1
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Jiang N, Li YB, Jin JY, Guo JY, Ding QR, Meng D, Zhi XL. Structural and functional insights into the epigenetic regulator MRG15. Acta Pharmacol Sin 2024; 45:879-889. [PMID: 38191914 PMCID: PMC11053006 DOI: 10.1038/s41401-023-01211-6] [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: 06/24/2023] [Accepted: 12/05/2023] [Indexed: 01/10/2024] Open
Abstract
MORF4-related gene on chromosome 15 (MRG15), a chromatin remodeller, is evolutionally conserved and ubiquitously expressed in mammalian tissues and cells. MRG15 plays vital regulatory roles in DNA damage repair, cell proliferation and division, cellular senescence and apoptosis by regulating both gene activation and gene repression via associations with specific histone acetyltransferase and histone deacetylase complexes. Recently, MRG15 has also been shown to rhythmically regulate hepatic lipid metabolism and suppress carcinoma progression. The unique N-terminal chromodomain and C-terminal MRG domain in MRG15 synergistically regulate its interaction with different cofactors, affecting its functions in various cell types. Thus, how MRG15 elaborately regulates target gene expression and performs diverse functions in different cellular contexts is worth investigating. In this review, we provide an in-depth discussion of how MRG15 controls multiple physiological and pathological processes.
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Affiliation(s)
- Nan Jiang
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Yong-Bo Li
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jia-Yu Jin
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Jie-Yu Guo
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Qiu-Rong Ding
- CAS Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Dan Meng
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
| | - Xiu-Ling Zhi
- Department of Physiology and Pathophysiology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
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2
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Du WJ, Yang H, Tong F, Liu S, Zhang C, Chen Y, Yan Y, Xiang YW, Hua LY, Gong Y, Xu ZX, Liu X, Jiang X, Lu M, Guan JS, Han Q. Ash1L ameliorates psoriasis via limiting neuronal activity-dependent release of miR-let-7b. Br J Pharmacol 2024; 181:1107-1127. [PMID: 37766518 DOI: 10.1111/bph.16254] [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: 04/13/2023] [Revised: 09/12/2023] [Accepted: 09/16/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND AND PURPOSE Psoriasis is a common autoimmune skin disease that significantly diminishes patients' quality of life. Interactions between primary afferents of the somatosensory system and the cutaneous immune system mediate the pathogenesis of psoriasis. This study aims to elucidate the molecular mechanisms of how primary sensory neurons regulate psoriasis formation. EXPERIMENTAL APPROACH Skin and total RNA were extracted from wild-type (WT) and ASH1-like histone lysine methyltransferase (Ash1l+/- ) mice in both naive and imiquimod (IMQ)-induced psoriasis models. Immunohistochemistry, quantitative real-time polymerase chain reaction (qRT-PCR) and fluorescence-activated cell sorting (FACS) were then performed. Microfluidic chamber coculture was used to investigate the interaction between somatosensory neurons and bone marrow dendritic cells (BMDCs) ex vivo. Whole-cell patch clamp recordings were used to evaluate neuronal excitability after Ash1L haploinsufficiency in primary sensory neurons. KEY RESULTS The haploinsufficiency of ASH1L, a histone methyltransferase, in primary sensory neurons causes both neurite hyperinnervation and increased neuronal excitability, which promote miR-let-7b release from primary afferents in the skin in a neuronal activity-dependent manner. With a 'GUUGUGU' core sequence, miR-let-7b functions as an endogenous ligand of toll-like receptor 7 (TLR7) and stimulates the activation of dermal dendritic cells (DCs) and interleukin (IL)-23/IL-17 axis, ultimately exacerbating the symptoms of psoriasis. Thus, by limiting miR-let-7b release from primary afferents, ASH1L prevents dermal DC activation and ameliorates psoriasis. CONCLUSION AND IMPLICATIONS Somatosensory neuron ASH1L modulates the cutaneous immune system by limiting neuronal activity-dependent release of miR-let-7b, which can directly activate dermal DCs via TLR7 and ultimately lead to aggravated psoriatic lesion.
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Affiliation(s)
- Wan-Jie Du
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Huan Yang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Fang Tong
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Shuai Liu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Chen Zhang
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Yeying Chen
- Department of Immunology, Key Laboratory of Medical Molecular Virology (MOE, NHC, CAMS), School of Basic Medical Sciences and Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Yuze Yan
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Yan-Wei Xiang
- School of Rehabilitation Science, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Ling-Yang Hua
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Ye Gong
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhi-Xiang Xu
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
| | - Xiaoyan Liu
- Department of Biomedical Engineering, Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Southern University of Science and Technology, Shenzhen, China
| | - Xingyu Jiang
- Department of Biomedical Engineering, Shenzhen Key Laboratory of Smart Healthcare Engineering, Guangdong Provincial Key Laboratory of Advanced Biomaterials, Southern University of Science and Technology, Shenzhen, China
| | - Mingfang Lu
- Department of Immunology, Key Laboratory of Medical Molecular Virology (MOE, NHC, CAMS), School of Basic Medical Sciences and Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Ji-Song Guan
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Qingjian Han
- State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, Department of Neurosurgery, Huashan Hospital, Fudan University, Shanghai, China
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3
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Cordova I, Blesson A, Savatt JM, Sveden A, Mahida S, Hazlett H, Rooney Riggs E, Chopra M. Expansion of the Genotypic and Phenotypic Spectrum of ASH1L-Related Syndromic Neurodevelopmental Disorder. Genes (Basel) 2024; 15:423. [PMID: 38674358 PMCID: PMC11049257 DOI: 10.3390/genes15040423] [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: 02/15/2024] [Revised: 03/21/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Pathogenic ASH1L variants have been reported in probands with broad phenotypic presentations, including intellectual disability, autism spectrum disorder, attention deficit hyperactivity disorder, seizures, congenital anomalies, and other skeletal, muscular, and sleep differences. Here, we review previously published individuals with pathogenic ASH1L variants and report three further probands with novel ASH1L variants and previously unreported phenotypic features, including mixed receptive language disorder and gait disturbances. These novel data from the Brain Gene Registry, an accessible repository of clinically derived genotypic and phenotypic data, have allowed for the expansion of the phenotypic and genotypic spectrum of this condition.
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Affiliation(s)
- Ineke Cordova
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA 17822, USA; (I.C.); (E.R.R.)
| | - Alyssa Blesson
- Department of Neurology and Developmental Medicine, Kennedy Krieger Institute, Baltimore, MD 21205, USA
| | - Juliann M. Savatt
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA 17822, USA; (I.C.); (E.R.R.)
| | - Abigail Sveden
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Sonal Mahida
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Heather Hazlett
- Department of Psychiatry, University of North Carolina Intellectual and Developmental Disability Research Center, Chapel Hill, NC 27510, USA
| | - Erin Rooney Riggs
- Autism and Developmental Medicine Institute, Geisinger, Danville, PA 17822, USA; (I.C.); (E.R.R.)
| | - Maya Chopra
- Rosamund Stone Zander Translational Neuroscience Center, Boston Children’s Hospital, Boston, MA 02115, USA
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Dutta M, Qamar T, Kushavah U, Siddiqi MI, Kar S. Exploring host epigenetic enzymes as targeted therapies for visceral leishmaniasis: in silico design and in vitro efficacy of KDM6B and ASH1L inhibitors. Mol Divers 2024:10.1007/s11030-024-10824-w. [PMID: 38522046 DOI: 10.1007/s11030-024-10824-w] [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: 12/28/2023] [Accepted: 02/18/2024] [Indexed: 03/25/2024]
Abstract
In order to combat various infectious diseases, the utilization of host-directed therapies as an alternative to chemotherapy has gained a lot of attention in the recent past, since it bypasses the existing limitations of conventional therapies. The use of host epigenetic enzymes like histone lysine methyltransferases and lysine demethylases as potential drug targets has successfully been employed for controlling various inflammatory diseases like rheumatoid arthritis and acute leukemia. In our earlier study, we have already shown that the functional knockdown of KDM6B and ASH1L in the experimental model of visceral leishmaniasis has resulted in a significant reduction of organ parasite burden. Herein, we performed a high throughput virtual screening against KDM6B and ASH1L using > 53,000 compounds that were obtained from the Maybridge library and PubChem Database, followed by molecular docking to evaluate their docking score/Glide Gscore. Based on their docking scores, the selected inhibitors were later assessed for their in vitro anti-leishmanial efficacy. Out of all inhibitors designed against KDM6B and ASH1L, HTS09796, GSK-J4 and AS-99 particularly showed promising in vitro activity with IC50 < 5 µM against both extracellular promastigote and intracellular amastigote forms of L. donovani. In vitro drug interaction studies of these inhibitors further demonstrated their synergistic interaction with amphotericin-B and miltefosine. However, GSK-J4 makes an exception by displaying an in different mode of interaction with miltefosine. Collectively, our in silico and in vitro studies acted as a platform to identify the applicability of these inhibitors targeted against KDM6B and ASH1L for anti-leishmanial therapy.
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Affiliation(s)
- Mukul Dutta
- Infectious Diseases & Immunology Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032, India
- Molecular Microbiology & Immunology Division, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Tooba Qamar
- Molecular Microbiology & Immunology Division, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
- Department of Clinical Immunology and Rheumatology, Sanjay Gandhi Post Graduate Institute of Medical Sciences (SGPGIMS), Lucknow, Uttar Pradesh, 226014, India
| | - Unnati Kushavah
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Mohammad Imran Siddiqi
- Biochemistry and Structural Biology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Susanta Kar
- Infectious Diseases & Immunology Division, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Jadavpur, Kolkata, 700032, India.
- Molecular Microbiology & Immunology Division, CSIR-Central Drug Research Institute, BS-10/1, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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5
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Holguin-Cruz JA, Bui JM, Jha A, Na D, Gsponer J. Widespread alteration of protein autoinhibition in human cancers. Cell Syst 2024; 15:246-263.e7. [PMID: 38366601 DOI: 10.1016/j.cels.2024.01.009] [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: 01/31/2019] [Revised: 06/20/2023] [Accepted: 01/26/2024] [Indexed: 02/18/2024]
Abstract
Autoinhibition is a prevalent allosteric regulatory mechanism in signaling proteins. Reduced autoinhibition underlies the tumorigenic effect of some known cancer drivers, but whether autoinhibition is altered generally in cancer remains elusive. Here, we demonstrate that cancer-associated missense mutations, in-frame insertions/deletions, and fusion breakpoints are enriched within inhibitory allosteric switches (IASs) across all cancer types. Selection for IASs that are recurrently mutated in cancers identifies established and unknown cancer drivers. Recurrent missense mutations in IASs of these drivers are associated with distinct, cancer-specific changes in molecular signaling. For the specific case of PPP3CA, the catalytic subunit of calcineurin, we provide insights into the molecular mechanisms of altered autoinhibition by cancer mutations using biomolecular simulations, and demonstrate that such mutations are associated with transcriptome changes consistent with increased calcineurin signaling. Our integrative study shows that autoinhibition-modulating genetic alterations are positively selected for by cancer cells.
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Affiliation(s)
- Jorge A Holguin-Cruz
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jennifer M Bui
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Ashwani Jha
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Jörg Gsponer
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
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6
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Al-Harthi S, Li H, Winkler A, Szczepski K, Deng J, Grembecka J, Cierpicki T, Jaremko Ł. MRG15 activates histone methyltransferase activity of ASH1L by recruiting it to the nucleosomes. Structure 2023; 31:1200-1207.e5. [PMID: 37527654 DOI: 10.1016/j.str.2023.07.001] [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: 03/18/2023] [Revised: 05/16/2023] [Accepted: 07/05/2023] [Indexed: 08/03/2023]
Abstract
ASH1L is a histone methyltransferase that regulates gene expression through methylation of histone H3 on lysine K36. While the catalytic SET domain of ASH1L has low intrinsic activity, several studies found that it can be vastly enhanced by the interaction with MRG15 protein and proposed allosteric mechanism of releasing its autoinhibited conformation. Here, we found that full-length MRG15, but not the MRG domain alone, can enhance the activity of the ASH1L SET domain. In addition, we showed that catalytic activity of MRG15-ASH1L depends on nucleosome binding mediated by MRG15 chromodomain. We found that in solution MRG15 binds to ASH1L, but has no impact on the conformation of the SET domain autoinhibitory loop or the S-adenosylmethionine cofactor binding site. Moreover, MRG15 binding did not impair the potency of small molecule inhibitors of ASH1L. These findings suggest that MRG15 functions as an adapter that enhances ASH1L catalytic activity by recruiting nucleosome substrate.
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Affiliation(s)
- Samah Al-Harthi
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Bioscience Program, Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Hao Li
- Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510D, Ann Arbor, MI 48108, USA
| | - Alyssa Winkler
- Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510D, Ann Arbor, MI 48108, USA
| | - Kacper Szczepski
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Bioscience Program, Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Jing Deng
- Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510D, Ann Arbor, MI 48108, USA
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510D, Ann Arbor, MI 48108, USA
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, 1150 West Medical Center Dr, MSRB I, Room 4510D, Ann Arbor, MI 48108, USA.
| | - Łukasz Jaremko
- Smart-Health Initiative (SHI) and Red Sea Research Center (RSRC), Bioscience Program, Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
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7
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Seni S, Singh RK, Prasad M. Dynamics of epigenetic control in plants via SET domain containing proteins: Structural and functional insights. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194966. [PMID: 37532097 DOI: 10.1016/j.bbagrm.2023.194966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/25/2023] [Accepted: 07/28/2023] [Indexed: 08/04/2023]
Abstract
Plants control expression of their genes in a way that involves manipulating the chromatin structural dynamics in order to adapt to environmental changes and carry out developmental processes. Histone modifications like histone methylation are significant epigenetic marks which profoundly and globally modify chromatin, potentially affecting the expression of several genes. Methylation of histones is catalyzed by histone lysine methyltransferases (HKMTs), that features an evolutionary conserved domain known as SET [Su(var)3-9, E(Z), Trithorax]. This methylation is directed at particular lysine (K) residues on H3 or H4 histone. Plant SET domain group (SDG) proteins are categorized into different classes that have been conserved through evolution, and each class have specificity that influences how the chromatin structure operates. The domains discovered in plant SET domain proteins have typically been linked to protein-protein interactions, suggesting that majority of the SDGs function in complexes. Additionally, SDG-mediated histone mark deposition also affects alternative splicing events. In present review, we discussed the diversity of SDGs in plants including their structural properties. Additionally, we have provided comprehensive summary of the functions of the SDG-domain containing proteins in plant developmental processes and response to environmental stimuli have also been highlighted.
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Affiliation(s)
- Sushmita Seni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Roshan Kumar Singh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Manoj Prasad
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India; Department of Plant Sciences, University of Hyderabad, Hyderabad, Telangana 500046, India.
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8
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Möller M, Ridenour JB, Wright DF, Martin FA, Freitag M. H4K20me3 is important for Ash1-mediated H3K36me3 and transcriptional silencing in facultative heterochromatin in a fungal pathogen. PLoS Genet 2023; 19:e1010945. [PMID: 37747878 PMCID: PMC10553808 DOI: 10.1371/journal.pgen.1010945] [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: 04/20/2023] [Revised: 10/05/2023] [Accepted: 08/30/2023] [Indexed: 09/27/2023] Open
Abstract
Facultative heterochromatin controls development and differentiation in many eukaryotes. In metazoans, plants, and many filamentous fungi, facultative heterochromatin is characterized by transcriptional repression and enrichment with nucleosomes that are trimethylated at histone H3 lysine 27 (H3K27me3). While loss of H3K27me3 results in derepression of transcriptional gene silencing in many species, additional up- and downstream layers of regulation are necessary to mediate control of transcription in chromosome regions enriched with H3K27me3. Here, we investigated the effects of one histone mark on histone H4, namely H4K20me3, in the fungus Zymoseptoria tritici, a globally important pathogen of wheat. Deletion of kmt5, the gene encoding the sole methyltransferase responsible for H4K20 methylation, resulted in global derepression of transcription, especially in regions of facultative heterochromatin. Derepression in the absence of H4K20me3 not only affected known genes but also a large number of novel, previously undetected transcripts generated from regions of facultative heterochromatin on accessory chromosomes. Transcriptional activation in kmt5 deletion strains was accompanied by a complete loss of Ash1-mediated H3K36me3 and chromatin reorganization affecting H3K27me3 and H3K4me2 distribution in regions of facultative heterochromatin. Strains with H4K20L, M or Q mutations in the single histone H4 gene of Z. tritici recapitulated these chromatin changes, suggesting that H4K20me3 is important for Ash1-mediated H3K36me3. The ∆kmt5 mutants we obtained were more sensitive to genotoxic stressors than wild type and both, ∆kmt5 and ∆ash1, showed greatly increased rates of accessory chromosome loss. Taken together, our results provide insights into an unsuspected mechanism involved in the assembly and maintenance of facultative heterochromatin.
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Affiliation(s)
- Mareike Möller
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, United States of America
| | - John B. Ridenour
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, United States of America
| | - Devin F. Wright
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, United States of America
| | - Faith A. Martin
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, United States of America
| | - Michael Freitag
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, United States of America
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9
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Maritz C, Khaleghi R, Yancoskie MN, Diethelm S, Brülisauer S, Ferreira NS, Jiang Y, Sturla SJ, Naegeli H. ASH1L-MRG15 methyltransferase deposits H3K4me3 and FACT for damage verification in nucleotide excision repair. Nat Commun 2023; 14:3892. [PMID: 37393406 PMCID: PMC10314917 DOI: 10.1038/s41467-023-39635-7] [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: 09/09/2022] [Accepted: 06/22/2023] [Indexed: 07/03/2023] Open
Abstract
To recognize DNA adducts, nucleotide excision repair (NER) deploys the XPC sensor, which detects damage-induced helical distortions, followed by engagement of TFIIH for lesion verification. Accessory players ensure that this factor handover takes place in chromatin where DNA is tightly wrapped around histones. Here, we describe how the histone methyltransferase ASH1L, once activated by MRG15, helps XPC and TFIIH to navigate through chromatin and induce global-genome NER hotspots. Upon UV irradiation, ASH1L adds H3K4me3 all over the genome (except in active gene promoters), thus priming chromatin for XPC relocations from native to damaged DNA. The ASH1L-MRG15 complex further recruits the histone chaperone FACT to DNA lesions. In the absence of ASH1L, MRG15 or FACT, XPC is misplaced and persists on damaged DNA without being able to deliver the lesions to TFIIH. We conclude that ASH1L-MRG15 makes damage verifiable by the NER machinery through the sequential deposition of H3K4me3 and FACT.
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Affiliation(s)
- Corina Maritz
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Reihaneh Khaleghi
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Michelle N Yancoskie
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Sarah Diethelm
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Sonja Brülisauer
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Natalia Santos Ferreira
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland
| | - Yang Jiang
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zurich, Zurich, Switzerland
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich, Switzerland.
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10
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Rodriguez Araya E, Merli ML, Cribb P, de Souza VC, Serra E. Deciphering Divergent Trypanosomatid Nuclear Complexes by Analyzing Interactomic Datasets with AlphaFold2 and Genetic Approaches. ACS Infect Dis 2023; 9:1267-1282. [PMID: 37167453 DOI: 10.1021/acsinfecdis.3c00148] [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: 05/13/2023]
Abstract
Acetylation signaling pathways in trypanosomatids, a group of early branching organisms, are poorly understood due to highly divergent protein sequences. To overcome this challenge, we used interactomic datasets and AlphaFold2 (AF2)-multimer to predict direct interactions and validated them using yeast two and three-hybrid assays. We focused on MORF4 related gene (MRG) domain-containing proteins and their interactions, typically found in histone acetyltransferase/deacetylase complexes. The results identified a structurally conserved complex, TcTINTIN, which is orthologous to human and yeast trimer independent of NuA4 for transcription interaction (TINTIN) complexes; and another trimeric complex involving an MRG domain, only seen in trypanosomatids. The identification of a key component of TcTINTIN, TcMRGBP, would not have been possible through traditional homology-based methods. We also conducted molecular dynamics simulations, revealing a conformational change that potentially affects its affinity for TcBDF6. The study also revealed a novel way in which an MRG domain participates in simultaneous interactions with two MRG binding proteins binding two different surfaces, a phenomenon not previously reported. Overall, this study demonstrates the potential of using AF2-processed interactomic datasets to identify protein complexes in deeply branched eukaryotes, which can be challenging to study based on sequence similarity. The findings provide new insights into the acetylation signaling pathways in trypanosomatids, specifically highlighting the importance of MRG domain-containing proteins in forming complexes, which may have important implications for understanding the biology of these organisms and developing new therapeutics. On the other hand, our validation of AF2 models for the determination of multiprotein complexes illuminates the power of using such artificial intelligence-derived tools in the future development of biology.
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Affiliation(s)
- Elvio Rodriguez Araya
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Suipacha 590, CP2000 Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, CP2000 Rosario, Argentina
| | - Marcelo L Merli
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Suipacha 590, CP2000 Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, CP2000 Rosario, Argentina
| | - Pamela Cribb
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Suipacha 590, CP2000 Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, CP2000 Rosario, Argentina
| | | | - Esteban Serra
- Instituto de Biología Molecular y Celular de Rosario, CONICET, Suipacha 590, CP2000 Rosario, Argentina
- Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, CP2000 Rosario, Argentina
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11
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Devoucoux M, Roques C, Lachance C, Lashgari A, Joly-Beauparlant C, Jacquet K, Alerasool N, Prudente A, Taipale M, Droit A, Lambert JP, Hussein SMI, Côté J. MRG Proteins Are Shared by Multiple Protein Complexes With Distinct Functions. Mol Cell Proteomics 2022; 21:100253. [PMID: 35636729 PMCID: PMC9253478 DOI: 10.1016/j.mcpro.2022.100253] [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: 08/10/2021] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
MRG15/MORF4L1 is a highly conserved protein in eukaryotes that contains a chromodomain (CHD) recognizing methylation of lysine 36 on histone H3 (H3K36me3) in chromatin. Intriguingly, it has been reported in the literature to interact with several different factors involved in chromatin modifications, gene regulation, alternative mRNA splicing, and DNA repair by homologous recombination. To get a complete and reliable picture of associations in physiological conditions, we used genome editing and tandem affinity purification to analyze the stable native interactome of human MRG15, its paralog MRGX/MORF4L2 that lacks the CHD, and MRGBP (MRG-binding protein) in isogenic K562 cells. We found stable interchangeable association of MRG15 and MRGX with the NuA4/TIP60 histone acetyltransferase/chromatin remodeler, Sin3B histone deacetylase/demethylase, ASH1L histone methyltransferase, and PALB2-BRCA2 DNA repair protein complexes. These associations were further confirmed and analyzed by CRISPR tagging of endogenous proteins and comparison of expressed isoforms. Importantly, based on structural information, point mutations could be introduced that specifically disrupt MRG15 association with some complexes but not others. Most interestingly, we also identified a new abundant native complex formed by MRG15/X-MRGBP-BRD8-EP400NL (EP400 N-terminal like) that is functionally similar to the yeast TINTIN (Trimer Independent of NuA4 for Transcription Interactions with Nucleosomes) complex. Our results show that EP400NL, being homologous to the N-terminal region of NuA4/TIP60 subunit EP400, creates TINTIN by competing for BRD8 association. Functional genomics indicate that human TINTIN plays a role in transcription of specific genes. This is most likely linked to the H4ac-binding bromodomain of BRD8 along the H3K36me3-binding CHD of MRG15 on the coding region of transcribed genes. Taken together, our data provide a complete detailed picture of human MRG proteins-associated protein complexes, which are essential to understand and correlate their diverse biological functions in chromatin-based nuclear processes.
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Affiliation(s)
- Maëva Devoucoux
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Quebec, Canada
| | - Céline Roques
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Quebec, Canada
| | - Catherine Lachance
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Quebec, Canada
| | - Anahita Lashgari
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Quebec, Canada; Department of Molecular Medicine, Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center, Big Data Research Center, Université Laval, Quebec City, Quebec, Canada
| | - Charles Joly-Beauparlant
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, Quebec City, Quebec, Canada; Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Karine Jacquet
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Quebec, Canada
| | - Nader Alerasool
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Alexandre Prudente
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Quebec, Canada
| | - Mikko Taipale
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Arnaud Droit
- Axe Neurosciences, Centre de Recherche du CHU de Québec-Université Laval, Pavillon CHUL, Quebec City, Quebec, Canada; Faculty of Medicine, Université Laval, Quebec City, Quebec, Canada
| | - Jean-Philippe Lambert
- Department of Molecular Medicine, Laval University Cancer Research Center, CHU de Québec-Université Laval Research Center, Big Data Research Center, Université Laval, Quebec City, Quebec, Canada
| | - Samer M I Hussein
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Quebec, Canada
| | - Jacques Côté
- St. Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Quebec, Canada.
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12
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Taylor-Papadimitriou J, Burchell JM. Histone Methylases and Demethylases Regulating Antagonistic Methyl Marks: Changes Occurring in Cancer. Cells 2022; 11:1113. [PMID: 35406676 PMCID: PMC8997813 DOI: 10.3390/cells11071113] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 02/06/2023] Open
Abstract
Epigenetic regulation of gene expression is crucial to the determination of cell fate in development and differentiation, and the Polycomb (PcG) and Trithorax (TrxG) groups of proteins, acting antagonistically as complexes, play a major role in this regulation. Although originally identified in Drosophila, these complexes are conserved in evolution and the components are well defined in mammals. Each complex contains a protein with methylase activity (KMT), which can add methyl groups to a specific lysine in histone tails, histone 3 lysine 27 (H3K27), by PcG complexes, and H3K4 and H3K36 by TrxG complexes, creating transcriptionally repressive or active marks, respectively. Histone demethylases (KDMs), identified later, added a new dimension to histone methylation, and mutations or changes in levels of expression are seen in both methylases and demethylases and in components of the PcG and TrX complexes across a range of cancers. In this review, we focus on both methylases and demethylases governing the methylation state of the suppressive and active marks and consider their action and interaction in normal tissues and in cancer. A picture is emerging which indicates that the changes which occur in cancer during methylation of histone lysines can lead to repression of genes, including tumour suppressor genes, or to the activation of oncogenes. Methylases or demethylases, which are themselves tumour suppressors, are highly mutated. Novel targets for cancer therapy have been identified and a methylase (KMT6A/EZH2), which produces the repressive H3K27me3 mark, and a demethylase (KDM1A/LSD1), which demethylates the active H3K4me2 mark, are now under clinical evaluation.
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13
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Redington J, Deveryshetty J, Kanikkannan L, Miller I, Korolev S. Structural Insight into the Mechanism of PALB2 Interaction with MRG15. Genes (Basel) 2021; 12:genes12122002. [PMID: 34946951 PMCID: PMC8701324 DOI: 10.3390/genes12122002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/08/2021] [Accepted: 12/11/2021] [Indexed: 12/21/2022] Open
Abstract
The tumor suppressor protein partner and localizer of BRCA2 (PALB2) orchestrates the interactions between breast cancer susceptibility proteins 1 and 2 (BRCA1, -2) that are critical for genome stability, homologous recombination (HR) and DNA repair. PALB2 mutations predispose patients to a spectrum of cancers, including breast and ovarian cancers. PALB2 localizes HR machinery to chromatin and links it with transcription through multiple DNA and protein interactions. This includes its interaction with MRG15 (Morf-related gene on chromosome 15), which is part of many transcription complexes, including the HAT-associated and the HDAC-associated complexes. This interaction is critical for PALB2 localization in actively transcribed genes, where transcription/replication conflicts lead to frequent replication stress and DNA breaks. We solved the crystal structure of the MRG15 MRG domain bound to the PALB2 peptide and investigated the effect of several PALB2 mutations, including patient-derived variants. PALB2 interacts with an extended surface of the MRG that is known to interact with other proteins. This, together with a nanomolar affinity, suggests that the binding of MRG15 partners, including PALB2, to this region is mutually exclusive. Breast cancer-related mutations of PALB2 cause only minor attenuation of the binding affinity. New data reveal the mechanism of PALB2-MRG15 binding, advancing our understanding of PALB2 function in chromosome maintenance and tumorigenesis.
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14
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A loss-of-function variant in SUV39H2 identified in autism-spectrum disorder causes altered H3K9 trimethylation and dysregulation of protocadherin β-cluster genes in the developing brain. Mol Psychiatry 2021; 26:7550-7559. [PMID: 34262135 DOI: 10.1038/s41380-021-01199-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 05/21/2021] [Accepted: 06/10/2021] [Indexed: 02/06/2023]
Abstract
Recent evidence has documented the potential roles of histone-modifying enzymes in autism-spectrum disorder (ASD). Aberrant histone H3 lysine 9 (H3K9) dimethylation resulting from genetic variants in histone methyltransferases is known for neurodevelopmental and behavioral anomalies. However, a systematic examination of H3K9 methylation dynamics in ASD is lacking. Here we resequenced nine genes for histone methyltransferases and demethylases involved in H3K9 methylation in individuals with ASD and healthy controls using targeted next-generation sequencing. We identified a novel rare variant (A211S) in the SUV39H2, which was predicted to be deleterious. The variant showed strongly reduced histone methyltransferase activity in vitro. In silico analysis showed that the variant destabilizes the hydrophobic core and allosterically affects the enzyme activity. The Suv39h2-KO mice displayed hyperactivity and reduced behavioral flexibility in learning the tasks that required complex behavioral adaptation, which is relevant for ASD. The Suv39h2 deficit evoked an elevated expression of a subset of protocadherin β (Pcdhb) cluster genes in the embryonic brain, which is attributable to the loss of H3K9 trimethylation (me3) at the gene promoters. Reduced H3K9me3 persisted in the cerebellum of Suv39h2-deficient mice to an adult stage. Congruently, reduced expression of SUV39H1 and SUV39H2 in the postmortem brain samples of ASD individuals was observed, underscoring the role of H3K9me3 deficiency in ASD etiology. The present study provides direct evidence for the role of SUV39H2 in ASD and suggests a molecular cascade of SUV39H2 dysfunction leading to H3K9me3 deficiency followed by an untimely, elevated expression of Pcdhb cluster genes during early neurodevelopment.
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15
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Sato K, Kumar A, Hamada K, Okada C, Oguni A, Machiyama A, Sakuraba S, Nishizawa T, Nureki O, Kono H, Ogata K, Sengoku T. Structural basis of the regulation of the normal and oncogenic methylation of nucleosomal histone H3 Lys36 by NSD2. Nat Commun 2021; 12:6605. [PMID: 34782608 PMCID: PMC8593083 DOI: 10.1038/s41467-021-26913-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 10/28/2021] [Indexed: 12/24/2022] Open
Abstract
Dimethylated histone H3 Lys36 (H3K36me2) regulates gene expression, and aberrant H3K36me2 upregulation, resulting from either the overexpression or point mutation of the dimethyltransferase NSD2, is found in various cancers. Here we report the cryo-electron microscopy structure of NSD2 bound to the nucleosome. Nucleosomal DNA is partially unwrapped, facilitating NSD2 access to H3K36. NSD2 interacts with DNA and H2A along with H3. The NSD2 autoinhibitory loop changes its conformation upon nucleosome binding to accommodate H3 in its substrate-binding cleft. Kinetic analysis revealed that two oncogenic mutations, E1099K and T1150A, increase NSD2 catalytic turnover. Molecular dynamics simulations suggested that in both mutants, the autoinhibitory loop adopts an open state that can accommodate H3 more often than the wild-type. We propose that E1099K and T1150A destabilize the interactions that keep the autoinhibitory loop closed, thereby enhancing catalytic turnover. Our analyses guide the development of specific inhibitors of NSD2.
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Affiliation(s)
- Ko Sato
- grid.268441.d0000 0001 1033 6139Department of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004 Japan
| | - Amarjeet Kumar
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215 Japan
| | - Keisuke Hamada
- grid.268441.d0000 0001 1033 6139Department of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004 Japan
| | - Chikako Okada
- grid.268441.d0000 0001 1033 6139Department of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004 Japan
| | - Asako Oguni
- grid.268441.d0000 0001 1033 6139Department of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004 Japan
| | - Ayumi Machiyama
- grid.268441.d0000 0001 1033 6139Department of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa 236-0004 Japan
| | - Shun Sakuraba
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215 Japan
| | - Tomohiro Nishizawa
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan ,grid.268441.d0000 0001 1033 6139Present Address: Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045 Japan
| | - Osamu Nureki
- grid.26999.3d0000 0001 2151 536XDepartment of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033 Japan
| | - Hidetoshi Kono
- Institute for Quantum Life Science, National Institutes for Quantum Science and Technology, 8-1-7 Umemidai, Kizugawa, Kyoto 619-0215 Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan.
| | - Toru Sengoku
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-0004, Japan.
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16
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Lindehell H, Glotov A, Dorafshan E, Schwartz YB, Larsson J. The role of H3K36 methylation and associated methyltransferases in chromosome-specific gene regulation. SCIENCE ADVANCES 2021; 7:eabh4390. [PMID: 34597135 PMCID: PMC10938550 DOI: 10.1126/sciadv.abh4390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 08/11/2021] [Indexed: 06/13/2023]
Abstract
In Drosophila, two chromosomes require special mechanisms to balance their transcriptional output to the rest of the genome. These are the male-specific lethal complex targeting the male X chromosome and Painting of fourth targeting chromosome 4. Here, we explore the role of histone H3 methylated at lysine-36 (H3K36) and the associated methyltransferases—Set2, NSD, and Ash1—in these two chromosome-specific systems. We show that the loss of Set2 impairs the MSL complex–mediated dosage compensation; however, the effect is not recapitulated by H3K36 replacement and indicates an alternative target of Set2. Unexpectedly, balanced transcriptional output from the fourth chromosome requires intact H3K36 and depends on the additive functions of NSD and Ash1. We conclude that H3K36 methylation and the associated methyltransferases are important factors to balance transcriptional output of the male X chromosome and the fourth chromosome. Furthermore, our study highlights the pleiotropic effects of these enzymes.
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Affiliation(s)
- Henrik Lindehell
- Department of Molecular Biology, Umeå University, SE-90187 Umeå, Sweden
| | - Alexander Glotov
- Department of Molecular Biology, Umeå University, SE-90187 Umeå, Sweden
| | - Eshagh Dorafshan
- Department of Molecular Biology, Umeå University, SE-90187 Umeå, Sweden
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17
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Davidovich C, Zhang Q. Allosteric regulation of histone lysine methyltransferases: from context-specific regulation to selective drugs. Biochem Soc Trans 2021; 49:591-607. [PMID: 33769454 PMCID: PMC8106495 DOI: 10.1042/bst20200238] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 02/06/2023]
Abstract
Histone lysine methyltransferases (HKMTs) are key regulators of many cellular processes. By definition, HKMTs catalyse the methylation of lysine residues in histone proteins. The enzymatic activities of HKMTs are under precise control, with their allosteric regulation emerging as a prevalent paradigm. We review the molecular mechanisms of allosteric regulation of HKMTs using well-studied histone H3 (K4, K9, K27 and K36) methyltransferases as examples. We discuss the current advances and future potential in targeting allosteric sites of HKMTs for drug development.
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Affiliation(s)
- Chen Davidovich
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
- EMBL-Australia and the ARC Centre of Excellence in Advanced Molecular Imaging, Clayton, Victoria, Australia
| | - Qi Zhang
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, Victoria, Australia
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18
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Gsell C, Richly H, Coin F, Naegeli H. A chromatin scaffold for DNA damage recognition: how histone methyltransferases prime nucleosomes for repair of ultraviolet light-induced lesions. Nucleic Acids Res 2020; 48:1652-1668. [PMID: 31930303 PMCID: PMC7038933 DOI: 10.1093/nar/gkz1229] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/18/2019] [Accepted: 12/23/2019] [Indexed: 02/07/2023] Open
Abstract
The excision of mutagenic DNA adducts by the nucleotide excision repair (NER) pathway is essential for genome stability, which is key to avoiding genetic diseases, premature aging, cancer and neurologic disorders. Due to the need to process an extraordinarily high damage density embedded in the nucleosome landscape of chromatin, NER activity provides a unique functional caliper to understand how histone modifiers modulate DNA damage responses. At least three distinct lysine methyltransferases (KMTs) targeting histones have been shown to facilitate the detection of ultraviolet (UV) light-induced DNA lesions in the difficult to access DNA wrapped around histones in nucleosomes. By methylating core histones, these KMTs generate docking sites for DNA damage recognition factors before the chromatin structure is ultimately relaxed and the offending lesions are effectively excised. In view of their function in priming nucleosomes for DNA repair, mutations of genes coding for these KMTs are expected to cause the accumulation of DNA damage promoting cancer and other chronic diseases. Research on the question of how KMTs modulate DNA repair might pave the way to the development of pharmacologic agents for novel therapeutic strategies.
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Affiliation(s)
- Corina Gsell
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Winterthurerstrasse 260, 8057 Zurich, Switzerland
| | - Holger Richly
- Boehringer Ingelheim Pharma, Department of Molecular Biology, Birkendorfer Str. 65, 88397 Biberach an der Riß, Germany
| | - Frédéric Coin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Equipe Labélisée Ligue contre le Cancer, Illkirch Cedex, Strasbourg, France
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Winterthurerstrasse 260, 8057 Zurich, Switzerland
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19
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Liu S, Tian M, He F, Li J, Xie H, Liu W, Zhang Y, Zhang R, Yi M, Che F, Ma X, Zheng Y, Deng H, Wang G, Chen L, Sun X, Xu Y, Wang J, Zang Y, Han M, Wang X, Guan H, Ge Y, Wu C, Wang H, Liang H, Li H, Ran N, Yang Z, Huang H, Wei Y, Zheng X, Sun X, Feng X, Zheng L, Zhu T, Luo W, Chen Q, Yan Y, Huang Z, Jing Z, Guo Y, Zhang X, Schaaf CP, Xing J, Wang C, Yu F, Guan JS. Mutations in ASH1L confer susceptibility to Tourette syndrome. Mol Psychiatry 2020; 25:476-490. [PMID: 31673123 DOI: 10.1038/s41380-019-0560-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 08/12/2019] [Accepted: 08/19/2019] [Indexed: 12/31/2022]
Abstract
Tourette syndrome (TS) is a childhood-onset neuropsychiatric disorder characterized by repetitive motor movements and vocal tics. The clinical manifestations of TS are complex and often overlap with other neuropsychiatric disorders. TS is highly heritable; however, the underlying genetic basis and molecular and neuronal mechanisms of TS remain largely unknown. We performed whole-exome sequencing of a hundred trios (probands and their parents) with detailed records of their clinical presentations and identified a risk gene, ASH1L, that was both de novo mutated and associated with TS based on a transmission disequilibrium test. As a replication, we performed follow-up targeted sequencing of ASH1L in additional 524 unrelated TS samples and replicated the association (P value = 0.001). The point mutations in ASH1L cause defects in its enzymatic activity. Therefore, we established a transgenic mouse line and performed an array of anatomical, behavioral, and functional assays to investigate ASH1L function. The Ash1l+/- mice manifested tic-like behaviors and compulsive behaviors that could be rescued by the tic-relieving drug haloperidol. We also found that Ash1l disruption leads to hyper-activation and elevated dopamine-releasing events in the dorsal striatum, all of which could explain the neural mechanisms for the behavioral abnormalities in mice. Taken together, our results provide compelling evidence that ASH1L is a TS risk gene.
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Affiliation(s)
- Shiguo Liu
- Medical Genetic Department, The Affiliated Hospital of Qingdao University, Qingdao, China.,The Prenatal Diagnosis Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Miaomiao Tian
- School of Life Sciences, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Fan He
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders & Beijing Institute for Brain Disorders Center of Schizophrenia, Beijing Anding Hospital, Capital Medical University, Beijing, China
| | - Jiani Li
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Hong Xie
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.,Institute of Brain-Intelligence Technology, Zhangjiang Laboratory & Shanghai Research Center for Brain Science and Brain-Inspired Intelligence, Shanghai, 201210, China
| | - Wenmiao Liu
- Medical Genetic Department, The Affiliated Hospital of Qingdao University, Qingdao, China.,The Prenatal Diagnosis Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yeting Zhang
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Ru Zhang
- Medical Genetic Department, The Affiliated Hospital of Qingdao University, Qingdao, China.,The Prenatal Diagnosis Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Mingji Yi
- Developmental Behavioral Pediatric Department, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Fengyuan Che
- Department of Neurology, Linyi People's Hospital, Linyi, China
| | - Xu Ma
- National Research Institute for Family Planning, Beijing, China
| | - Yi Zheng
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders & Beijing Institute for Brain Disorders Center of Schizophrenia, Beijing Anding Hospital, Capital Medical University, Beijing, China
| | - Hao Deng
- Center for Experimental Medicine & Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Guiju Wang
- Child Healthcare Department, Rizhao people's Hospital, Rizhao, China
| | - Lang Chen
- Department of Pediatrics, Fujian Provincial Hospital, Provincial Clinical Medical College Affiliated to Fujian Medical University, Fuzhou, China
| | - Xue Sun
- Department of Medical Record, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yinglei Xu
- Medical Genetic Department, The Affiliated Hospital of Qingdao University, Qingdao, China.,The Prenatal Diagnosis Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Jingli Wang
- Medical Genetic Department, The Affiliated Hospital of Qingdao University, Qingdao, China.,The Prenatal Diagnosis Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yucui Zang
- Medical Genetic Department, The Affiliated Hospital of Qingdao University, Qingdao, China.,The Prenatal Diagnosis Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Mengmeng Han
- Medical Genetic Department, The Affiliated Hospital of Qingdao University, Qingdao, China.,The Prenatal Diagnosis Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiuhai Wang
- Department of Biology, Qingdao University, Qingdao, China
| | - Hongzai Guan
- Department of Clinical Laboratory Diagnosis, Qingdao University, Qingdao, China
| | - Yinlin Ge
- Department of Biochemistry and Molecular Biology, Qingdao University, Qingdao, China
| | - Chunmei Wu
- Department of Clinical Laboratory Diagnosis, Qingdao University, Qingdao, China
| | - Haiyan Wang
- Department of Blood Transfusion, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Hui Liang
- Department of Public Health, Qingdao University, Qingdao, China
| | - Hui Li
- Physical Examination Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Ni Ran
- Developmental Behavioral Pediatric Department, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhaochuan Yang
- Developmental Behavioral Pediatric Department, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Huanhuan Huang
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders & Beijing Institute for Brain Disorders Center of Schizophrenia, Beijing Anding Hospital, Capital Medical University, Beijing, China
| | - Yanzhao Wei
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders & Beijing Institute for Brain Disorders Center of Schizophrenia, Beijing Anding Hospital, Capital Medical University, Beijing, China
| | - Xueping Zheng
- Department of Neurology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xiangrong Sun
- Medical Genetic Department, The Affiliated Hospital of Qingdao University, Qingdao, China.,The Prenatal Diagnosis Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xueying Feng
- Developmental Behavioral Pediatric Department, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Lanlan Zheng
- Department of Psychiatry, The Third Hospital of Chaoyang District of Beijing, Beijing, China
| | - Tao Zhu
- School of Life Sciences, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,Institute of Laboratory Animal Science, Chinese Academy of Medical Sciences and Comparative Medical Center, Peking Union Medical College, Beijing, China
| | - Wenhan Luo
- School of Life Sciences, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Qinan Chen
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Yuze Yan
- School of Life Sciences, IDG/McGovern Institute for Brain Research, Tsinghua University, Beijing, China.,School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Zuzhou Huang
- Department of Blood Transfusion, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Zhongcui Jing
- Department of Blood Transfusion, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yixia Guo
- Developmental Behavioral Pediatric Department, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Xuzhan Zhang
- Physical Examination Center, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Christian P Schaaf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Department of Genetics; Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Jinchuan Xing
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Chuanyue Wang
- The National Clinical Research Center for Mental Disorders & Beijing Key Laboratory of Mental Disorders & Beijing Institute for Brain Disorders Center of Schizophrenia, Beijing Anding Hospital, Capital Medical University, Beijing, China.
| | - Fuli Yu
- Human Genome Sequencing Center, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
| | - Ji-Song Guan
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China. .,CAS Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China.
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20
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Abstract
Trithorax histone methyltransferase Ash1/ASH1L is tightly regulated because it activates developmental gene transcription and counteracts Polycomb silencing. In this issue of Structure, Lee et al. (2019) and Hou et al. (2019) report the crystal structure of ASH1L bound to its activator MRG15 and suggest a mechanism that releases ASH1L auto-inhibition.
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Genetic Dissection Reveals the Role of Ash1 Domains in Counteracting Polycomb Repression. G3-GENES GENOMES GENETICS 2019; 9:3801-3812. [PMID: 31540973 PMCID: PMC6829142 DOI: 10.1534/g3.119.400579] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Antagonistic functions of Polycomb and Trithorax proteins are essential for proper development of all metazoans. While the Polycomb proteins maintain the repressed state of many key developmental genes, the Trithorax proteins ensure that these genes stay active in cells where they have to be expressed. Ash1 is the Trithorax protein that was proposed to counteract Polycomb repression by methylating lysine 36 of histone H3. However, it was recently shown that genetic replacement of Drosophila histone H3 with the variant that carried Arginine instead of Lysine at position 36 did not impair the ability of Ash1 to counteract Polycomb repression. This argues that Ash1 counteracts Polycomb repression by methylating yet unknown substrate(s) and that it is time to look beyond Ash1 methyltransferase SET domain, at other evolutionary conserved parts of the protein that received little attention. Here we used Drosophila genetics to demonstrate that Ash1 requires each of the BAH, PHD and SET domains to counteract Polycomb repression, while AT hooks are dispensable. Our findings argue that, in vivo, Ash1 acts as a multimer. Thereby it can combine the input of the SET domain and PHD-BAH cassette residing in different peptides. Finally, using new loss of function alleles, we show that zygotic Ash1 is required to prevent erroneous repression of homeotic genes of the bithorax complex in the embryo.
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22
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Bilokapic S, Halic M. Nucleosome and ubiquitin position Set2 to methylate H3K36. Nat Commun 2019; 10:3795. [PMID: 31439846 PMCID: PMC6706414 DOI: 10.1038/s41467-019-11726-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 08/01/2019] [Indexed: 12/19/2022] Open
Abstract
Histone H3 lysine 36 methylation (H3K36me) is a conserved histone modification deposited by the Set2 methyltransferases. Recent findings show that over-expression or mutation of Set2 enzymes promotes cancer progression, however, mechanisms of H3K36me are poorly understood. Set2 enzymes show spurious activity on histones and histone tails, and it is unknown how they obtain specificity to methylate H3K36 on the nucleosome. In this study, we present 3.8 Å cryo-EM structure of Set2 bound to the mimic of H2B ubiquitinated nucleosome. Our structure shows that Set2 makes extensive interactions with the H3 αN, the H3 tail, the H2A C-terminal tail and stabilizes DNA in the unwrapped conformation, which positions Set2 to specifically methylate H3K36. Moreover, we show that ubiquitin contributes to Set2 positioning on the nucleosome and stimulates the methyltransferase activity. Notably, our structure uncovers interfaces that can be targeted by small molecules for development of future cancer therapies.
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Affiliation(s)
- Silvija Bilokapic
- Department of Structural Biology, St. Jude Children's Research Hospital, 263 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Mario Halic
- Department of Structural Biology, St. Jude Children's Research Hospital, 263 Danny Thomas Place, Memphis, TN, 38105, USA.
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