in the catalysis of H3K4me1 at enhancers and provide additional support for an active role of H3K4me1 in enhancer-promoter interactions and transcription in mammalian cells.
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Affiliation(s)
- Naoki Kubo
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA; Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
| | - Poshen B Chen
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA; Genome Institute of Singapore, Agency for Science, Technology and Research (A(∗)STAR), Singapore, Singapore; Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, 7 Engineering Drive 1, Singapore 117574, Singapore
| | - Rong Hu
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Zhen Ye
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA; Center for Epigenomics, Department of Cellular and Molecular Medicine, Moores Cancer Center and Institute of Genome Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.
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10
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Ahmed IA, Liu M, Gomez D. Nuclear Control of Vascular Smooth Muscle Cell Plasticity during Vascular Remodeling. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:525-538. [PMID: 37820925 PMCID: PMC10988766 DOI: 10.1016/j.ajpath.2023.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 09/18/2023] [Accepted: 09/27/2023] [Indexed: 10/13/2023]
Abstract
Control of vascular smooth muscle cell (SMC) gene expression is an essential process for establishing and maintaining lineage identity, contractility, and plasticity. Most mechanisms (epigenetic, transcriptional, and post-transcriptional) implicated in gene regulation occur in the nucleus. Still, intranuclear pathways are directly impacted by modifications in the extracellular environment in conditions of adaptive or maladaptive remodeling. Integration of extracellular, cellular, and genomic information into the nucleus through epigenetic and transcriptional control of genome organization plays a major role in regulating SMC functions and phenotypic transitions during vascular remodeling and diseases. This review aims to provide a comprehensive update on nuclear mechanisms, their interactions, and their integration in controlling SMC homeostasis and dysfunction. It summarizes and discusses the main nuclear mechanisms preponderant in SMCs in the context of vascular disease, such as atherosclerosis, with an emphasis on studies employing in vivo cell-specific loss-of-function and single-cell omics approaches.
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Affiliation(s)
- Ibrahim A Ahmed
- Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania; Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Mingjun Liu
- Department of Pathology, New York University, New York, New York
| | - Delphine Gomez
- Pittsburgh Heart, Lung, and Blood Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, Pennsylvania; Division of Cardiology, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania.
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11
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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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12
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Wang Z, Ren B. Role of H3K4 monomethylation in gene regulation. Curr Opin Genet Dev 2024; 84:102153. [PMID: 38278054 PMCID: PMC11065453 DOI: 10.1016/j.gde.2024.102153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/02/2024] [Accepted: 01/02/2024] [Indexed: 01/28/2024]
Abstract
Methylation of histone H3 on the lysine-4 residue (H3K4me) is found throughout the eukaryotic domain, and its initial discovery as a conserved epigenetic mark of active transcription from yeast to mammalian cells has contributed to the histone code hypothesis. However, recent studies have raised questions on whether the different forms of H3K4me play a direct role in gene regulation or are simply by-products of the transcription process. Here, we review the often-conflicting experimental evidence, focusing on the monomethylation of lysine 4 on histone H3 that has been linked to the transcriptional state of enhancers in metazoans. We suggest that this epigenetic mark acts in a context-dependent manner to directly facilitate the transcriptional output of the genome and the establishment of cellular identity.
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Affiliation(s)
- Zhaoning Wang
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA. https://twitter.com/@ZhaoningWang
| | - Bing Ren
- Department of Cellular and Molecular Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA; Center for Epigenomics, University of California San Diego School of Medicine, La Jolla, CA, USA; Institute of Genomic Medicine, University of California San Diego School of Medicine, La Jolla, CA, USA.
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13
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Terzi Cizmecioglu N. Roles and Regulation of H3K4 Methylation During Mammalian Early Embryogenesis and Embryonic Stem Cell Differentiation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024. [PMID: 38231346 DOI: 10.1007/5584_2023_794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2024]
Abstract
From generation of germ cells, fertilization, and throughout early mammalian embryonic development, the chromatin undergoes significant alterations to enable precise regulation of gene expression and genome use. Methylation of histone 3 lysine 4 (H3K4) correlates with active regions of the genome, and it has emerged as a dynamic mark throughout this timeline. The pattern and the level of H3K4 methylation are regulated by methyltransferases and demethylases. These enzymes, as well as their protein partners, play important roles in early embryonic development and show phenotypes in embryonic stem cell self-renewal and differentiation. The various roles of H3K4 methylation are interpreted by dedicated chromatin reader proteins, linking this modification to broader molecular and cellular phenotypes. In this review, we discuss the regulation of different levels of H3K4 methylation, their distinct accumulation pattern, and downstream molecular roles with an early embryogenesis perspective.
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14
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Wang J, Chen Y, Xiao Z, Liu X, Liu C, Huang K, Chen H. Phase Separation of Chromatin Structure-related Biomolecules: A Driving Force for Epigenetic Regulations. Curr Protein Pept Sci 2024; 25:553-566. [PMID: 38551058 DOI: 10.2174/0113892037296216240301074253] [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: 01/03/2024] [Revised: 02/12/2024] [Accepted: 02/16/2024] [Indexed: 07/25/2024]
Abstract
Intracellularly, membrane-less organelles are formed by spontaneous fusion and fission of macro-molecules in a process called phase separation, which plays an essential role in cellular activities. In certain disease states, such as cancers and neurodegenerative diseases, aberrant phase separations take place and participate in disease progression. Chromatin structure-related proteins, based on their characteristics and upon external stimuli, phase separate to exert functions like genome assembly, transcription regulation, and signal transduction. Moreover, many chromatin structure-related proteins, such as histones, histone-modifying enzymes, DNA-modifying enzymes, and DNA methylation binding proteins, are involved in epigenetic regulations through phase separation. This review introduces phase separation and how phase separation affects epigenetics with a focus on chromatin structure-related molecules.
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Affiliation(s)
- Jiao Wang
- Wuhan No.1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Yuchen Chen
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Zixuan Xiao
- ISA Wenhua Wuhan High School, Fenglin Road, Junshan New Town, Wuhan Economics & Technological Development Zone, Wuhan, Hubei 430119, China
| | - Xikai Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China
| | - Chengyu Liu
- Wuhan No.1 Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430000, China
| | - Kun Huang
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hong Chen
- Tongji School of Pharmacy, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
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15
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Gökbuget D, Boileau RM, Lenshoek K, Blelloch R. MLL3/MLL4 enzymatic activity shapes DNA replication timing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.07.569680. [PMID: 38106216 PMCID: PMC10723431 DOI: 10.1101/2023.12.07.569680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Mammalian genomes are replicated in a precise order during S phase, which is cell-type-specific1-3 and correlates with local transcriptional activity2,4-8, chromatin modifications9 and chromatin architecture1,10,11,12. However, the causal relationships between these features and the key regulators of DNA replication timing (RT) are largely unknown. Here, machine learning was applied to quantify chromatin features, including epigenetic marks, histone variants and chromatin architectural factors, best predicting local RT under steady-state and RT changes during early embryonic stem (ES) cell differentiation. About one-third of genome exhibited RT changes during the differentiation. Combined, chromatin features predicted steady-state RT and RT changes with high accuracy. Of these features, histone H3 lysine 4 monomethylation (H3K4me1) catalyzed by MLL3/4 (also known as KMT2C/D) emerged as a top predictor. Loss of Mll3/4 (but not Mll3 alone) or their enzymatic activity resulted in erasure of genome-wide RT dynamics during ES cell differentiation. Sites that normally gain H3K4me1 in a MLL3/4-dependent fashion during the transition failed to transition towards earlier RT, often with transcriptional activation unaffected. Further analysis revealed a requirement for MLL3/4 in promoting DNA replication initiation zones through MCM2 recruitment, providing a direct link for its role in regulating RT. Our results uncover MLL3/4-dependent H3K4me1 as a functional regulator of RT and highlight a causal relationship between the epigenome and RT that is largely uncoupled from transcription. These findings uncover a previously unknown role for MLL3/4-dependent chromatin functions which is likely relevant to the numerous diseases associated with MLL3/4 mutations.
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Affiliation(s)
- Deniz Gökbuget
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Ryan M. Boileau
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
- Present address: Department of Biomedical Engineering, Duke University, Durham, NC, USA
| | - Kayla Lenshoek
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
| | - Robert Blelloch
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, Center for Reproductive Sciences, University of California San Francisco, San Francisco, CA, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA
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16
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Shpargel KB, Quickstad G. SETting up the genome: KMT2D and KDM6A genomic function in the Kabuki syndrome craniofacial developmental disorder. Birth Defects Res 2023; 115:1885-1898. [PMID: 37800171 PMCID: PMC11190966 DOI: 10.1002/bdr2.2253] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 10/07/2023]
Abstract
BACKGROUND Kabuki syndrome is a congenital developmental disorder that is characterized by distinctive facial gestalt and skeletal abnormalities. Although rare, the disorder shares clinical features with several related craniofacial syndromes that manifest from mutations in chromatin-modifying enzymes. Collectively, these clinical studies underscore the crucial, concerted functions of chromatin factors in shaping developmental genome structure and driving cellular transcriptional states. Kabuki syndrome predominantly results from mutations in KMT2D, a histone H3 lysine 4 methylase, or KDM6A, a histone H3 lysine 27 demethylase. AIMS In this review, we summarize the research efforts to model Kabuki syndrome in vivo to understand the cellular and molecular mechanisms that lead to the craniofacial and skeletal pathogenesis that defines the disorder. DISCUSSION As several studies have indicated the importance of KMT2D and KDM6A function through catalytic-independent mechanisms, we highlight noncanonical roles for these enzymes as recruitment centers for alternative chromatin and transcriptional machinery.
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Affiliation(s)
- Karl B. Shpargel
- Department of GeneticsUniversity of North CarolinaChapel HillNorth CarolinaUSA
| | - Gabrielle Quickstad
- Department of GeneticsUniversity of North CarolinaChapel HillNorth CarolinaUSA
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17
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Saadeldin IM, Bang S, Maigoro AY, Yun SH, Kim SI, Lee S, Cho J. Proteomic Analysis and Reprogramming Potential of the Porcine Intra-Ooplasmic Nanovesicles. Cell Reprogram 2023; 25:238-250. [PMID: 37725012 DOI: 10.1089/cell.2023.0050] [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] [Indexed: 09/21/2023] Open
Abstract
Oocytes contain reprogramming machinery that can transform somatic cells into totipotent cells. In this study, we aimed to isolate and characterize nanovesicles from mature porcine oocytes and described them for the first time as "intra-ooplasmic vesicles (IOVs)". Isolated IOVs had an average diameter of 186.3 ± 10.8 nm. Proteomic analysis revealed 467 peptide reads, with the top 20 proteins related to reprogramming, antioxidative defense, cytoskeleton, heat shock proteins, and metabolism. Protein-protein interaction and gene ontology analysis indicated that these proteins were involved in various biological pathways, including protein folding, metabolism, and cellular responses to stress. Supplementing cultured fibroblasts with IOVs resulted in the expression of the pluripotency marker OCT4 and the early trophoblastic marker CDX2 and increased expression of the corresponding mRNAs together with increasing KLF4 and SALL4 expression. IOV treatment of fibroblasts for 14 consecutive days resulted in changes in cell morphology, with increased expression of ZEB2 and YBX3 as markers for epithelial-to-mesenchymal transition (EMT). These results provide a rationale for further characterization of IOVs, investigation of potential reprogramming capabilities for EMT, and the generation of induced pluripotent or oligopotent stem cells.
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Affiliation(s)
- Islam M Saadeldin
- Laboratory of Theriogenology, College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
- Research Institute of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Seonggyu Bang
- Laboratory of Theriogenology, College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Abdulkadir Y Maigoro
- Department of Life Sciences, Incheon National University, Incheon, Republic of Korea
| | - Sung Ho Yun
- Korea Basic Science Institute (KBSI), Ochang, Republic of Korea
| | - Seung Ii Kim
- Korea Basic Science Institute (KBSI), Ochang, Republic of Korea
| | - Sanghoon Lee
- Laboratory of Theriogenology, College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Jongki Cho
- Laboratory of Theriogenology, College of Veterinary Medicine, Chungnam National University, Daejeon, Republic of Korea
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18
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Tsukahara T, Kethireddy S, Bonefas K, Chen A, Sutton BLM, Dou Y, Iwase S, Sutton MA. Division of labor among H3K4 Methyltransferases Defines Distinct Facets of Homeostatic Plasticity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558734. [PMID: 37790395 PMCID: PMC10542164 DOI: 10.1101/2023.09.20.558734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Heterozygous mutations in any of the six H3K4 methyltransferases (KMT2s) result in monogenic neurodevelopmental disorders, indicating nonredundant yet poorly understood roles of this enzyme family in neurodevelopment. Recent evidence suggests that histone methyltransferase activity may not be central to KMT2 functions; however, the enzymatic activity is evolutionarily conserved, implicating the presence of selective pressure to maintain the catalytic activity. Here, we show that H3K4 methylation is dynamically regulated during prolonged alteration of neuronal activity. The perturbation of H3K4me by the H3.3K4M mutant blocks synaptic scaling, a form of homeostatic plasticity that buffers the impact of prolonged reductions or increases in network activity. Unexpectedly, we found that the six individual enzymes are all necessary for synaptic scaling and that the roles of KMT2 enzymes segregate into evolutionary-defined subfamilies: KMT2A and KMT2B (fly-Trx homologs) for synaptic downscaling, KMT2C and KMT2D (Trr homologs) for upscaling, and KMT2F and KMT2G (dSet homologs) for both directions. Selective blocking of KMT2A enzymatic activity by a small molecule and targeted disruption of the enzymatic domain both blocked the synaptic downscaling and interfered with the activity-dependent transcriptional program. Furthermore, our study revealed specific phases of synaptic downscaling, i.e., induction and maintenance, in which KMT2A and KMT2B play distinct roles. These results suggest that mammalian brains have co-opted intricate H3K4me installation to achieve stability of the expanding neuronal circuits.
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Affiliation(s)
- Takao Tsukahara
- Michigan Neuroscience Institute, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan
| | - Saini Kethireddy
- College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, Michigan
| | - Katherine Bonefas
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, Michigan
| | - Alex Chen
- Neuroscience Graduate Program, University of Michigan, Ann Arbor, Michigan
| | - Brendan LM Sutton
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Yali Dou
- Department of Medicine and Department of Biochemistry and Molecular Medicine, Keck School of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Shigeki Iwase
- Michigan Neuroscience Institute, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Human Genetics, University of Michigan, Ann Arbor, Michigan
| | - Michael A. Sutton
- Michigan Neuroscience Institute, University of Michigan Medical School, Ann Arbor, Michigan
- Department of Molecular & Integrative Physiology, University of Michigan, Ann Arbor, Michigan
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19
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Wu X, Wu X, Xie W. Activation, decommissioning, and dememorization: enhancers in a life cycle. Trends Biochem Sci 2023; 48:673-688. [PMID: 37221124 DOI: 10.1016/j.tibs.2023.04.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 04/15/2023] [Accepted: 04/18/2023] [Indexed: 05/25/2023]
Abstract
Spatiotemporal regulation of cell type-specific gene expression is essential to convert a zygote into a complex organism that contains hundreds of distinct cell types. A class of cis-regulatory elements called enhancers, which have the potential to enhance target gene transcription, are crucial for precise gene expression programs during development. Following decades of research, many enhancers have been discovered and how enhancers become activated has been extensively studied. However, the mechanisms underlying enhancer silencing are less well understood. We review current understanding of enhancer decommissioning and dememorization, both of which enable enhancer silencing. We highlight recent progress from genome-wide perspectives that have revealed the life cycle of enhancers and how its dynamic regulation underlies cell fate transition, development, cell regeneration, and epigenetic reprogramming.
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Affiliation(s)
- Xiaotong Wu
- Tsinghua-Peking Center for Life Sciences, New Cornerstone Science Laboratory, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China; Laboratory of Molecular Developmental Biology, State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Xi Wu
- Tsinghua-Peking Center for Life Sciences, New Cornerstone Science Laboratory, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Wei Xie
- Tsinghua-Peking Center for Life Sciences, New Cornerstone Science Laboratory, MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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Sun Z, Lin Y, Islam MT, Koche R, Hedehus L, Liu D, Huang C, Vierbuchen T, Sawyers CL, Helin K. Chromatin regulation of transcriptional enhancers and cell fate by the Sotos syndrome gene NSD1. Mol Cell 2023; 83:2398-2416.e12. [PMID: 37402365 PMCID: PMC10529604 DOI: 10.1016/j.molcel.2023.06.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 04/27/2023] [Accepted: 06/05/2023] [Indexed: 07/06/2023]
Abstract
Nuclear receptor-binding SET-domain protein 1 (NSD1), a methyltransferase that catalyzes H3K36me2, is essential for mammalian development and is frequently dysregulated in diseases, including Sotos syndrome. Despite the impacts of H3K36me2 on H3K27me3 and DNA methylation, the direct role of NSD1 in transcriptional regulation remains largely unknown. Here, we show that NSD1 and H3K36me2 are enriched at cis-regulatory elements, particularly enhancers. NSD1 enhancer association is conferred by a tandem quadruple PHD (qPHD)-PWWP module, which recognizes p300-catalyzed H3K18ac. By combining acute NSD1 depletion with time-resolved epigenomic and nascent transcriptomic analyses, we demonstrate that NSD1 promotes enhancer-dependent gene transcription by facilitating RNA polymerase II (RNA Pol II) pause release. Notably, NSD1 can act as a transcriptional coactivator independent of its catalytic activity. Moreover, NSD1 enables the activation of developmental transcriptional programs associated with Sotos syndrome pathophysiology and controls embryonic stem cell (ESC) multilineage differentiation. Collectively, we have identified NSD1 as an enhancer-acting transcriptional coactivator that contributes to cell fate transition and Sotos syndrome development.
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Affiliation(s)
- Zhen Sun
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Yuan Lin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Mohammed T Islam
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Richard Koche
- Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lin Hedehus
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Biotech Research and Innovation Centre, University of Copenhagen 2200 Copenhagen N, Denmark
| | - Dingyu Liu
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Chang Huang
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Division of Cancer Biology, Institute of Cancer Research, London SW7 3RP, UK
| | - Thomas Vierbuchen
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Stem Cell Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Charles L Sawyers
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Kristian Helin
- Cell Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Biotech Research and Innovation Centre, University of Copenhagen 2200 Copenhagen N, Denmark; Division of Cancer Biology, Institute of Cancer Research, London SW7 3RP, UK.
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