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Jin X, Wang Y, Chen J, Niu M, Yang Y, Zhang Q, Bao G. Novel dual-targeting inhibitors of NSD2 and HDAC2 for the treatment of liver cancer: structure-based virtual screening, molecular dynamics simulation, and in vitro and in vivo biological activity evaluations. J Enzyme Inhib Med Chem 2024; 39:2289355. [PMID: 38059332 DOI: 10.1080/14756366.2023.2289355] [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: 07/19/2023] [Accepted: 11/26/2023] [Indexed: 12/08/2023] Open
Abstract
Liver cancer exhibits a high degree of heterogeneity and involves intricate mechanisms. Recent research has revealed the significant role of histone lysine methylation and acetylation in the epigenetic regulation of liver cancer development. In this study, five inhibitors capable of targeting both histone lysine methyltransferase nuclear receptor-binding SET domain 2 (NSD2) and histone deacetylase 2 (HDAC2) were identified using a structure-based virtual screening approach. Notably, DT-NH-1 displayed a potent inhibition of NSD2 (IC50 = 0.08 ± 0.03 μM) and HDAC2 (IC50 = 5.24 ± 0.87 nM). DT-NH-1 also demonstrated a strong anti-proliferative activity against various liver cancer cell lines, particularly HepG2 cells, and exhibited a high level of biological safety. In an experimental xenograft model involving HepG2 cells, DT-NH-1 showed a significant reduction in tumour growth. Consequently, these findings indicate that DT-NH-1 will be a promising lead compound for the treatment of liver cancer with epigenetic dual-target inhibitors.
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Affiliation(s)
- Xing Jin
- Department of Laboratory Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Yuting Wang
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Jing Chen
- Department of Laboratory Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Miaomiao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Yang Yang
- Department of Laboratory Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
| | - Qiaoxuan Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine (Guangdong Provincial Hospital of Chinese Medicine), Guangzhou, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Guangyu Bao
- Department of Laboratory Medicine, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, China
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2
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Sinha J, Nickels JF, Thurm AR, Ludwig CH, Archibald BN, Hinks MM, Wan J, Fang D, Bintu L. The H3.3K36M oncohistone disrupts the establishment of epigenetic memory through loss of DNA methylation. Mol Cell 2024; 84:3899-3915.e7. [PMID: 39368466 DOI: 10.1016/j.molcel.2024.09.015] [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: 10/03/2023] [Revised: 05/31/2024] [Accepted: 09/13/2024] [Indexed: 10/07/2024]
Abstract
Histone H3.3 is frequently mutated in tumors, with the lysine 36 to methionine mutation (K36M) being a hallmark of chondroblastomas. While it is known that H3.3K36M changes the epigenetic landscape, its effects on gene expression dynamics remain unclear. Here, we use a synthetic reporter to measure the effects of H3.3K36M on silencing and epigenetic memory after recruitment of the ZNF10 Krüppel-associated box (KRAB) domain, part of the largest class of human repressors and associated with H3K9me3 deposition. We find that H3.3K36M, which decreases H3K36 methylation and increases histone acetylation, leads to a decrease in epigenetic memory and promoter methylation weeks after KRAB release. We propose a model for establishment and maintenance of epigenetic memory, where the H3K36 methylation pathway is necessary to maintain histone deacetylation and convert H3K9me3 domains into DNA methylation for stable epigenetic memory. Our quantitative model can inform oncogenic mechanisms and guide development of epigenetic editing tools.
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Affiliation(s)
- Joydeb Sinha
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jan F Nickels
- Niels Bohr Institute, University of Copenhagen, Copenhagen 2100, Denmark; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Abby R Thurm
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Connor H Ludwig
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Bella N Archibald
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Michaela M Hinks
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Jun Wan
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Dong Fang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.
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3
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Singh MK, Bonnell VA, Tojal Da Silva I, Santiago VF, Moraes MS, Adderley J, Doerig C, Palmisano G, Llinas M, Garcia CRS. A Plasmodium falciparum MORC protein complex modulates epigenetic control of gene expression through interaction with heterochromatin. eLife 2024; 12:RP92201. [PMID: 39412522 PMCID: PMC11483127 DOI: 10.7554/elife.92201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2024] Open
Abstract
Dynamic control of gene expression is critical for blood stage development of malaria parasites. Here, we used multi-omic analyses to investigate transcriptional regulation by the chromatin-associated microrchidia protein, MORC, during asexual blood stage development of the human malaria parasite Plasmodium falciparum. We show that PfMORC (PF3D7_1468100) interacts with a suite of nuclear proteins, including APETALA2 (ApiAP2) transcription factors (PfAP2-G5, PfAP2-O5, PfAP2-I, PF3D7_0420300, PF3D7_0613800, PF3D7_1107800, and PF3D7_1239200), a DNA helicase DS60 (PF3D7_1227100), and other chromatin remodelers (PfCHD1 and PfEELM2). Transcriptomic analysis of PfMORCHA-glmS knockdown parasites revealed 163 differentially expressed genes belonging to hypervariable multigene families, along with upregulation of genes mostly involved in host cell invasion. In vivo genome-wide chromatin occupancy analysis during both trophozoite and schizont stages of development demonstrates that PfMORC is recruited to repressed, multigene families, including the var genes in subtelomeric chromosomal regions. Collectively, we find that PfMORC is found in chromatin complexes that play a role in the epigenetic control of asexual blood stage transcriptional regulation and chromatin organization.
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Affiliation(s)
- Maneesh Kumar Singh
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São PauloSão PauloBrazil
| | - Victoria Ann Bonnell
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University ParkHarrisburgUnited States
- Huck Institutes Center for Eukaryotic Gene Regulation, Pennsylvania State University, University ParkHarrisburgUnited States
- Huck Institutes Center for Malaria Research, Pennsylvania State University, University ParkHarrisburgUnited States
| | | | | | - Miriam Santos Moraes
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São PauloSão PauloBrazil
| | - Jack Adderley
- School of Health and Biomedical Sciences, RMIT UniversityBundooraAustralia
| | - Christian Doerig
- School of Health and Biomedical Sciences, RMIT UniversityBundooraAustralia
| | - Giuseppe Palmisano
- Department of Parasitology, Institute of Biomedical Science, University of São PauloSão PauloBrazil
| | - Manuel Llinas
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University ParkHarrisburgUnited States
- Huck Institutes Center for Eukaryotic Gene Regulation, Pennsylvania State University, University ParkHarrisburgUnited States
- Huck Institutes Center for Malaria Research, Pennsylvania State University, University ParkHarrisburgUnited States
- Department of Chemistry, Pennsylvania State University, University ParkHarrisburgUnited States
| | - Celia RS Garcia
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São PauloSão PauloBrazil
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4
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Park S, Cho JH, Kim JH, Kim JA. Histone lysine methylation modifiers controlled by protein stability. Exp Mol Med 2024:10.1038/s12276-024-01329-5. [PMID: 39394462 DOI: 10.1038/s12276-024-01329-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 10/13/2024] Open
Abstract
Histone lysine methylation is pivotal in shaping the epigenetic landscape and is linked to cell physiology. Coordination of the activities of multiple histone lysine methylation modifiers, namely, methyltransferases and demethylases, modulates chromatin structure and dynamically alters the epigenetic landscape, orchestrating almost all DNA-templated processes, such as transcription, DNA replication, and DNA repair. The stability of modifier proteins, which is regulated by protein degradation, is crucial for their activity. Here, we review the current knowledge of modifier-protein degradation via specific pathways and its subsequent impact on cell physiology through epigenetic changes. By summarizing the functional links between the aberrant stability of modifier proteins and human diseases and highlighting efforts to target protein stability for therapeutic purposes, we aim to promote interest in defining novel pathways that regulate the degradation of modifiers and ultimately increase the potential for the development of novel therapeutic strategies.
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Affiliation(s)
- Sungryul Park
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jin Hwa Cho
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jeong-Hoon Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.
- Department of Bioscience, University of Science and Technology, Daejeon, South Korea.
| | - Jung-Ae Kim
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.
- Department of Bioscience, University of Science and Technology, Daejeon, South Korea.
- Aging Convergence Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea.
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5
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Shipman GA, Padilla R, Horth C, Hu B, Bareke E, Vitorino FN, Gongora JM, Garcia BA, Lu C, Majewski J. Systematic perturbations of SETD2, NSD1, NSD2, NSD3, and ASH1L reveal their distinct contributions to H3K36 methylation. Genome Biol 2024; 25:263. [PMID: 39390582 PMCID: PMC11465688 DOI: 10.1186/s13059-024-03415-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 10/01/2024] [Indexed: 10/12/2024] Open
Abstract
BACKGROUND Methylation of histone 3 lysine 36 (H3K36me) has emerged as an essential epigenetic component for the faithful regulation of gene expression. Despite its importance in development and disease, how the molecular agents collectively shape the H3K36me landscape is unclear. RESULTS We use mouse mesenchymal stem cells to perturb the H3K36me methyltransferases (K36MTs) and infer the activities of the five most prominent enzymes: SETD2, NSD1, NSD2, NSD3, and ASH1L. We find that H3K36me2 is the most abundant of the three methylation states and is predominantly deposited at intergenic regions by NSD1, and partly by NSD2. In contrast, H3K36me1/3 are most abundant within exons and are positively correlated with gene expression. We demonstrate that while SETD2 deposits most H3K36me3, it may also deposit H3K36me2 within transcribed genes. Additionally, loss of SETD2 results in an increase of exonic H3K36me1, suggesting other (K36MTs) prime gene bodies with lower methylation states ahead of transcription. While NSD1/2 establish broad intergenic H3K36me2 domains, NSD3 deposits H3K36me2 peaks on active promoters and enhancers. Meanwhile, the activity of ASH1L is restricted to the regulatory elements of developmentally relevant genes, and our analyses implicate PBX2 as a potential recruitment factor. CONCLUSIONS Within genes, SETD2 primarily deposits H3K36me3, while the other K36MTs deposit H3K36me1/2 independently of SETD2 activity. For the deposition of H3K36me1/2, we find a hierarchy of K36MT activities where NSD1 > NSD2 > NSD3 > ASH1L. While NSD1 and NSD2 are responsible for most genome-wide propagation of H3K36me2, the activities of NSD3 and ASH1L are confined to active regulatory elements.
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Affiliation(s)
- Gerry A Shipman
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Reinnier Padilla
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Cynthia Horth
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Bo Hu
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Eric Bareke
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada
| | - Francisca N Vitorino
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Joanna M Gongora
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Benjamin A Garcia
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada.
- McGill University Genome Centre, Montreal, QC, H3A 0G1, Canada.
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Yan L, Zheng M, Fan M, Yao R, Zou K, Feng S, Wu M. A Chemoselective Enrichment Strategy for In-Depth Coverage of the Methyllysine Proteome. Angew Chem Int Ed Engl 2024; 63:e202408564. [PMID: 39011605 DOI: 10.1002/anie.202408564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 07/01/2024] [Accepted: 07/15/2024] [Indexed: 07/17/2024]
Abstract
Proteomics is a powerful method to comprehensively understand cellular posttranslational modifications (PTMs). Owing to low abundance, tryptic peptides with PTMs are usually enriched for enhanced coverage by liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). Affinity chromatography for phosphoproteomes by metal-oxide and pan-specific antibodies for lysine acetylome allow identification of tens of thousands of modification sites. Lysine methylation is a significant PTM; however, only hundreds of methylation sites were identified by available approaches. Herein we report an aryl diazonium based chemoselective strategy that enables enrichment of monomethyllysine (Kme1) peptides through covalent bonds with extraordinary sensitivity. We identified more than 10000 Kme1 peptides from diverse cell lines and mouse tissues, which implied a wide lysine methylation impact on cellular processes. Furthermore, we found a significant amount of methyl marks that were not S-adenosyl methionine (SAM)-dependent by isotope labeling experiments.
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Affiliation(s)
- Lufeng Yan
- Department of Chemistry, School of Science, Westlake University, Hangzhou, 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang Province, China
| | - Manqian Zheng
- Department of Chemistry, Fudan University, Shanghai, 200438, China
| | - Mingzhu Fan
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, Zhejiang Province, China
- Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Westlake University, Hangzhou, 310024, Zhejiang Province, China
| | - Rui Yao
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang Province, China
| | - Kun Zou
- Department of Chemistry, School of Science, Westlake University, Hangzhou, 310030, Zhejiang Province, China
| | - Shan Feng
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, 310024, Zhejiang Province, China
- Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Westlake University, Hangzhou, 310024, Zhejiang Province, China
| | - Mingxuan Wu
- Department of Chemistry, School of Science, Westlake University, Hangzhou, 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, 310024, Zhejiang Province, China
- Institute of Natural Sciences, Westlake Institute for Advanced Study, Hangzhou, 310024, Zhejiang Province, China
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7
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Neeman B, Sudhakar S, Biswas A, Rosenblum J, Sidpra J, D’Arco F, Löbel U, Gómez-Chiari M, Serrano M, Bolasell M, Reddy K, Ben-Sira L, Zakzouk R, Al-Hashem A, Mirsky DM, Patel R, Radhakrishnan R, Shekdar K, Whitehead MT, Mankad K. Sotos Syndrome: Deep Neuroimaging Phenotyping Reveals a High Prevalence of Malformations of Cortical Development. AJNR Am J Neuroradiol 2024; 45:1570-1577. [PMID: 39147584 PMCID: PMC11448971 DOI: 10.3174/ajnr.a8364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Accepted: 05/16/2024] [Indexed: 08/17/2024]
Abstract
BACKGROUND AND PURPOSE Sotos syndrome is a rare autosomal dominant condition caused by pathogenic mutations in the NSD1 gene that presents with craniofacial dysmorphism, overgrowth, seizures, and neurodevelopmental delay. Macrocephaly, ventriculomegaly, and corpus callosal dysmorphism are typical neuroimaging features that have been described in the medical literature. The purpose of this study was to expand on the neuroimaging phenotype by detailed analysis of a large cohort of patients with genetically proved Sotos syndrome. MATERIALS AND METHODS This multicenter, multinational, retrospective observational cohort study systematically analyzed the clinical characteristics and neuroimaging features of 77 individuals with genetically diagnosed Sotos syndrome, via central consensus review with 3 pediatric neuroradiologists. RESULTS In addition to previously described features, malformations of cortical development were identified in most patients (95.0%), typically dysgyria (92.2%) and polymicrogyria (22.1%), varying in location and distribution. Incomplete rotation of the hippocampus was observed in 50.6% of patients and was associated with other imaging findings, in particular with dysgyria (100% versus 84.2%, P = .012). CONCLUSIONS Our findings show a link between the genetic-biochemical basis and the neuroimaging features and aid in better understanding the underlying clinical manifestations and possible treatment options. These findings have yet to be described to this extent and correspond with recent studies that show that NSD1 participates in brain development and has interactions with other known relevant genetic pathways.
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Affiliation(s)
- Bar Neeman
- From the Department of Radiology (B.N., L.B.-S.), Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
- Faculty of Medicine (B.N., L.B.-S.), Tel-Aviv University, Tel-Aviv, Israel
| | - Sniya Sudhakar
- Department of Radiology (S.S., A.B., F.D., U.L., K.M.), Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Asthik Biswas
- Department of Radiology (S.S., A.B., F.D., U.L., K.M.), Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Jessica Rosenblum
- Center of Medical Genetics (J.R.), Antwerp University Hospital/University of Antwerp, Antwerp, Belgium
| | - Jai Sidpra
- Developmental Biology and Cancer Section (J.S., K.M.), University College London Great Ormond Street Institute of Child Health, London, UK
| | - Felice D’Arco
- Department of Radiology (S.S., A.B., F.D., U.L., K.M.), Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Ulrike Löbel
- Department of Radiology (S.S., A.B., F.D., U.L., K.M.), Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Marta Gómez-Chiari
- Diagnostic Imaging Department (M.G.-C.), Hospital Sant Joan de Déu, Barcelona, Spain
- Institut de Recerca Sant Joan de Déu,(M.G.-C., M.S., M.B.), Barcelona, Spain
| | - Mercedes Serrano
- Institut de Recerca Sant Joan de Déu,(M.G.-C., M.S., M.B.), Barcelona, Spain
- Neuropediatric Department (M.S.), Hospital Sant Joan de Déu, U-703 Centre for Biomedical Research on Rare Diseases, Barcelona, Spain
| | - Mercè Bolasell
- Institut de Recerca Sant Joan de Déu,(M.G.-C., M.S., M.B.), Barcelona, Spain
- Department of Genetic and Molecular Medicine/IPER (M.B.), Institut de Recerca, Hospital Sant Joan de Déu Barcelona, Barcelona, Spain
| | - Kartik Reddy
- Department of Radiology and Imaging Sciences (K.R.), Emory University School of Medicine, Atlanta, Georgia
| | - Liat Ben-Sira
- From the Department of Radiology (B.N., L.B.-S.), Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
- Faculty of Medicine (B.N., L.B.-S.), Tel-Aviv University, Tel-Aviv, Israel
| | - Reem Zakzouk
- Division of Neuroradiology (R.Z.), Department of Radiology, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - Amal Al-Hashem
- Division of Genetics (A.A.-H.), Department of Pediatrics, Prince Sultan Military Medical City, Riyadh, Saudi Arabia
| | - David M. Mirsky
- Department of Radiology (D.M.M.), Children's Hospital Colorado, University of Colorado School of Medicine, Aurora, Colorado
| | - Rajan Patel
- Texas Children's Hospital (R.P.), Baylor College of Medicine, Houston, Texas
| | - Rupa Radhakrishnan
- Department of Radiology and Imaging Sciences (R.R.), Indiana University School of Medicine, Indianapolis, Indiana
| | - Karuna Shekdar
- Department of Radiology (K.S., M.T.W.), Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Matthew T. Whitehead
- Department of Radiology (K.S., M.T.W.), Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania
- Perelman School of Medicine (M.T.W.), University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kshitij Mankad
- Department of Radiology (S.S., A.B., F.D., U.L., K.M.), Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
- Developmental Biology and Cancer Section (J.S., K.M.), University College London Great Ormond Street Institute of Child Health, London, UK
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8
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Haider S, Farrona S. Decoding histone 3 lysine methylation: Insights into seed germination and flowering. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102598. [PMID: 38986392 DOI: 10.1016/j.pbi.2024.102598] [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: 04/01/2024] [Revised: 06/01/2024] [Accepted: 06/12/2024] [Indexed: 07/12/2024]
Abstract
Histone lysine methylation is a highly conserved epigenetic modification across eukaryotes that contributes to creating different dynamic chromatin states, which may result in transcriptional changes. Over the years, an accumulated set of evidence has shown that histone methylation allows plants to align their development with their surroundings, enabling them to respond and memorize past events due to changes in the environment. In this review, we discuss the molecular mechanisms of histone methylation in plants. Writers, readers, and erasers of Arabidopsis histone methylation marks are described with an emphasis on their role in two of the most important developmental transition phases in plants, seed germination and flowering. Further, the crosstalk between different methylation marks is also discussed. An overview of the mechanisms of histone methylation modifications and their biological outcomes will shed light on existing research gaps and may provide novel perspectives to increase crop yield and resistance in the era of global climate change.
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Affiliation(s)
- Saqlain Haider
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, Galway H91 TK33, Ireland
| | - Sara Farrona
- School of Biological and Chemical Sciences, College of Science and Engineering, University of Galway, Galway H91 TK33, Ireland.
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9
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Du Y, Cao L, Wang S, Guo L, Tan L, Liu H, Feng Y, Wu W. Differences in alternative splicing and their potential underlying factors between animals and plants. J Adv Res 2024; 64:83-98. [PMID: 37981087 PMCID: PMC11464654 DOI: 10.1016/j.jare.2023.11.017] [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: 05/07/2023] [Revised: 08/16/2023] [Accepted: 11/14/2023] [Indexed: 11/21/2023] Open
Abstract
BACKGROUND Alternative splicing (AS), a posttranscriptional process, contributes to the complexity of transcripts from a limited number of genes in a genome, and AS is considered a great source of genetic and phenotypic diversity in eukaryotes. In animals, AS is tightly regulated during the processes of cell growth and differentiation, and its dysregulation is involved in many diseases, including cancers. Likewise, in plants, AS occurs in all stages of plant growth and development, and it seems to play important roles in the rapid reprogramming of genes in response to environmental stressors. To date, the prevalence and functional roles of AS have been extensively reviewed in animals and plants. However, AS differences between animals and plants, especially their underlying molecular mechanisms and impact factors, are anecdotal and rarely reviewed. AIM OF REVIEW This review aims to broaden our understanding of AS roles in a variety of biological processes and provide insights into the underlying mechanisms and impact factors likely leading to AS differences between animals and plants. KEY SCIENTIFIC CONCEPTS OF REVIEW We briefly summarize the roles of AS regulation in physiological and biochemical activities in animals and plants. Then, we underline the differences in the process of AS between plants and animals and especially analyze the potential impact factors, such as gene exon/intron architecture, 5'/3' untranslated regions (UTRs), spliceosome components, chromatin dynamics and transcription speeds, splicing factors [serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs)], noncoding RNAs, and environmental stimuli, which might lead to the differences. Moreover, we compare the nonsense-mediated mRNA decay (NMD)-mediated turnover of the transcripts with a premature termination codon (PTC) in animals and plants. Finally, we summarize the current AS knowledge published in animals versus plants and discuss the potential development of disease therapies and superior crops in the future.
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Affiliation(s)
- Yunfei Du
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Lu Cao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Lingling Tan
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Hua Liu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China
| | - Ying Feng
- Key Laboratory of Nutrition, Metabolism and Food Safety, Shanghai Institute of Nutrition and Health (SINH), Chinese Academy of Sciences (CAS), Shanghai 200032, China.
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, 311300, Hangzhou, China.
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10
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Wei J, Shi Q, Li B, Yang H, Liu L, Zhou R, Feng Z, Yang Z, Zhan J, Xiong XF, Huang X, Wang Y. Discovery of a Highly Potent and Selective Inhibitor Targeting Protein Lysine Methyltransferase NSD2. J Med Chem 2024; 67:16056-16071. [PMID: 39230932 DOI: 10.1021/acs.jmedchem.4c00639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
The histone lysine methyltransferase NSD2 has been recognized as an attractive target for cancer treatment, due to the functional implication of its dysregulation in the initiation and progression of many cancers. Although considerable efforts have been made to develop NSD2 small-molecule inhibitors, highly potent and selective ones are still rarely available till now. Here, we report the discovery of a series of novel NSD2 inhibitors via an extensive SAR exploration of the privileged quinazoline scaffold within compound 8. The most promising compound 42 showed excellent NSD2 enzymatic inhibitory activity and good antiproliferative activity in cells. In addition, it demonstrated favorable pharmacokinetic properties and significantly inhibited the tumor growth in a RS411 tumor xenograft model with good safety. Taken together, compound 42 could be a promising NSD2 inhibitor and deserves further investigation.
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Affiliation(s)
- Jianwei Wei
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | | | - Bang Li
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Hong Yang
- Lingang Laboratory, Shanghai 200031, China
| | - Li Liu
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Ruilin Zhou
- Lingang Laboratory, Shanghai 200031, China
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, Jiangsu 210023, China
| | - Zongbo Feng
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Zhenjiao Yang
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Jinhong Zhan
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
| | - Xiao-Feng Xiong
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
- State Key Laboratory of Anti-Infective Drug Development, Guangzhou 510006, China
| | - Xun Huang
- Lingang Laboratory, Shanghai 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yuanxiang Wang
- Balance-Based Drug Discovery Laboratory, School of Pharmaceutical Sciences, Sun Yat-Sen University, Guangzhou 510006, China
- State Key Laboratory of Anti-Infective Drug Development, Guangzhou 510006, China
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11
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Xie J, Yu Z, Zhu Y, Zheng M, Zhu Y. Functions of Coenzyme A and Acyl-CoA in Post-Translational Modification and Human Disease. FRONT BIOSCI-LANDMRK 2024; 29:331. [PMID: 39344325 DOI: 10.31083/j.fbl2909331] [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: 12/02/2023] [Revised: 05/24/2024] [Accepted: 07/17/2024] [Indexed: 10/01/2024]
Abstract
Coenzyme A (CoA) is synthesized from pantothenate, L-cysteine and adenosine triphosphate (ATP), and plays a vital role in diverse physiological processes. Protein acylation is a common post-translational modification (PTM) that modifies protein structure, function and interactions. It occurs via the transfer of acyl groups from acyl-CoAs to various amino acids by acyltransferase. The characteristics and effects of acylation vary according to the origin, structure, and location of the acyl group. Acetyl-CoA, formyl-CoA, lactoyl-CoA, and malonyl-CoA are typical acyl group donors. The major acyl donor, acyl-CoA, enables modifications that impart distinct biological functions to both histone and non-histone proteins. These modifications are crucial for regulating gene expression, organizing chromatin, managing metabolism, and modulating the immune response. Moreover, CoA and acyl-CoA play significant roles in the development and progression of neurodegenerative diseases, cancer, cardiovascular diseases, and other health conditions. The goal of this review was to systematically describe the types of commonly utilized acyl-CoAs, their functions in protein PTM, and their roles in the progression of human diseases.
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Affiliation(s)
- Jumin Xie
- Hubei Key Laboratory of Renal Disease Occurrence and Intervention, Medical School, Hubei Polytechnic University, 435003 Huangshi, Hubei, China
| | - Zhang Yu
- Hubei Key Laboratory of Renal Disease Occurrence and Intervention, Medical School, Hubei Polytechnic University, 435003 Huangshi, Hubei, China
| | - Ying Zhu
- Hubei Key Laboratory of Renal Disease Occurrence and Intervention, Medical School, Hubei Polytechnic University, 435003 Huangshi, Hubei, China
| | - Mei Zheng
- Hubei Key Laboratory of Renal Disease Occurrence and Intervention, Medical School, Hubei Polytechnic University, 435003 Huangshi, Hubei, China
| | - Yanfang Zhu
- Department of Critical Care Medicine, Huangshi Hospital of TCM (Infectious Disease Hospital), 435003 Huangshi, Hubei, China
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12
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Lee MK, Park NH, Lee SY, Kim T. Context-Dependent and Locus-Specific Role of H3K36 Methylation in Transcriptional Regulation. J Mol Biol 2024:168796. [PMID: 39299382 DOI: 10.1016/j.jmb.2024.168796] [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: 06/17/2024] [Revised: 09/10/2024] [Accepted: 09/13/2024] [Indexed: 09/22/2024]
Abstract
H3K36 methylation is a critical histone modification involved in transcription regulation. It involves the mono (H3K36me1), di (H3K36me2), and/or tri-methylation (H3K36me3) of lysine 36 on histone H3 by methyltransferases. In yeast, Set2 catalyzes all three methylation states. By contrast, in higher eukaryotes, at least eight methyltransferases catalyze different methylation states, including SETD2 for H3K36me3 and the NSD family for H3K36me2 in vivo. Both Set2 and SETD2 interact with the phosphorylated CTD of RNA Pol II, which links H3K36 methylation to transcription. In yeast, H3K36me3 and H3K36me2 peak at the 3' ends of genes. In higher eukaryotes, this is also true for H3K36me3 but not for H3K36me2, which is enriched at the 5' ends of genes and intergenic regions, suggesting that H3K36me2 and H3K36me3 may play different regulatory roles. Whether H3K36me1 demonstrates preferential distribution remains unclear. H3K36me3 is essential for inhibiting transcription elongation. It also suppresses cryptic transcription by promoting histone deacetylation by the histone deacetylases Rpd3S (yeast) and variant NuRD (higher eukaryotes). H3K36me3 also facilitates DNA methylation by DNMT3B, thereby preventing spurious transcription initiation. H3K36me3 not only represses transcription since it promotes the activation of mRNA and cryptic promoters in response to environmental changes by targeting the histone acetyltransferase NuA3 in yeast. Further research is needed to elucidate the methylation state- and locus-specific functions of H3K36me1 and the mechanisms that regulate it.
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Affiliation(s)
- Min Kyung Lee
- Department of Life Sciences and Multitasking Macrophage Research Center, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Na Hyun Park
- Department of Life Sciences and Multitasking Macrophage Research Center, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Soo Young Lee
- Department of Life Sciences and Multitasking Macrophage Research Center, Ewha Womans University, Seoul 03760, Republic of Korea
| | - TaeSoo Kim
- Department of Life Sciences and Multitasking Macrophage Research Center, Ewha Womans University, Seoul 03760, Republic of Korea.
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13
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Caeiro LD, Verdun RE, Morey L. Histone H3 mutations and their impact on genome stability maintenance. Biochem Soc Trans 2024:BST20240177. [PMID: 39248209 DOI: 10.1042/bst20240177] [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: 06/26/2024] [Revised: 08/13/2024] [Accepted: 08/27/2024] [Indexed: 09/10/2024]
Abstract
Histones are essential for maintaining chromatin structure and function. Histone mutations lead to changes in chromatin compaction, gene expression, and the recruitment of DNA repair proteins to the DNA lesion. These disruptions can impair critical DNA repair pathways, such as homologous recombination and non-homologous end joining, resulting in increased genomic instability, which promotes an environment favorable to tumor development and progression. Understanding these mechanisms underscores the potential of targeting DNA repair pathways in cancers harboring mutated histones, offering novel therapeutic strategies to exploit their inherent genomic instability for better treatment outcomes. Here, we examine how mutations in histone H3 disrupt normal chromatin function and DNA damage repair processes and how these mechanisms can be exploited for therapeutic interventions.
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Affiliation(s)
- Lucas D Caeiro
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL 33136, U.S.A
- Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, U.S.A
| | - Ramiro E Verdun
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL 33136, U.S.A
- Division of Hematology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL 33136, U.S.A
- Geriatric Research, Education, and Clinical Center, Miami VA Healthcare System, Miami, FL, U.S.A
| | - Lluis Morey
- Sylvester Comprehensive Cancer Center, Biomedical Research Building, 1501 NW 10th Avenue, Miami, FL 33136, U.S.A
- Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL 33136, U.S.A
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14
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Xu J, Wang Q, Tang X, Feng X, Zhang X, Liu T, Wu F, Wang Q, Feng X, Tang Q, Lisch D, Lu Y. Drought-induced circular RNAs in maize roots: Separating signal from noise. PLANT PHYSIOLOGY 2024; 196:352-367. [PMID: 38669308 DOI: 10.1093/plphys/kiae229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 03/08/2024] [Accepted: 03/08/2024] [Indexed: 04/28/2024]
Abstract
Circular RNAs (circRNAs) play an important role in diverse biological processes; however, their origin and functions, especially in plants, remain largely unclear. Here, we used 2 maize (Zea mays) inbred lines, as well as 14 of their derivative recombination inbred lines with different drought sensitivity, to systematically characterize 8,790 circRNAs in maize roots under well-watered (WW) and water-stress (WS) conditions. We found that a diverse set of circRNAs expressed at significantly higher levels under WS. Enhanced expression of circRNAs was associated with longer flanking introns and an enrichment of long interspersed nuclear element retrotransposable elements. The epigenetic marks found at the back-splicing junctions of circRNA-producing genes were markedly different from canonical splicing, characterized by increased levels of H3K36me3/H3K4me1, as well as decreased levels of H3K9Ac/H3K27Ac. We found that genes expressing circRNAs are subject to relaxed selection. The significant enrichment of trait-associated sites along their genic regions suggested that genes giving rise to circRNAs were associated with plant survival rate under drought stress, implying that circRNAs play roles in plant drought responses. Furthermore, we found that overexpression of circMED16, one of the drought-responsive circRNAs, enhances drought tolerance in Arabidopsis (Arabidopsis thaliana). Our results provide a framework for understanding the intricate interplay of epigenetic modifications and how they contribute to the fine-tuning of circRNA expression under drought stress.
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Affiliation(s)
- Jie Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
- Key Laboratory of Agricultural Bioinformatics, Ministry of Education, Sichuan Agricultural University, Sichuan 611130, China
| | - Qi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Xin Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Xiaoju Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Xiaoyue Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Tianhong Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Fengkai Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Qingjun Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Xuanjun Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Qi Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Yanli Lu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Sichuan 611130, China
- Maize Research Institute, Sichuan Agricultural University, Sichuan 611130, China
- Key Laboratory of Biology and Genetic Improvement of Maize in Southwest Region, Ministry of Agriculture, Sichuan 611130, China
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15
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Yancoskie M, Khaleghi R, Gururajan A, Raghunathan A, Gupta A, Diethelm S, Maritz C, Sturla S, Krishnan M, Naegeli H. ASH1L guards cis-regulatory elements against cyclobutane pyrimidine dimer induction. Nucleic Acids Res 2024; 52:8254-8270. [PMID: 38884271 PMCID: PMC11317172 DOI: 10.1093/nar/gkae517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 05/29/2024] [Accepted: 06/04/2024] [Indexed: 06/18/2024] Open
Abstract
The histone methyltransferase ASH1L, first discovered for its role in transcription, has been shown to accelerate the removal of ultraviolet (UV) light-induced cyclobutane pyrimidine dimers (CPDs) by nucleotide excision repair. Previous reports demonstrated that CPD excision is most efficient at transcriptional regulatory elements, including enhancers, relative to other genomic sites. Therefore, we analyzed DNA damage maps in ASH1L-proficient and ASH1L-deficient cells to understand how ASH1L controls enhancer stability. This comparison showed that ASH1L protects enhancer sequences against the induction of CPDs besides stimulating repair activity. ASH1L reduces CPD formation at C-containing but not at TT dinucleotides, and no protection occurs against pyrimidine-(6,4)-pyrimidone photoproducts or cisplatin crosslinks. The diminished CPD induction extends to gene promoters but excludes retrotransposons. This guardian role against CPDs in regulatory elements is associated with the presence of H3K4me3 and H3K27ac histone marks, which are known to interact with the PHD and BRD motifs of ASH1L, respectively. Molecular dynamics simulations identified a DNA-binding AT hook of ASH1L that alters the distance and dihedral angle between neighboring C nucleotides to disfavor dimerization. The loss of this protection results in a higher frequency of C->T transitions at enhancers of skin cancers carrying ASH1L mutations compared to ASH1L-intact counterparts.
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Affiliation(s)
- Michelle N Yancoskie
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
| | - Reihaneh Khaleghi
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
| | - Anirvinya Gururajan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Aadarsh Raghunathan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Aryan Gupta
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Sarah Diethelm
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
| | - Corina Maritz
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zurich, Zurich 8092, Switzerland
| | - Marimuthu Krishnan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad 500032, India
| | - Hanspeter Naegeli
- Institute of Pharmacology and Toxicology, University of Zurich-Vetsuisse, Zurich 8057, Switzerland
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16
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Ma S, Long G, Jiang Z, Zhang Y, Sun L, Pan Y, You Q, Guo X. Recent advances in targeting histone H3 lysine 36 methyltransferases for cancer therapy. Eur J Med Chem 2024; 274:116532. [PMID: 38805937 DOI: 10.1016/j.ejmech.2024.116532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/14/2024] [Accepted: 05/22/2024] [Indexed: 05/30/2024]
Abstract
Histone H3 lysine 36 (H3K36) methylation is a typical epigenetic histone modification that is involved in various biological processes such as DNA transcription, repair and recombination in vivo. Mutations, translocations, and aberrant gene expression associated with H3K36 methyltransferases have been implicated in different malignancies such as acute myeloid leukemia, lung cancer, multiple myeloma, and others. Herein, we provided a comprehensive overview of the latest advances in small molecule inhibitors targeting H3K36 methyltransferases. We analyzed the structures and biological functions of the H3K36 methyltransferases family members. Additionally, we discussed the potential directions for future development of inhibitors targeting H3K36 methyltransferases.
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Affiliation(s)
- Sai Ma
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Guanlu Long
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Zheng Jiang
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Yan Zhang
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Liangkui Sun
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China
| | - Yun Pan
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China
| | - Qidong You
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
| | - Xiaoke Guo
- Jiangsu Key Laboratory of Drug Design and Optimization and State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 210009, China.
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17
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Goto N, Suke K, Yonezawa N, Nishihara H, Handa T, Sato Y, Kujirai T, Kurumizaka H, Yamagata K, Kimura H. ISWI chromatin remodeling complexes recruit NSD2 and H3K36me2 in pericentromeric heterochromatin. J Cell Biol 2024; 223:e202310084. [PMID: 38709169 PMCID: PMC11076809 DOI: 10.1083/jcb.202310084] [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: 10/20/2023] [Revised: 03/04/2024] [Accepted: 04/16/2024] [Indexed: 05/07/2024] Open
Abstract
Histone H3 lysine36 dimethylation (H3K36me2) is generally distributed in the gene body and euchromatic intergenic regions. However, we found that H3K36me2 is enriched in pericentromeric heterochromatin in some mouse cell lines. We here revealed the mechanism of heterochromatin targeting of H3K36me2. Among several H3K36 methyltransferases, NSD2 was responsible for inducing heterochromatic H3K36me2. Depletion and overexpression analyses of NSD2-associating proteins revealed that NSD2 recruitment to heterochromatin was mediated through the imitation switch (ISWI) chromatin remodeling complexes, such as BAZ1B-SMARCA5 (WICH), which directly binds to AT-rich DNA via a BAZ1B domain-containing AT-hook-like motifs. The abundance and stoichiometry of NSD2, SMARCA5, and BAZ1B could determine the localization of H3K36me2 in different cell types. In mouse embryos, H3K36me2 heterochromatin localization was observed at the two- to four-cell stages, suggesting its physiological relevance.
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Affiliation(s)
- Naoki Goto
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
| | - Kazuma Suke
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Japan
| | - Nao Yonezawa
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Japan
| | - Hidenori Nishihara
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara, Japan
| | - Tetsuya Handa
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Yuko Sato
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
| | - Tomoya Kujirai
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Hitoshi Kurumizaka
- Institute for Quantitative Biosciences, The University of Tokyo, Tokyo, Japan
| | - Kazuo Yamagata
- Faculty of Biology-Oriented Science and Technology, Kindai University, Kinokawa, Japan
| | - Hiroshi Kimura
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Japan
- Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Yokohama, Japan
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18
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Zheng YQ, Huang HH, Chen SX, Xu XE, Li ZM, Li YH, Chen SZ, Luo WX, Guo Y, Liu W, Li EM, Xu LY. Discovery and validation of combined biomarkers for the diagnosis of esophageal intraepithelial neoplasia and esophageal squamous cell carcinoma. J Proteomics 2024; 304:105233. [PMID: 38925350 DOI: 10.1016/j.jprot.2024.105233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 06/19/2024] [Accepted: 06/22/2024] [Indexed: 06/28/2024]
Abstract
Early diagnosis and intervention of esophageal squamous cell carcinoma (ESCC) can improve the prognosis. The purpose of this study was to identify biomarkers for ESCC and esophageal precancerous lesions (intraepithelial neoplasia, IEN). Based on the proteomic and genomic data of esophageal tissue including previously reported data, up-regulated proteins with copy number amplification in esophageal cancer were screened as candidate biomarkers. Five proteins, including KDM2A, RAD9A, ECT2, CYHR1 and TONSL, were confirmed by immunohistochemistry on ESCC and normal esophagus (NE). Then, we investigated the expression of 5 proteins in 236 participants (60 NEs, 93 IENs and 83 ESCCs) which were randomly divided into training set and test set. When distinguishing ESCC from NE, the area under curve (AUC) of the multiprotein model was 0.940 in the training set, while the lowest AUC of a protein was 0.735. In the test set, the results were similar. When distinguishing ESCC from IEN or distinguishing IEN from NE, the diagnostic efficiency of the multi-protein models were also improved compared with that of single protein. Our findings suggest that combined detection of KDM2A, RAD9A, ECT2, CYHR1 and TONSL can be used as potential biomarkers for the early diagnosis of ESCC and precancerous lesion development prediction. SIGNIFICANCE: Candidate biomarkers including KDM2A, RAD9A, ECT2, CYHR1 and TONSL screened by integrating genomic and proteomic data from the esophagus can be used as potential biomarkers for the early diagnosis of esophageal squamous cell carcinoma and precancerous lesion development prediction.
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Affiliation(s)
- Ya-Qi Zheng
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong 515041, China; Department of Pathology, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510000, China
| | - Hai-Hua Huang
- Department of Pathology, Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Shu-Xian Chen
- Department of Digestive Endoscopy, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Xiu-E Xu
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Zhi-Mao Li
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Yue-Hong Li
- Department of Digestive Endoscopy, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Su-Zuan Chen
- Department of Digestive Endoscopy, First Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Wen-Xiong Luo
- Department of Endoscopy, Shantou Central Hospital, Shantou, Guangdong 515041, China
| | - Yi Guo
- Department of Endoscopy, Cancer Hospital of Shantou University Medical College, Shantou, Guangdong 515041, China
| | - Wei Liu
- College of Science, Heilongjiang Institute of Technology, Harbin, Heilongjiang 150000, China
| | - En-Min Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Department of Biochemistry and Molecular Biology, Shantou University Medical College, Shantou, Guangdong 515041, China.
| | - Li-Yan Xu
- Guangdong Provincial Key Laboratory of Infectious Diseases and Molecular Immunopathology, Institute of Oncologic Pathology, Cancer Research Center, Shantou University Medical College, Shantou, Guangdong 515041, China.
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19
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Jayakrishnan M, Havlová M, Veverka V, Regnard C, Becker P. Genomic context-dependent histone H3K36 methylation by three Drosophila methyltransferases and implications for dedicated chromatin readers. Nucleic Acids Res 2024; 52:7627-7649. [PMID: 38813825 PMCID: PMC11260483 DOI: 10.1093/nar/gkae449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/03/2024] [Accepted: 05/28/2024] [Indexed: 05/31/2024] Open
Abstract
Methylation of histone H3 at lysine 36 (H3K36me3) marks active chromatin. The mark is interpreted by epigenetic readers that assist transcription and safeguard the integrity of the chromatin fiber. The chromodomain protein MSL3 binds H3K36me3 to target X-chromosomal genes in male Drosophila for dosage compensation. The PWWP-domain protein JASPer recruits the JIL1 kinase to active chromatin on all chromosomes. Unexpectedly, depletion of K36me3 had variable, locus-specific effects on the interactions of those readers. This observation motivated a systematic and comprehensive study of K36 methylation in a defined cellular model. Contrasting prevailing models, we found that K36me1, K36me2 and K36me3 each contribute to distinct chromatin states. A gene-centric view of the changing K36 methylation landscape upon depletion of the three methyltransferases Set2, NSD and Ash1 revealed local, context-specific methylation signatures. Set2 catalyzes K36me3 predominantly at transcriptionally active euchromatin. NSD places K36me2/3 at defined loci within pericentric heterochromatin and on weakly transcribed euchromatic genes. Ash1 deposits K36me1 at regions with enhancer signatures. The genome-wide mapping of MSL3 and JASPer suggested that they bind K36me2 in addition to K36me3, which was confirmed by direct affinity measurement. This dual specificity attracts the readers to a broader range of chromosomal locations and increases the robustness of their actions.
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Affiliation(s)
- Muhunden Jayakrishnan
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-Universität, Munich, Germany
| | - Magdalena Havlová
- Institute of Organic Chemistry and Biochemistry (IOCB) of the Czech Academy of Sciences, Prague, Czech Republic
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry (IOCB) of the Czech Academy of Sciences, Prague, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Catherine Regnard
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-Universität, Munich, Germany
| | - Peter B Becker
- Biomedical Center, Molecular Biology Division, Ludwig-Maximilians-Universität, Munich, Germany
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20
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Chen L, Zhang M, Yang X, Wang Y, Huang T, Li X, Ban Y, Li Q, Yang Q, Zhang Y, Zheng Y, Wang D, Wang X, Shi X, Zhang M, Sun Y, Wu J. Methyl-CpG-binding 2 K271 lactylation-mediated M2 macrophage polarization inhibits atherosclerosis. Theranostics 2024; 14:4256-4277. [PMID: 39113793 PMCID: PMC11303070 DOI: 10.7150/thno.94738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 06/18/2024] [Indexed: 08/10/2024] Open
Abstract
Rationale: Posttranslational modifications of proteins have not been addressed in studies aimed at elucidating the cardioprotective effect of exercise in atherosclerotic cardiovascular disease (ASCVD). In this study, we reveal a novel mechanism by which exercise ameliorates atherosclerosis via lactylation. Methods: Using ApoE-/- mice in an exercise model, proteomics analysis was used to identify exercise-induced specific lactylation of MeCP2 at lysine 271 (K271). Mutation of the MeCP2 K271 lactylation site in aortic plaque macrophages was achieved by recombinant adenoviral transfection. Explore the molecular mechanisms by which motility drives MeCP2 K271 lactylation to improve plaque stability using ATAC-Seq, CUT &Tag and molecular biology. Validation of the potential target RUNX1 for exercise therapy using Ro5-3335 pharmacological inhibition. Results: we showed that in ApoE-/- mice, methyl-CpG-binding protein 2 (MeCP2) K271 lactylation was observed in aortic root plaque macrophages, promoting pro-repair M2 macrophage polarization, reducing the plaque area, shrinking necrotic cores, reducing plaque lipid deposition, and increasing collagen content. Adenoviral transfection, by introducing a mutant at lysine 271, overexpressed MeCP2 K271 lactylation, which enhanced exercise-induced M2 macrophage polarization and increased plaque stability. Mechanistically, the exercise-induced atheroprotective effect requires an interaction between MeCP2 K271 lactylation and H3K36me3, leading to increased chromatin accessibility and transcriptional repression of RUNX1. In addition, the pharmacological inhibition of the transcription factor RUNX1 exerts atheroprotective effects by promoting the polarization of plaque macrophages towards the pro-repair M2 phenotype. Conclusions: These findings reveal a novel mechanism by which exercise ameliorates atherosclerosis via MeCP2 K271 lactylation-H3K36me3/RUNX1. Interventions that enhance MeCP2 K271 lactylation have been shown to increase pro-repair M2 macrophage infiltration, thereby promoting plaque stabilization and reducing the risk of atherosclerotic cardiovascular disease. We also established RUNX1 as a potential drug target for exercise therapy, thereby providing guidance for the discovery of new targets.
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Affiliation(s)
- Liangqi Chen
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
| | - Meiju Zhang
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
| | - Xueyan Yang
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
| | - Yanan Wang
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
| | - Tuo Huang
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
| | - Xin Li
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
| | - Yunting Ban
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
| | - Qifeng Li
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
| | - Qingyuan Yang
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
| | - Yongxiang Zhang
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
| | - Yang Zheng
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
| | - Di Wang
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
| | - Xiaoqi Wang
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
| | - Xiujie Shi
- The Clinical Skills Center, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Maomao Zhang
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
| | - Yong Sun
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
| | - Jian Wu
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
- The Key Laboratory of Myocardial Ischemia, Chinese Ministry of Education, Harbin, China
- Cardiac Rehabilitation Center, Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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21
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Pathak R, Esnault C, Radhakrishnan R, Singh PK, Zhang H, Dale R, Anand A, Bedwell GJ, Engelman AN, Rabi A, Hormoz S, Singh P, Levin HL. The role of LEDGF in transcription is exploited by HIV-1 to position integration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.29.601340. [PMID: 39005447 PMCID: PMC11244883 DOI: 10.1101/2024.06.29.601340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
HIV-1 integration occurs across actively transcribed genes due to the interaction of integrase with host chromatin factor LEDGF. Although LEDGF was originally isolated as a co-activator that stimulates promoter activity in purified systems, this role is inconsistent with LEDGF-mediated integration across gene bodies and with data indicating LEDGF is a histone chaperone that promotes transcriptional elongation. We found LEDGF is enriched in pronounced peaks that match the enrichments of H3K4me3 and RNA Pol II at transcription start sites (TSSs) of active promoters. Our genome-wide chromatin mapping revealed that MLL1 had a dominant role in recruiting LEDGF to promoters and the presence of LEDGF recruits RNA Pol II. Enrichment of LEDGF at TSSs correlates strongly with levels of integration across the transcribed sequences, indicating that LEDGF at TSSs contributed to integration across gene bodies. Although the N-terminal Pro-Trp-Trp-Pro (PWWP) domain of LEDGF interacts with nucleosomes containing H3K36me3, a modification thought to recruit LEDGF to chromatin, we found H3K36me3 does not contribute to gene specificity of integration. These data support a dual role model of LEDGF where it is tethered to promoters by MLL1 and recruits RNA Pol II. Subsequently, LEDGF travels across genes to effect HIV-1 integration. Our data also provides a mechanistic context for the contribution made by LEDGF to MLL1-based infant acute leukemia and acute myeloid leukemia in adults.
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22
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Yabe K, Kamio A, Oya S, Kakutani T, Hirayama M, Tanaka Y, Inagaki S. H3K9 methylation regulates heterochromatin silencing through incoherent feedforward loops. SCIENCE ADVANCES 2024; 10:eadn4149. [PMID: 38924413 PMCID: PMC11204290 DOI: 10.1126/sciadv.adn4149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 05/22/2024] [Indexed: 06/28/2024]
Abstract
Histone H3 lysine-9 methylation (H3K9me) is a hallmark of the condensed and transcriptionally silent heterochromatin. It remains unclear how H3K9me controls transcription silencing and how cells delimit H3K9me domains to avoid silencing essential genes. Here, using Arabidopsis genetic systems that induce H3K9me2 in genes and transposons de novo, we show that H3K9me2 accumulation paradoxically also causes the deposition of the euchromatic mark H3K36me3 by a SET domain methyltransferase, ASHH3. ASHH3-induced H3K36me3 confers anti-silencing by preventing the demethylation of H3K4me1 by LDL2, which mediates transcriptional silencing downstream of H3K9me2. These results demonstrate that H3K9me2 not only facilitates but orchestrates silencing by actuating antagonistic silencing and anti-silencing pathways, providing insights into the molecular basis underlying proper partitioning of chromatin domains and the creation of metastable epigenetic variation.
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Affiliation(s)
| | | | - Satoyo Oya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | | | - Mami Hirayama
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Yuriko Tanaka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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23
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Mouro Pinto R, Murtha R, Azevedo A, Douglas C, Kovalenko M, Ulloa J, Crescenti S, Burch Z, Oliver E, Vitalo A, Mota-Silva E, Riggs MJ, Correia K, Elezi E, Demelo B, Carroll JB, Gillis T, Gusella JF, MacDonald ME, Wheeler VC. Identification of genetic modifiers of Huntington's disease somatic CAG repeat instability by in vivo CRISPR-Cas9 genome editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.08.597823. [PMID: 38895438 PMCID: PMC11185783 DOI: 10.1101/2024.06.08.597823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Huntington's disease (HD), one of >50 inherited repeat expansion disorders (Depienne and Mandel, 2021), is a dominantly-inherited neurodegenerative disease caused by a CAG expansion in HTT (The Huntington's Disease Collaborative Research Group, 1993). Inherited CAG repeat length is the primary determinant of age of onset, with human genetic studies underscoring that the property driving disease is the CAG length-dependent propensity of the repeat to further expand in brain (Swami et al ., 2009; GeM-HD, 2015; Hensman Moss et al ., 2017; Ciosi et al ., 2019; GeM-HD, 2019; Hong et al ., 2021). Routes to slowing somatic CAG expansion therefore hold great promise for disease-modifying therapies. Several DNA repair genes, notably in the mismatch repair (MMR) pathway, modify somatic expansion in HD mouse models (Wheeler and Dion, 2021). To identify novel modifiers of somatic expansion, we have used CRISPR-Cas9 editing in HD knock-in mice to enable in vivo screening of expansion-modifier candidates at scale. This has included testing of HD onset modifier genes emerging from human genome-wide association studies (GWAS), as well as interactions between modifier genes, thereby providing new insight into pathways underlying CAG expansion and potential therapeutic targets.
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24
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Weirich S, Kusevic D, Schnee P, Reiter J, Pleiss J, Jeltsch A. Discovery of NSD2 non-histone substrates and design of a super-substrate. Commun Biol 2024; 7:707. [PMID: 38851815 PMCID: PMC11162472 DOI: 10.1038/s42003-024-06395-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 05/29/2024] [Indexed: 06/10/2024] Open
Abstract
The human protein lysine methyltransferase NSD2 catalyzes dimethylation at H3K36. It has very important roles in development and disease but many mechanistic features and its full spectrum of substrate proteins are unclear. Using peptide SPOT array methylation assays, we investigate the substrate sequence specificity of NSD2 and discover strong readout of residues between G33 (-3) and P38 (+2) on H3K36. Unexpectedly, we observe that amino acid residues different from natural ones in H3K36 are preferred at some positions. Combining four preferred residues led to the development of a super-substrate which is methylated much faster by NSD2 at peptide and protein level. Molecular dynamics simulations demonstrate that this activity increase is caused by distinct hyperactive conformations of the enzyme-peptide complex. To investigate the substrate spectrum of NSD2, we conducted a proteome wide search for nuclear proteins matching the specificity profile and discovered 22 peptide substrates of NSD2. In protein methylation studies, we identify K1033 of ATRX and K819 of FANCM as NSD2 methylation sites and also demonstrate their methylation in human cells. Both these proteins have important roles in DNA repair strengthening the connection of NSD2 and H3K36 methylation to DNA repair.
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Affiliation(s)
- Sara Weirich
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Denis Kusevic
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Philipp Schnee
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Jessica Reiter
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Albert Jeltsch
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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25
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Chen R, Zhao MJ, Li YM, Liu AH, Wang RX, Mei YC, Chen X, Du HN. Di- and tri-methylation of histone H3K36 play distinct roles in DNA double-strand break repair. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1089-1105. [PMID: 38842635 DOI: 10.1007/s11427-024-2543-9] [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: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 06/07/2024]
Abstract
Histone H3 Lys36 (H3K36) methylation and its associated modifiers are crucial for DNA double-strand break (DSB) repair, but the mechanism governing whether and how different H3K36 methylation forms impact repair pathways is unclear. Here, we unveil the distinct roles of H3K36 dimethylation (H3K36me2) and H3K36 trimethylation (H3K36me3) in DSB repair via non-homologous end joining (NHEJ) or homologous recombination (HR). Yeast cells lacking H3K36me2 or H3K36me3 exhibit reduced NHEJ or HR efficiency. yKu70 and Rfa1 bind H3K36me2- or H3K36me3-modified peptides and chromatin, respectively. Disrupting these interactions impairs yKu70 and Rfa1 recruitment to damaged H3K36me2- or H3K36me3-rich loci, increasing DNA damage sensitivity and decreasing repair efficiency. Conversely, H3K36me2-enriched intergenic regions and H3K36me3-enriched gene bodies independently recruit yKu70 or Rfa1 under DSB stress. Importantly, human KU70 and RPA1, the homologs of yKu70 and Rfa1, exclusively associate with H3K36me2 and H3K36me3 in a conserved manner. These findings provide valuable insights into how H3K36me2 and H3K36me3 regulate distinct DSB repair pathways, highlighting H3K36 methylation as a critical element in the choice of DSB repair pathway.
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Affiliation(s)
- Runfa Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, Wuhan University, Wuhan, 430072, China
| | - Meng-Jie Zhao
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, Wuhan University, Wuhan, 430072, China
| | - Yu-Min Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, Wuhan University, Wuhan, 430072, China
| | - Ao-Hui Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, Wuhan University, Wuhan, 430072, China
| | - Ru-Xin Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, Wuhan University, Wuhan, 430072, China
| | - Yu-Chao Mei
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, Wuhan University, Wuhan, 430072, China
| | - Xuefeng Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Wuhan University, Wuhan, 430072, China
| | - Hai-Ning Du
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, Wuhan University, Wuhan, 430072, China.
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26
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Chen JJ, Moy C, Pagé V, Monnin C, El-Hajj ZW, Avizonis DZ, Reyes-Lamothe R, Tanny JC. The Rtf1/Prf1-dependent histone modification axis counteracts multi-drug resistance in fission yeast. Life Sci Alliance 2024; 7:e202302494. [PMID: 38514187 PMCID: PMC10958104 DOI: 10.26508/lsa.202302494] [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: 11/26/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
RNA polymerase II transcription elongation directs an intricate pattern of histone modifications. This pattern includes a regulatory cascade initiated by the elongation factor Rtf1, leading to monoubiquitylation of histone H2B, and subsequent methylation of histone H3 on lysine 4. Previous studies have defined the molecular basis for these regulatory relationships, but it remains unclear how they regulate gene expression. To address this question, we investigated a drug resistance phenotype that characterizes defects in this axis in the model eukaryote Schizosaccharomyces pombe (fission yeast). The mutations caused resistance to the ribonucleotide reductase inhibitor hydroxyurea (HU) that correlated with a reduced effect of HU on dNTP pools, reduced requirement for the S-phase checkpoint, and blunting of the transcriptional response to HU treatment. Mutations in the C-terminal repeat domain of the RNA polymerase II large subunit Rpb1 led to similar phenotypes. Moreover, all the HU-resistant mutants also exhibited resistance to several azole-class antifungal agents. Our results suggest a novel, shared gene regulatory function of the Rtf1-H2Bub1-H3K4me axis and the Rpb1 C-terminal repeat domain in controlling fungal drug tolerance.
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Affiliation(s)
- Jennifer J Chen
- https://ror.org/01pxwe438 Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Calvin Moy
- https://ror.org/01pxwe438 Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Viviane Pagé
- https://ror.org/01pxwe438 Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
| | - Cian Monnin
- https://ror.org/01pxwe438 Metabolomics Innovation Resource, Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Ziad W El-Hajj
- https://ror.org/01pxwe438 Department of Biology, McGill University, Montreal, Canada
| | - Daina Z Avizonis
- https://ror.org/01pxwe438 Metabolomics Innovation Resource, Goodman Cancer Institute, McGill University, Montreal, Canada
| | - Rodrigo Reyes-Lamothe
- https://ror.org/01pxwe438 Department of Biology, McGill University, Montreal, Canada
| | - Jason C Tanny
- https://ror.org/01pxwe438 Department of Pharmacology and Therapeutics, McGill University, Montreal, Canada
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27
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Ren L, Ma W, Wang Y. Predicting RNA polymerase II transcriptional elongation pausing and associated histone code. Brief Bioinform 2024; 25:bbae246. [PMID: 38783706 PMCID: PMC11116834 DOI: 10.1093/bib/bbae246] [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: 01/22/2024] [Revised: 04/12/2024] [Accepted: 05/07/2024] [Indexed: 05/25/2024] Open
Abstract
RNA Polymerase II (Pol II) transcriptional elongation pausing is an integral part of the dynamic regulation of gene transcription in the genome of metazoans. It plays a pivotal role in many vital biological processes and disease progression. However, experimentally measuring genome-wide Pol II pausing is technically challenging and the precise governing mechanism underlying this process is not fully understood. Here, we develop RP3 (RNA Polymerase II Pausing Prediction), a network regularized logistic regression machine learning method, to predict Pol II pausing events by integrating genome sequence, histone modification, gene expression, chromatin accessibility, and protein-protein interaction data. RP3 can accurately predict Pol II pausing in diverse cellular contexts and unveil the transcription factors that are associated with the Pol II pausing machinery. Furthermore, we utilize a forward feature selection framework to systematically identify the combination of histone modification signals associated with Pol II pausing. RP3 is freely available at https://github.com/AMSSwanglab/RP3.
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Affiliation(s)
- Lixin Ren
- School of Mathematics and Physics, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Wanbiao Ma
- School of Mathematics and Physics, University of Science and Technology Beijing, 30 Xueyuan Road, Haidian District, Beijing 100083, China
| | - Yong Wang
- CEMS, NCMIS, MDIS, Academy of Mathematics and Systems Science, National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, 55 Zhongguancun East Road, Haidian District, Beijing 100190, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, 19A Yuquan Road, Shijingshan District, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 32 Jiaochang Donglu, Wuhua District, Kunming 650223, China
- Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 1 Xiangshan Zhi Nong, West Lake District, Hangzhou 330106, China
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28
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Shi TH, Sugishita H, Gotoh Y. Crosstalk within and beyond the Polycomb repressive system. J Cell Biol 2024; 223:e202311021. [PMID: 38506728 PMCID: PMC10955045 DOI: 10.1083/jcb.202311021] [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: 11/06/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/21/2024] Open
Abstract
The development of multicellular organisms depends on spatiotemporally controlled differentiation of numerous cell types and their maintenance. To generate such diversity based on the invariant genetic information stored in DNA, epigenetic mechanisms, which are heritable changes in gene function that do not involve alterations to the underlying DNA sequence, are required to establish and maintain unique gene expression programs. Polycomb repressive complexes represent a paradigm of epigenetic regulation of developmentally regulated genes, and the roles of these complexes as well as the epigenetic marks they deposit, namely H3K27me3 and H2AK119ub, have been extensively studied. However, an emerging theme from recent studies is that not only the autonomous functions of the Polycomb repressive system, but also crosstalks of Polycomb with other epigenetic modifications, are important for gene regulation. In this review, we summarize how these crosstalk mechanisms have improved our understanding of Polycomb biology and how such knowledge could help with the design of cancer treatments that target the dysregulated epigenome.
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Affiliation(s)
- Tianyi Hideyuki Shi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroki Sugishita
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- International Research Center for Neurointelligence, The University of Tokyo, Tokyo, Japan
| | - Yukiko Gotoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- International Research Center for Neurointelligence, The University of Tokyo, Tokyo, Japan
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29
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Wang Z, Zhang YX, Shi JZ, Yan Y, Zhao LL, Kou JJ, He YY, Xie XM, Zhang SJ, Pang XB. RNA m6A methylation and regulatory proteins in pulmonary arterial hypertension. Hypertens Res 2024; 47:1273-1287. [PMID: 38438725 DOI: 10.1038/s41440-024-01607-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 11/12/2023] [Accepted: 01/27/2024] [Indexed: 03/06/2024]
Abstract
m6A (N6‑methyladenosine) is the most common and abundant apparent modification in mRNA of eukaryotes. The modification of m6A is regulated dynamically and reversibly by methyltransferase (writer), demethylase (eraser), and binding protein (reader). It plays a significant role in various processes of mRNA metabolism, including regulation of transcription, maturation, translation, degradation, and stability. Pulmonary arterial hypertension (PAH) is a malignant cardiopulmonary vascular disease characterized by abnormal proliferation of pulmonary artery smooth muscle cells. Despite the existence of several effective and targeted therapies, there is currently no cure for PAH and the prognosis remains poor. Recent studies have highlighted the crucial role of m6A modification in cardiovascular diseases. Investigating the role of RNA m6A methylation in PAH could provide valuable insights for drug development. This review aims to explore the mechanism and function of m6A in the pathogenesis of PAH and discuss the potential targeting of RNA m6A methylation modification as a treatment for PAH.
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Affiliation(s)
- Zhe Wang
- School of Pharmacy, Henan University, Henan, China
| | - Yi-Xuan Zhang
- Department of Anesthesiology, Huaihe Hospital of Henan University, Henan, China
| | - Jun-Zhuo Shi
- School of Pharmacy, Henan University, Henan, China
| | - Yi Yan
- Heart Center and Shanghai Institute of Pediatric Congenital Heart Disease, Shanghai Children's Medical Center, National Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lu-Ling Zhao
- School of Pharmacy, Henan University, Henan, China
| | - Jie-Jian Kou
- Department of Pharmacy, Huaihe Hospital of Henan University, Henan, China
| | - Yang-Yang He
- School of Pharmacy, Henan University, Henan, China
| | - Xin-Mei Xie
- School of Pharmacy, Henan University, Henan, China.
| | - Si-Jin Zhang
- Department of Cardiology, Guangdong Cardiovascular Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China.
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Zhang X, Yang Y, Wang L, Qin Y. Histone H2B lysine 122 and lysine 130, as the putative targets of Penicillium oxalicum LaeA, play important roles in asexual development, expression of secondary metabolite gene clusters, and extracellular glycoside hydrolase synthesis. World J Microbiol Biotechnol 2024; 40:179. [PMID: 38668807 DOI: 10.1007/s11274-024-03978-0] [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: 10/17/2023] [Accepted: 04/03/2024] [Indexed: 05/01/2024]
Abstract
Core histones in the nucleosome are subject to a wide variety of posttranslational modifications (PTMs), such as methylation, phosphorylation, ubiquitylation, and acetylation, all of which are crucial in shaping the structure of the chromatin and the expression of the target genes. A putative histone methyltransferase LaeA/Lae1, which is conserved in numerous filamentous fungi, functions as a global regulator of fungal growth, virulence, secondary metabolite formation, and the production of extracellular glycoside hydrolases (GHs). LaeA's direct histone targets, however, were not yet recognized. Previous research has shown that LaeA interacts with core histone H2B. Using S-adenosyl-L-methionine (SAM) as a methyl group donor and recombinant human histone H2B as the substrate, it was found that Penicillium oxalicum LaeA can transfer the methyl groups to the C-terminal lysine (K) 108 and K116 residues in vitro. The H2BK108 and H2BK116 sites on recombinant histone correspond to P. oxalicum H2BK122 and H2BK130, respectively. H2BK122A and H2BK130A, two mutants with histone H2B K122 or K130 mutation to alanine (A), were constructed in P. oxalicum. The mutants H2BK122A and H2BK130A demonstrated altered asexual development and decreased extracellular GH production, consistent with the findings of the laeA gene deletion strain (ΔlaeA). The transcriptome data showed that when compared to wild-type (WT) of P. oxalicum, 38 of the 47 differentially expressed (fold change ≥ 2, FDR ≤ 0.05) genes that encode extracellular GHs showed the same expression pattern in the three mutants ΔlaeA, H2BK122A, and H2BK130A. The four secondary metabolic gene clusters that considerably decreased expression in ΔlaeA also significantly decreased in H2BK122A or H2BK130A. The chromatin of promotor regions of the key cellulolytic genes cel7A/cbh1 and cel7B/eg1 compacted in the ΔlaeA, H2BK122A, and H2BK130A mutants, according to the results of chromatin accessibility real-time PCR (CHART-PCR). The chromatin accessibility index dropped. The histone binding pocket of the LaeA-methyltransf_23 domain is compatible with particular histone H2B peptides, providing appropriate electrostatic and steric compatibility to stabilize these peptides, according to molecular docking. The findings of the study demonstrate that H2BK122 and H2BK130, which are histone targets of P. oxalicum LaeA in vitro, are crucial for fungal conidiation, the expression of gene clusters encoding secondary metabolites, and the production of extracellular GHs.
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Affiliation(s)
- Xiujun Zhang
- National Glycoengineering Research Center, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Yuhong Yang
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Lushan Wang
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China
| | - Yuqi Qin
- National Glycoengineering Research Center, Shandong University, Qingdao, China.
- State Key Laboratory of Microbial Technology, Microbial Technology Institute, Shandong University, Qingdao, China.
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31
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Zhimulev I, Vatolina T, Levitsky V, Tsukanov A. Developmental and Housekeeping Genes: Two Types of Genetic Organization in the Drosophila Genome. Int J Mol Sci 2024; 25:4068. [PMID: 38612878 PMCID: PMC11012173 DOI: 10.3390/ijms25074068] [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: 12/29/2023] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
We developed a procedure for locating genes on Drosophila melanogaster polytene chromosomes and described three types of chromosome structures (gray bands, black bands, and interbands), which differed markedly in morphological and genetic properties. This was reached through the use of our original methods of molecular and genetic analysis, electron microscopy, and bioinformatics data processing. Analysis of the genome-wide distribution of these properties led us to a bioinformatics model of the Drosophila genome organization, in which the genome was divided into two groups of genes. One was constituted by 65, in which the genome was divided into two groups, 62 genes that are expressed in most cell types during life cycle and perform basic cellular functions (the so-called "housekeeping genes"). The other one was made up of 3162 genes that are expressed only at particular stages of development ("developmental genes"). These two groups of genes are so different that we may state that the genome has two types of genetic organization. Different are the timings of their expression, chromatin packaging levels, the composition of activating and deactivating proteins, the sizes of these genes, the lengths of their introns, the organization of the promoter regions of the genes, the locations of origin recognition complexes (ORCs), and DNA replication timings.
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Affiliation(s)
- Igor Zhimulev
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Science, 630090 Novosibirsk, Russia;
| | - Tatyana Vatolina
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Science, 630090 Novosibirsk, Russia;
| | - Victor Levitsky
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Science, 630090 Novosibirsk, Russia; (V.L.); (A.T.)
| | - Anton Tsukanov
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Science, 630090 Novosibirsk, Russia; (V.L.); (A.T.)
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Huang X, Chen Y, Xiao Q, Shang X, Liu Y. Chemical inhibitors targeting histone methylation readers. Pharmacol Ther 2024; 256:108614. [PMID: 38401773 DOI: 10.1016/j.pharmthera.2024.108614] [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: 12/19/2023] [Revised: 02/01/2024] [Accepted: 02/15/2024] [Indexed: 02/26/2024]
Abstract
Histone methylation reader domains are protein modules that recognize specific histone methylation marks, such as methylated or unmethylated lysine or arginine residues on histones. These reader proteins play crucial roles in the epigenetic regulation of gene expression, chromatin structure, and DNA damage repair. Dysregulation of these proteins has been linked to various diseases, including cancer, neurodegenerative diseases, and developmental disorders. Therefore, targeting these proteins with chemical inhibitors has emerged as an attractive approach for therapeutic intervention, and significant progress has been made in this area. In this review, we will summarize the development of inhibitors targeting histone methylation readers, including MBT domains, chromodomains, Tudor domains, PWWP domains, PHD fingers, and WD40 repeat domains. For each domain, we will briefly discuss its identification and biological/biochemical functions, and then focus on the discovery of inhibitors tailored to target this domain, summarizing the property and potential application of most inhibitors. We will also discuss the structural basis for the potency and selectivity of these inhibitors, which will aid in further lead generation and optimization. Finally, we will also address the challenges and strategies involved in the development of these inhibitors. It should facilitate the rational design and development of novel chemical scaffolds and new targeting strategies for histone methylation reader domains with the help of this body of data.
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Affiliation(s)
- Xiaolei Huang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Yichang Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Qin Xiao
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Xinci Shang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Yanli Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China.
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Chen S, Zhang Z, Peng H, Jiang S, Xu C, Ma X, Zhang L, Zhou H, Xing X, Chen L, Wang Q, Chen W, Li D. Histone H3K36me3 mediates the genomic instability of Benzo[a]pyrene in human bronchial epithelial cells. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2024; 346:123564. [PMID: 38367693 DOI: 10.1016/j.envpol.2024.123564] [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: 07/14/2023] [Revised: 11/13/2023] [Accepted: 02/11/2024] [Indexed: 02/19/2024]
Abstract
Histone modifications maintain genomic stability and orchestrate gene expression at the chromatin level. Benzo [a]pyrene (BaP) is the ubiquitous carcinogen widely spread in the environment, but the role and regulatory mechanism of histone modification in its toxic effects remain largely undefined. In this study, we found a dose-dependent reduction of histone H3 methylations at lysine4, lysine9, lysine27, lysine36 in HBE cells treated with BaP. We observed that inhibiting H3K27 and H3K36 methylation impaired cell proliferation, whereas the loss of H3K4, H3K9, H3K27, and H3K36 methylation led to increased genomic instability and delayed DNA repair. H3K36 mutation at both H3.1 and H3.3 exhibited the most significant impacts. In addition, we found that the expression of SET domain containing 2 (SETD2), the unique methyltransferase catalyzed H3K36me3, was downregulated by BaP dose-dependently in vitro and in vivo. Knockdown of SETD2 aggravated DNA damage of BaP exposure, which was consistent with the effects of H3K36 mutation. With the aid of chromatin immunoprecipitation (ChIP) -seq and RNA-seq, we found that H3K36me3 was responsible for transcriptional regulation of genes involved in pathways related to cell survival, lung cancer, metabolism and inflammation. The enhanced enrichment of H3K36me3 in genes (CYP1A1, ALDH1A3, ACOXL, WNT5A, WNT7A, RUNX2, IL1R2) was positively correlated with their expression levels, while the reduction of H3K36me3 distribution in genes (PPARGC1A, PDE4D, GAS1, RNF19A, KSR1) were in accordance with the downregulation of gene expression. Taken together, our findings emphasize the critical roles and mechanisms of histone lysine methylation in mediating cellular homeostasis during BaP exposure.
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Affiliation(s)
- Shen Chen
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Zhengbao Zhang
- Guangxi Key Laboratory of Environmental Exposomics and Entire Lifecycle Health, Department of Toxicology, School of Public Health, Guilin Medical University, Guilin, 541199, Guangxi, China
| | - Honghao Peng
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Shuyun Jiang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Chi Xu
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xingyu Ma
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Liying Zhang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Hao Zhou
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xiumei Xing
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Liping Chen
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Qing Wang
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Wen Chen
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Daochuan Li
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, Department of Toxicology, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China.
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Piao L, Gao Y, Xu X, Su Y, Wang YD, Zhou J, Gao Y, Fang J, Li Q, Chang S, Kong R. Discovery of potent small molecule inhibitors of histone lysine methyltransferase NSDs. Eur J Med Chem 2024; 268:116264. [PMID: 38412693 DOI: 10.1016/j.ejmech.2024.116264] [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: 11/28/2023] [Revised: 01/31/2024] [Accepted: 02/18/2024] [Indexed: 02/29/2024]
Abstract
Nuclear receptor binding SET domain (NSD) proteins are a class of histone lysine methyltransferases and implicated in multiple cancer types with aberrant expression and involvement of cancer related signaling pathways. In this study, a series of small-molecule compounds including compound 2 and 3 are identified against the SET domain of NSDs through structure-based virtual screening. Our lead compound 3 exhibits potent inhibitory activities in vitro towards the NSD2-SET and NSD3-SET with an IC50 of 0.81 μM and 0.84 μM, respectively, and efficiently inhibits histone H3 lysine 36 dimethylation and decreases the expression of NSDs-targeted genes in non-small cell lung cancer cells at 100 nM. Compound 3 suppresses cell proliferation and reduces the clonogenicity in H460 and H1299 non-small cell lung cancer cells, and induces s-phase cell cycle arrest and apoptosis. These data establish our compounds as a valuable tool-kit for the study of the biological roles of NSDs in cancer.
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Affiliation(s)
- Lianhua Piao
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, Jiangsu, 213001, China
| | - Ying Gao
- Primary Biotechnology Co., Ltd., Changzhou, 213125, China
| | - Xiaoshuang Xu
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, Jiangsu, 213001, China
| | - Yangyang Su
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, Jiangsu, 213001, China
| | | | - Jie Zhou
- Suzhou Medinoah Co., Ltd., Suzhou, 215125, China
| | - Yang Gao
- Suzhou Medinoah Co., Ltd., Suzhou, 215125, China
| | - Jin Fang
- Suzhou Medinoah Co., Ltd., Suzhou, 215125, China
| | - Qihui Li
- Primary Biotechnology Co., Ltd., Changzhou, 213125, China
| | - Shan Chang
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, Jiangsu, 213001, China.
| | - Ren Kong
- Institute of Bioinformatics and Medical Engineering, Jiangsu University of Technology, Changzhou, Jiangsu, 213001, China.
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35
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Chen Y, Chen K, Zhu H, Qin H, Liu J, Cao X. Methyltransferase Setd2 prevents T cell-mediated autoimmune diseases via phospholipid remodeling. Proc Natl Acad Sci U S A 2024; 121:e2314561121. [PMID: 38359295 PMCID: PMC10895270 DOI: 10.1073/pnas.2314561121] [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: 08/23/2023] [Accepted: 12/16/2023] [Indexed: 02/17/2024] Open
Abstract
Coordinated metabolic reprogramming and epigenetic remodeling are critical for modulating T cell function and differentiation. However, how the epigenetic modification controls Th17/Treg cell balance via metabolic reprogramming remains obscure. Here, we find that Setd2, a histone H3K36 trimethyltransferase, suppresses Th17 development but promotes iTreg cell polarization via phospholipid remodeling. Mechanistically, Setd2 up-regulates transcriptional expression of lysophosphatidylcholine acyltransferase 4 (Lpcat4) via directly catalyzing H3K36me3 of Lpcat4 gene promoter in T cells. Lpcat4-mediated phosphatidylcholine PC(16:0,18:2) generation in turn limits endoplasmic reticulum stress and oxidative stress. These changes decrease HIF-1α transcriptional activity and thus suppress Th17 but enhance Treg development. Consistent with this regulatory paradigm, T cell deficiency of Setd2 aggravates neuroinflammation and demyelination in experimental autoimmune encephalomyelitis due to imbalanced Th17/Treg cell differentiation. Overall, our data reveal that Setd2 acts as an epigenetic brake for T cell-mediated autoimmunity through phospholipid remodeling, suggesting potential targets for treating neuroinflammatory diseases.
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Affiliation(s)
- Yali Chen
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing100005, China
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Naval Medical University, Shanghai200433, China
| | - Kun Chen
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing100005, China
- Translational Medical Center for Stem Cell Therapy, Shanghai East Hospital, School of Life Sciences and Technology, Tongji University, Shanghai200120, China
| | - Ha Zhu
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Naval Medical University, Shanghai200433, China
| | - Hua Qin
- Institute of Immunology, College of Life Sciences, Nankai University, Tianjin300071, China
| | - Juan Liu
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Naval Medical University, Shanghai200433, China
| | - Xuetao Cao
- Department of Immunology, Center for Immunotherapy, Institute of Basic Medical Sciences, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing100005, China
- National Key Laboratory of Immunity and Inflammation, Institute of Immunology, Naval Medical University, Shanghai200433, China
- Institute of Immunology, College of Life Sciences, Nankai University, Tianjin300071, China
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Owings KG, Chow CY. A Drosophila screen identifies a role for histone methylation in ER stress preconditioning. G3 (BETHESDA, MD.) 2024; 14:jkad265. [PMID: 38098286 PMCID: PMC11021027 DOI: 10.1093/g3journal/jkad265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 11/02/2023] [Indexed: 12/26/2023]
Abstract
Stress preconditioning occurs when transient, sublethal stress events impact an organism's ability to counter future stresses. Although preconditioning effects are often noted in the literature, very little is known about the underlying mechanisms. To model preconditioning, we exposed a panel of genetically diverse Drosophila melanogaster to a sublethal heat shock and measured how well the flies survived subsequent exposure to endoplasmic reticulum (ER) stress. The impact of preconditioning varied with genetic background, ranging from dying half as fast to 4 and a half times faster with preconditioning compared to no preconditioning. Subsequent association and transcriptional analyses revealed that histone methylation, and transcriptional regulation are both candidate preconditioning modifier pathways. Strikingly, almost all subunits (7/8) in the Set1/COMPASS complex were identified as candidate modifiers of preconditioning. Functional analysis of Set1 knockdown flies demonstrated that loss of Set1 led to the transcriptional dysregulation of canonical ER stress genes during preconditioning. Based on these analyses, we propose a preconditioning model in which Set1 helps to establish an interim transcriptional "memory" of previous stress events, resulting in a preconditioned response to subsequent stress.
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Affiliation(s)
- Katie G Owings
- Department of Human Genetics, University of Utah School of Medicine, EIHG 5200, 15 North 2030 East, Salt Lake City, UT 84112, USA
| | - Clement Y Chow
- Department of Human Genetics, University of Utah School of Medicine, EIHG 5200, 15 North 2030 East, Salt Lake City, UT 84112, USA
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Long Y, Mao C, Liu S, Tao Y, Xiao D. Epigenetic modifications in obesity-associated diseases. MedComm (Beijing) 2024; 5:e496. [PMID: 38405061 PMCID: PMC10893559 DOI: 10.1002/mco2.496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/27/2024] Open
Abstract
The global prevalence of obesity has reached epidemic levels, significantly elevating the susceptibility to various cardiometabolic conditions and certain types of cancer. In addition to causing metabolic abnormalities such as insulin resistance (IR), elevated blood glucose and lipids, and ectopic fat deposition, obesity can also damage pancreatic islet cells, endothelial cells, and cardiomyocytes through chronic inflammation, and even promote the development of a microenvironment conducive to cancer initiation. Improper dietary habits and lack of physical exercise are important behavioral factors that increase the risk of obesity, which can affect gene expression through epigenetic modifications. Epigenetic alterations can occur in early stage of obesity, some of which are reversible, while others persist over time and lead to obesity-related complications. Therefore, the dynamic adjustability of epigenetic modifications can be leveraged to reverse the development of obesity-associated diseases through behavioral interventions, drugs, and bariatric surgery. This review provides a comprehensive summary of the impact of epigenetic regulation on the initiation and development of obesity-associated cancers, type 2 diabetes, and cardiovascular diseases, establishing a theoretical basis for prevention, diagnosis, and treatment of these conditions.
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Affiliation(s)
- Yiqian Long
- Department of Pathology, Xiangya HospitalCentral South UniversityChangshaHunanChina
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, School of Basic MedicineCentral South UniversityChangshaHunanChina
| | - Chao Mao
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, School of Basic MedicineCentral South UniversityChangshaHunanChina
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic MedicineCentral South UniversityChangshaChina
| | - Shuang Liu
- Department of Pathology, Xiangya HospitalCentral South UniversityChangshaHunanChina
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, School of Basic MedicineCentral South UniversityChangshaHunanChina
- Department of Oncology, Institute of Medical Sciences, National Clinical Research Center for Geriatric DisordersXiangya HospitalCentral South UniversityChangshaHunanChina
| | - Yongguang Tao
- Department of Pathology, Xiangya HospitalCentral South UniversityChangshaHunanChina
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, School of Basic MedicineCentral South UniversityChangshaHunanChina
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic MedicineCentral South UniversityChangshaChina
- Hunan Key Laboratory of Early Diagnosis and Precision Therapy in Lung Cancer, Department of Thoracic SurgerySecond Xiangya HospitalCentral South UniversityChangshaHunanChina
| | - Desheng Xiao
- Department of Pathology, Xiangya HospitalCentral South UniversityChangshaHunanChina
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, School of Basic MedicineCentral South UniversityChangshaHunanChina
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Ko EK, Anderson A, D'souza C, Zou J, Huang S, Cho S, Alawi F, Prouty S, Lee V, Yoon S, Krick K, Horiuchi Y, Ge K, Seykora JT, Capell BC. Disruption of H3K36 methylation provokes cellular plasticity to drive aberrant glandular formation and squamous carcinogenesis. Dev Cell 2024; 59:187-198.e7. [PMID: 38198888 PMCID: PMC10872381 DOI: 10.1016/j.devcel.2023.12.007] [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: 01/11/2023] [Revised: 09/06/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Abstract
Chromatin organization is essential for maintaining cell-fate trajectories and developmental programs. Here, we find that disruption of H3K36 methylation dramatically impairs normal epithelial differentiation and development, which promotes increased cellular plasticity and enrichment of alternative cell fates. Specifically, we observe a striking increase in the aberrant generation of excessive epithelial glandular tissues, including hypertrophic salivary, sebaceous, and meibomian glands, as well as enhanced squamous tumorigenesis. These phenotypic and gene expression manifestations are associated with loss of H3K36me2 and rewiring of repressive H3K27me3, changes we also observe in human patients with glandular hyperplasia. Collectively, these results have identified a critical role for H3K36 methylation in both in vivo epithelial cell-fate decisions and the prevention of squamous carcinogenesis and suggest that H3K36 methylation modulation may offer new avenues for the treatment of numerous common disorders driven by altered glandular function, which collectively affect large segments of the human population.
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Affiliation(s)
- Eun Kyung Ko
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Amy Anderson
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Carina D'souza
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Jonathan Zou
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sijia Huang
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Penn Institute of Biomedical Informatics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Sohyun Cho
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Faizan Alawi
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Penn School of Dental Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Stephen Prouty
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Vivian Lee
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Ophthalmology, Scheie Eye Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Sora Yoon
- Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Keegan Krick
- Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Yoko Horiuchi
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Kai Ge
- National Institute of Diabetes and Digestive and Kidney Diseases, National Institute of Health, Bethesda, MD 20892, USA
| | - John T Seykora
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Brian C Capell
- Department of Dermatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Penn Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA; Department of Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Abramson Cancer Center, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA; Penn Institute for Regenerative Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA.
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Huang Y, Tang M, Hu Z, Cai B, Chen G, Jiang L, Xia Y, Guan P, Li X, Mao Z, Wan X, Lu W. SMYD3 promotes endometrial cancer through epigenetic regulation of LIG4/XRCC4/XLF complex in non-homologous end joining repair. Oncogenesis 2024; 13:3. [PMID: 38191478 PMCID: PMC10774296 DOI: 10.1038/s41389-023-00503-0] [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: 01/22/2023] [Revised: 11/30/2023] [Accepted: 12/07/2023] [Indexed: 01/10/2024] Open
Abstract
Endometrial cancer (EC) stands as one of the most prevalent malignancies affecting the female genital tract, witnessing a rapid surge in incidence globally. Despite the well-established association of histone methyltransferase SMYD3 with the development and progression of various cancers, its specific oncogenic role in endometrial cancer remains unexplored. In the present study, we report that the expression level of SMYD3 is significantly upregulated in EC samples and associated with EC progression. Through meticulous in vivo and in vitro experiments, we reveal that depletion of SMYD3 curtails cell proliferation, migration, and invasion capabilities, leading to compromised non-homologous end joining repair (NHEJ) and heightened sensitivity of EC cells to radiation. Furthermore, our pathway enrichment analysis underscores the pivotal involvement of the DNA damage repair pathway in regulating EC progression. Mechanistically, in response to DNA damage, SMYD3 is recruited to these sites in a PARP1-dependent manner, specifically methylating LIG4. This methylation sets off a sequential assembly of the LIG4/XRCC4/XLF complex, actively participating in the NHEJ pathway and thereby fostering EC progression. Notably, our findings highlight the promise of SMYD3 as a crucial player in NHEJ repair and its direct correlation with EC progression. Intriguingly, pharmacological intervention targeting SMYD3 with its specific inhibitor, BCI-121, emerges as a potent strategy, markedly suppressing the tumorigenicity of EC cells and significantly enhancing the efficacy of radiotherapy. Collectively, our comprehensive data position SMYD3 as a central factor in NHEJ repair and underscore its potential as a promising pharmacological target for endometrial cancer therapy, validated through both in vitro and in vivo systems.
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Affiliation(s)
- Yujia Huang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Ming Tang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
| | - Zhiyi Hu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Bailian Cai
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Guofang Chen
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Lijun Jiang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Yan Xia
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Pujun Guan
- Department of Radiology, West China Hospital, Sichuan University, Chengdu, 610000, China
| | - Xiaoqi Li
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Zhiyong Mao
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Xiaoping Wan
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
| | - Wen Lu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
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40
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Shao R, Suo J, Zhang Z, Kong M, Ma Y, Wen Y, Liu M, Zhuang L, Ge K, Bi Q, Zhang C, Zou W. H3K36 methyltransferase NSD1 protects against osteoarthritis through regulating chondrocyte differentiation and cartilage homeostasis. Cell Death Differ 2024; 31:106-118. [PMID: 38012390 PMCID: PMC10781997 DOI: 10.1038/s41418-023-01244-8] [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: 08/17/2023] [Revised: 10/31/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023] Open
Abstract
Osteoarthritis (OA) is one of the most common joint diseases, there are no effective disease-modifying drugs, and the pathological mechanisms of OA need further investigation. Here, we show that H3K36 methylations were decreased in senescent chondrocytes and age-related osteoarthritic cartilage. Prrx1-Cre inducible H3.3K36M transgenic mice showed articular cartilage destruction and osteophyte formation. Conditional knockout Nsd1Prrx1-Cre mice, but not Nsd2Prrx1-Cre or Setd2Prrx1-Cre mice, replicated the phenotype of K36M/+; Prrx1-Cre mice. Immunostaining results showed decreased anabolic and increased catabolic activities in Nsd1Prrx1-Cre mice, along with decreased chondrogenic differentiation. Transcriptome and ChIP-seq data revealed that Osr2 was a key factor affected by Nsd1. Intra-articular delivery of Osr2 adenovirus effectively improved the homeostasis of articular cartilage in Nsd1Prrx1-Cre mice. In human osteoarthritic cartilages, both mRNA and protein levels of NSD1 and OSR2 were decreased. Our results indicate that NSD1-induced H3K36 methylations and OSR2 expression play important roles in articular cartilage homeostasis and OA. Targeting H3K36 methylation and OSR2 would be a novel strategy for OA treatment.
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Affiliation(s)
- Rui Shao
- Institute of Microsurgery on Extremities, and Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Jinlong Suo
- Institute of Microsurgery on Extremities, and Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Zhong Zhang
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Sciences, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Mingxiang Kong
- Department of Orthopedics, Rehabilitation center, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, 310014, China
| | - Yiyang Ma
- Institute of Microsurgery on Extremities, and Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Yang Wen
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Sciences, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Mengxue Liu
- Institute of Microsurgery on Extremities, and Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China
| | - Lenan Zhuang
- Adipocyte Biology and Gene Regulation Section, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, 20892, USA
| | - Kai Ge
- Adipocyte Biology and Gene Regulation Section, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD, 20892, USA
| | - Qing Bi
- Department of Orthopedics, Rehabilitation center, Zhejiang Provincial People's Hospital, Hangzhou, Zhejiang, 310014, China
| | - Changqing Zhang
- Institute of Microsurgery on Extremities, and Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China.
| | - Weiguo Zou
- Institute of Microsurgery on Extremities, and Department of Orthopedic Surgery, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, 200233, China.
- State Key Laboratory of Cell Biology, CAS Center for Excellence in Molecular Cell Sciences, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Shanghai, 200031, China.
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41
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He L, Yu C, Qin S, Zheng E, Liu X, Liu Y, Yu S, Liu Y, Dou X, Shang Z, Wang Y, Wang Y, Zhou X, Liu B, Zhong Y, Liu Z, Lu J, Sun L. The proteasome component PSMD14 drives myelomagenesis through a histone deubiquitinase activity. Mol Cell 2023; 83:4000-4016.e6. [PMID: 37935198 DOI: 10.1016/j.molcel.2023.10.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/03/2023] [Accepted: 10/17/2023] [Indexed: 11/09/2023]
Abstract
While 19S proteasome regulatory particle (RP) inhibition is a promising new avenue for treating bortezomib-resistant myeloma, the anti-tumor impact of inhibiting 19S RP component PSMD14 could not be explained by a selective inhibition of proteasomal activity. Here, we report that PSMD14 interacts with NSD2 on chromatin, independent of 19S RP. Functionally, PSMD14 acts as a histone H2AK119 deubiquitinase, facilitating NSD2-directed H3K36 dimethylation. Integrative genomic and epigenomic analyses revealed the functional coordination of PSMD14 and NSD2 in transcriptional activation of target genes (e.g., RELA) linked to myelomagenesis. Reciprocally, RELA transactivates PSMD14, forming a PSMD14/NSD2-RELA positive feedback loop. Remarkably, PSMD14 inhibitors enhance bortezomib sensitivity and fosters anti-myeloma synergy. PSMD14 expression is elevated in myeloma and inversely correlated with overall survival. Our study uncovers an unappreciated function of PSMD14 as an epigenetic regulator and a myeloma driver, supporting the pursuit of PSMD14 as a therapeutic target to overcome the treatment limitation of myeloma.
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Affiliation(s)
- Lin He
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University Health Science Center, Beijing 100191, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University International Cancer Institute, Peking University Health Science Center, Beijing 100191, China
| | - Chunyu Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Sen Qin
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University International Cancer Institute, Peking University Health Science Center, Beijing 100191, China
| | - Enrun Zheng
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University International Cancer Institute, Peking University Health Science Center, Beijing 100191, China
| | - Xinhua Liu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Yanhua Liu
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University Health Science Center, Beijing 100191, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University International Cancer Institute, Peking University Health Science Center, Beijing 100191, China
| | - Shimiao Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University International Cancer Institute, Peking University Health Science Center, Beijing 100191, China
| | - Yang Liu
- Peking University Institute of Hematology, Collaborative Innovation Center of Hematology, Peking University People's Hospital, Beijing 100044, China
| | - Xuelin Dou
- Peking University Institute of Hematology, Collaborative Innovation Center of Hematology, Peking University People's Hospital, Beijing 100044, China
| | - Zesen Shang
- Department of Orthopedics, Peking University Third Hospital, Beijing 100191, China
| | - Yizhou Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University International Cancer Institute, Peking University Health Science Center, Beijing 100191, China
| | - Yue Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University International Cancer Institute, Peking University Health Science Center, Beijing 100191, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Xuehong Zhou
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University International Cancer Institute, Peking University Health Science Center, Beijing 100191, China
| | - Boning Liu
- Peking University Institute of Hematology, Collaborative Innovation Center of Hematology, Peking University People's Hospital, Beijing 100044, China
| | - Yuping Zhong
- Department of Hematology, Qingdao Municipal Hospital, School of Medicine, Qingdao University, Qingdao 266003, China
| | - Zhiqiang Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Jin Lu
- Peking University Institute of Hematology, Collaborative Innovation Center of Hematology, Peking University People's Hospital, Beijing 100044, China
| | - Luyang Sun
- Department of Integration of Chinese and Western Medicine, School of Basic Medical Sciences, State Key Laboratory of Vascular Homeostasis and Remodeling, Peking University Health Science Center, Beijing 100191, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University International Cancer Institute, Peking University Health Science Center, Beijing 100191, China.
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Al-Fakhar MSQ, Bilgin N, Moesgaard L, Witecka A, Drozak J, Kongsted J, Mecinović J. The Role of Trp79 in β-Actin on Histidine Methyltransferase SETD3 Catalysis. Chembiochem 2023; 24:e202300490. [PMID: 37581408 DOI: 10.1002/cbic.202300490] [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: 07/03/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 08/16/2023]
Abstract
Nτ -methylation of His73 in actin by histidine methyltransferase SETD3 plays an important role in stabilising actin filaments in eukaryotes. Mutations in actin and overexpression of SETD3 have been related to human diseases, including cancer. Here, we investigated the importance of Trp79 in β-actin on productive human SETD3 catalysis. Substitution of Trp79 in β-actin peptides by its chemically diverse analogues reveals that the hydrophobic Trp79 binding pocket modulates the catalytic activity of SETD3, and that retaining a bulky and hydrophobic amino acid at position 79 is important for efficient His73 methylation by SETD3. Molecular dynamics simulations show that the Trp79 binding pocket of SETD3 is ideally shaped to accommodate large and hydrophobic Trp79, contributing to the favourable release of water molecules upon binding. Our results demonstrate that the distant Trp79 binding site plays an important role in efficient SETD3 catalysis, contributing to the identification of new SETD3 substrates and the development of chemical probes targeting the biomedically important SETD3.
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Affiliation(s)
- Mays S Q Al-Fakhar
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Nurgül Bilgin
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Laust Moesgaard
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Apolonia Witecka
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Jakub Drozak
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
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Depierre D, Perrois C, Schickele N, Lhoumaud P, Abdi-Galab M, Fosseprez O, Heurteau A, Margueron R, Cuvier O. Chromatin in 3D distinguishes dMes-4/NSD and Hypb/dSet2 in protecting genes from H3K27me3 silencing. Life Sci Alliance 2023; 6:e202302038. [PMID: 37684044 PMCID: PMC10491495 DOI: 10.26508/lsa.202302038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Cell type-specific barcoding of genomes requires the establishment of hundreds of heterochromatin domains where heterochromatin-associated repressive complexes hinder chromatin accessibility thereby silencing genes. At heterochromatin-euchromatin borders, regulation of accessibility not only depends on the delimitation of heterochromatin but may also involve interplays with nearby genes and their transcriptional activity, or alternatively on histone modifiers, chromatin barrier insulators, and more global demarcation of chromosomes into 3D compartmentalized domains and topological-associating domain (TADs). Here, we show that depletion of H3K36 di- or tri-methyl histone methyltransferases dMes-4/NSD or Hypb/dSet2 induces reproducible increasing levels of H3K27me3 at heterochromatin borders including in nearby promoters, thereby repressing hundreds of genes. Furthermore, dMes-4/NSD influences genes demarcated by insulators and TAD borders, within chromatin hubs, unlike transcription-coupled action of Hypb/dSet2 that protects genes independently of TADs. Insulator mutants recapitulate the increase of H3K27me3 upon dMes-4/NSD depletion unlike Hypb/dSet2. Hi-C data demonstrate how dMes-4/NSD blocks propagation of long-range interactions onto active regions. Our data highlight distinct mechanisms protecting genes from H3K27me3 silencing, highlighting a direct influence of H3K36me on repressive TADs.
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Affiliation(s)
- David Depierre
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology, Molecular, Cellular and Developmental Biology (MCD/UMR5087), CNRS, Université Paul Sabatier de Toulouse, Toulouse, France
| | - Charlène Perrois
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology, Molecular, Cellular and Developmental Biology (MCD/UMR5087), CNRS, Université Paul Sabatier de Toulouse, Toulouse, France
| | - Naomi Schickele
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology, Molecular, Cellular and Developmental Biology (MCD/UMR5087), CNRS, Université Paul Sabatier de Toulouse, Toulouse, France
| | - Priscillia Lhoumaud
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology, Molecular, Cellular and Developmental Biology (MCD/UMR5087), CNRS, Université Paul Sabatier de Toulouse, Toulouse, France
| | - Mahdia Abdi-Galab
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology, Molecular, Cellular and Developmental Biology (MCD/UMR5087), CNRS, Université Paul Sabatier de Toulouse, Toulouse, France
| | - Olivier Fosseprez
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology, Molecular, Cellular and Developmental Biology (MCD/UMR5087), CNRS, Université Paul Sabatier de Toulouse, Toulouse, France
| | - Alexandre Heurteau
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology, Molecular, Cellular and Developmental Biology (MCD/UMR5087), CNRS, Université Paul Sabatier de Toulouse, Toulouse, France
| | - Raphaël Margueron
- Institut Curie, Paris Sciences et Lettres Research University; INSERM U934/ CNRS UMR3215, Paris, France
| | - Olivier Cuvier
- Chromatin Dynamics and Cell Proliferation, Center of Integrative Biology, Molecular, Cellular and Developmental Biology (MCD/UMR5087), CNRS, Université Paul Sabatier de Toulouse, Toulouse, France
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Serdyukova K, Swearingen AR, Coradin M, Nevo M, Tran H, Bajric E, Brumbaugh J. Leveraging dominant-negative histone H3 K-to-M mutations to study chromatin during differentiation and development. Development 2023; 150:dev202169. [PMID: 37846748 PMCID: PMC10617616 DOI: 10.1242/dev.202169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2023]
Abstract
Histone modifications are associated with regulation of gene expression that controls a vast array of biological processes. Often, these associations are drawn by correlating the genomic location of a particular histone modification with gene expression or phenotype; however, establishing a causal relationship between histone marks and biological processes remains challenging. Consequently, there is a strong need for experimental approaches to directly manipulate histone modifications. A class of mutations on the N-terminal tail of histone H3, lysine-to-methionine (K-to-M) mutations, was identified as dominant-negative inhibitors of histone methylation at their respective and specific residues. The dominant-negative nature of K-to-M mutants makes them a valuable tool for studying the function of specific methylation marks on histone H3. Here, we review recent applications of K-to-M mutations to understand the role of histone methylation during development and homeostasis. We highlight important advantages and limitations that require consideration when using K-to-M mutants, particularly in a developmental context.
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Affiliation(s)
- Ksenia Serdyukova
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO 80045, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Alison R. Swearingen
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO 80045, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mariel Coradin
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO 80045, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Mika Nevo
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO 80045, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Huong Tran
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO 80045, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Emir Bajric
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO 80045, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Justin Brumbaugh
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado Boulder, Boulder, CO 80309, USA
- University of Colorado Cancer Center, Anschutz Medical Campus, Aurora, CO 80045, USA
- Charles C. Gates Center for Regenerative Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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45
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Li YM, Mei YC, Liu AH, Wang RX, Chen R, Du HN. Gcn5- and Bre1-mediated Set2 degradation promotes chronological aging of Saccharomyces cerevisiae. Cell Rep 2023; 42:113186. [PMID: 37796660 DOI: 10.1016/j.celrep.2023.113186] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 07/19/2023] [Accepted: 09/13/2023] [Indexed: 10/07/2023] Open
Abstract
Loss of transcription-coupled histone H3 lysine 36 trimethylation (H3K36me3) contributes to shorter lifespans in eukaryotes. However, the molecular mechanism of the decline of H3K36me3 during aging remains poorly understood. Here, we report that the degradation of the methyltransferase Set2 is the cause of decreased H3K36me3 levels during chronological aging in budding yeast. We show that Set2 protein degradation during cellular senescence and chronological aging is mainly mediated by the ubiquitin-conjugating E2 enzyme Ubc3 and the E3 ligase Bre1. Lack of Bre1 or abolishment of the ubiquitination stabilizes Set2 protein, sustains H3K36me3 levels at the aging-related gene loci, and upregulates their gene expression, thus leading to extended chronological lifespan. We further illustrate that Gcn5-mediated Set2 acetylation is a prerequisite for Bre1-catalyzed Set2 polyubiquitination and proteolysis during aging. We propose that two sequential post-translational modifications regulate Set2 homeostasis, suggesting a potential strategy to target the Gcn5-Bre1-Set2 axis for intervention of longevity.
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Affiliation(s)
- Yu-Min Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, RNA Institute, Wuhan University, Wuhan 430072, China
| | - Yu-Chao Mei
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, RNA Institute, Wuhan University, Wuhan 430072, China
| | - Ao-Hui Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, RNA Institute, Wuhan University, Wuhan 430072, China
| | - Ru-Xin Wang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, RNA Institute, Wuhan University, Wuhan 430072, China
| | - Runfa Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, RNA Institute, Wuhan University, Wuhan 430072, China
| | - Hai-Ning Du
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Frontier Science Center for Immunology and Metabolism, Hubei Clinical Research Center of Emergency and Resuscitation, Emergency Center of Zhongnan Hospital, RNA Institute, Wuhan University, Wuhan 430072, China.
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Shipman GA, Padilla R, Horth C, Hu B, Bareke E, Vitorino FN, Gongora JM, Garcia BA, Lu C, Majewski J. Systematic perturbations of SETD2, NSD1, NSD2, NSD3 and ASH1L reveals their distinct contributions to H3K36 methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.27.559313. [PMID: 37905045 PMCID: PMC10614729 DOI: 10.1101/2023.09.27.559313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Background Methylation of histone 3 lysine 36 (H3K36me) has emerged as an essential epigenetic component for the faithful regulation of gene expression. Despite its importance in development, disease, and cancer, how the molecular agents collectively shape the H3K36me landscape is unclear. Results We use a mouse mesenchymal stem cell model to perturb the H3K36me deposition machinery and infer the activities of the five most prominent players: SETD2, NSD1, NSD2, NSD3, and ASH1L. We find that H3K36me2 is the most abundant of the three methylation states and is predominantly deposited at intergenic regions by NSD1, and partly by NSD2. In contrast, H3K36me1/3 are most abundant within exons and are positively correlated with gene expression. We demonstrate that while SETD2 deposits most H3K36me3, it also deposits H3K36me2 within transcribed genes. Additionally, loss of SETD2 results in an increase of exonic H3K36me1, suggesting other H3K36 methyltransferases (K36MTs) prime gene bodies with lower methylation states ahead of transcription. Through a reductive approach, we uncover the distribution patterns of NSD3- and ASH1L-catalyzed H3K36me2. While NSD1/2 establish broad intergenic H3K36me2 domains, NSD3 deposits H3K36me2 peaks on active promoters and enhancers. Meanwhile, the activity of ASH1L is restricted to the regulatory elements of developmentally relevant genes, and our analyses implicate PBX2 as a potential recruitment factor. Conclusions Within genes, SETD2 deposits both H3K36me2/3, while the other K36MTs are capable of depositing H3K36me1/2 independently of SETD2 activity. For the deposition of H3K36me1/2, we find a hierarchy of K36MT activities where NSD1>NSD2>NSD3>ASH1L. While NSD1 and NSD2 are responsible for most genome-wide propagation of H3K36me2, the activities of NSD3 and ASH1L are confined to active regulatory elements.
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Sinha J, Nickels JF, Thurm AR, Ludwig CH, Archibald BN, Hinks MM, Wan J, Fang D, Bintu L. The H3.3 K36M oncohistone disrupts the establishment of epigenetic memory through loss of DNA methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.13.562147. [PMID: 37873347 PMCID: PMC10592807 DOI: 10.1101/2023.10.13.562147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Histone H3.3 is frequently mutated in cancers, with the lysine 36 to methionine mutation (K36M) being a hallmark of chondroblastomas. While it is known that H3.3K36M changes the cellular epigenetic landscape, it remains unclear how it affects the dynamics of gene expression. Here, we use a synthetic reporter to measure the effect of H3.3K36M on silencing and epigenetic memory after recruitment of KRAB: a member of the largest class of human repressors, commonly used in synthetic biology, and associated with H3K9me3. We find that H3.3K36M, which decreases H3K36 methylation, leads to a decrease in epigenetic memory and promoter methylation weeks after KRAB release. We propose a new model for establishment and maintenance of epigenetic memory, where H3K36 methylation is necessary to convert H3K9me3 domains into DNA methylation for stable epigenetic memory. Our quantitative model can inform oncogenic mechanisms and guide development of epigenetic editing tools.
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Affiliation(s)
- Joydeb Sinha
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jan F. Nickels
- Niels Bohr Institute, University of Copenhagen, Copenhagen 2100, Denmark
| | - Abby R. Thurm
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | - Connor H. Ludwig
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Bella N. Archibald
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Michaela M. Hinks
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Jun Wan
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Dong Fang
- Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Lacramioara Bintu
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
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48
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Koutná E, Lux V, Kouba T, Škerlová J, Nováček J, Srb P, Hexnerová R, Šváchová H, Kukačka Z, Novák P, Fábry M, Poepsel S, Veverka V. Multivalency of nucleosome recognition by LEDGF. Nucleic Acids Res 2023; 51:10011-10025. [PMID: 37615563 PMCID: PMC10570030 DOI: 10.1093/nar/gkad674] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 07/01/2023] [Accepted: 08/09/2023] [Indexed: 08/25/2023] Open
Abstract
Eukaryotic transcription is dependent on specific histone modifications. Their recognition by chromatin readers triggers complex processes relying on the coordinated association of transcription regulatory factors. Although various modification states of a particular histone residue often lead to differential outcomes, it is not entirely clear how they are discriminated. Moreover, the contribution of intrinsically disordered regions outside of the specialized reader domains to nucleosome binding remains unexplored. Here, we report the structures of a PWWP domain from transcriptional coactivator LEDGF in complex with the H3K36 di- and trimethylated nucleosome, indicating that both methylation marks are recognized by PWWP in a highly conserved manner. We identify a unique secondary interaction site for the PWWP domain at the interface between the acidic patch and nucleosomal DNA that might contribute to an H3K36-methylation independent role of LEDGF. We reveal DNA interacting motifs in the intrinsically disordered region of LEDGF that discriminate between the intra- or extranucleosomal DNA but remain dynamic in the context of dinucleosomes. The interplay between the LEDGF H3K36-methylation reader and protein binding module mediated by multivalent interactions of the intrinsically disordered linker with chromatin might help direct the elongation machinery to the vicinity of RNA polymerase II, thereby facilitating productive elongation.
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Affiliation(s)
- Eliška Koutná
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
| | - Vanda Lux
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Tomáš Kouba
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Jana Škerlová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | | | - Pavel Srb
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Rozálie Hexnerová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Hana Šváchová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Zdeněk Kukačka
- Institute of Microbiology of the Czech Academy of Sciences, Prague 142 20, Czech Republic
| | - Petr Novák
- Institute of Microbiology of the Czech Academy of Sciences, Prague 142 20, Czech Republic
| | - Milan Fábry
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Simon Poepsel
- Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, Cologne 509 31, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne 509 31, Germany
| | - Václav Veverka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
- Department of Cell Biology, Faculty of Science, Charles University, Prague 128 00, Czech Republic
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Perez MF, Sarkies P. Histone methyltransferase activity affects metabolism in human cells independently of transcriptional regulation. PLoS Biol 2023; 21:e3002354. [PMID: 37883365 PMCID: PMC10602318 DOI: 10.1371/journal.pbio.3002354] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 09/27/2023] [Indexed: 10/28/2023] Open
Abstract
The N-terminal tails of eukaryotic histones are frequently posttranslationally modified. The role of these modifications in transcriptional regulation is well-documented. However, the extent to which the enzymatic processes of histone posttranslational modification might affect metabolic regulation is less clear. Here, we investigated how histone methylation might affect metabolism using metabolomics, proteomics, and RNA-seq data from cancer cell lines, primary tumour samples and healthy tissue samples. In cancer, the expression of histone methyltransferases (HMTs) was inversely correlated to the activity of NNMT, an enzyme previously characterised as a methyl sink that disposes of excess methyl groups carried by the universal methyl donor S-adenosyl methionine (SAM or AdoMet). In healthy tissues, histone methylation was inversely correlated to the levels of an alternative methyl sink, PEMT. These associations affected the levels of multiple histone marks on chromatin genome-wide but had no detectable impact on transcriptional regulation. We show that HMTs with a variety of different associations to transcription are co-regulated by the Retinoblastoma (Rb) tumour suppressor in human cells. Rb-mutant cancers show increased total HMT activity and down-regulation of NNMT. Together, our results suggest that the total activity of HMTs affects SAM metabolism, independent of transcriptional regulation.
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Affiliation(s)
- Marcos Francisco Perez
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
- Department of Cells and Tissues, Instituto de Biologia Molecular de Barcelona (IBMB), CSIC, Barcelona, Spain
| | - Peter Sarkies
- Department of Biochemistry, University of Oxford, Oxford, United Kingdom
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50
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Li H, Mo P, Zhang J, Xie Z, Liu X, Chen H, Yang L, Liu M, Zhang H, Wang P, Zhang Z. Methionine biosynthesis enzyme MoMet2 is required for rice blast fungus pathogenicity by promoting virulence gene expression via reducing 5mC modification. PLoS Genet 2023; 19:e1010927. [PMID: 37733784 PMCID: PMC10547190 DOI: 10.1371/journal.pgen.1010927] [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: 04/12/2023] [Revised: 10/03/2023] [Accepted: 08/20/2023] [Indexed: 09/23/2023] Open
Abstract
The emergence of fungicide resistance severely threatens crop production by limiting the availability and application of established fungicides. Therefore, it is urgent to identify new fungicidal targets for controlling plant diseases. Here, we characterized the function of a conserved homoserine O-acetyltransferase (HOA) from the rice blast fungus Magnaporthe oryzae that could serve as the candidate antifungal target. Deletion of the MoMET2 and MoCYS2 genes encoding HOAs perturbed the biosynthesis of methionine and S-adenyl methionine, a methyl group donor for epigenetic modifications, and severely attenuated the development and virulence of M. oryzae. The ∆Momet2 mutant is significantly increased in 5-methylcytosine (5mC) modification that represses the expression of genes required for pathogenicity, including MoGLIK and MoCDH-CYT. We further showed that host-induced gene silencing (HIGS) targeting MoMET2 and MoCYS2 effectively controls rice blasts. Our studies revealed the importance of HOA in the development and virulence of M. oryzae, which suggests the potential feasibility of HOA as new targets for novel anti-rice blast measurements.
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Affiliation(s)
- Huimin Li
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Pengcheng Mo
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Jun Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Zhuoer Xie
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
| | - Xinyu Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Han Chen
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Leiyun Yang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Muxing Liu
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Haifeng Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
| | - Ping Wang
- Department of Microbiology, Immunology, and Parasitology, Louisiana State University Health Sciences Center, New Orleans, Louisiana, United States of America
| | - Zhengguang Zhang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, and Key Laboratory of Integrated Management of Crop Diseases and Pests, Ministry of Education, Nanjing, China
- The Key Laboratory of Plant Immunity, Nanjing Agricultural University, Nanjing, China
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