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Funabiki H, Wassing IE, Jia Q, Luo JD, Carroll T. Coevolution of the CDCA7-HELLS ICF-related nucleosome remodeling complex and DNA methyltransferases. eLife 2023; 12:RP86721. [PMID: 37769127 PMCID: PMC10538959 DOI: 10.7554/elife.86721] [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: 09/30/2023] Open
Abstract
5-Methylcytosine (5mC) and DNA methyltransferases (DNMTs) are broadly conserved in eukaryotes but are also frequently lost during evolution. The mammalian SNF2 family ATPase HELLS and its plant ortholog DDM1 are critical for maintaining 5mC. Mutations in HELLS, its activator CDCA7, and the de novo DNA methyltransferase DNMT3B, cause immunodeficiency-centromeric instability-facial anomalies (ICF) syndrome, a genetic disorder associated with the loss of DNA methylation. We here examine the coevolution of CDCA7, HELLS and DNMTs. While DNMT3, the maintenance DNA methyltransferase DNMT1, HELLS, and CDCA7 are all highly conserved in vertebrates and green plants, they are frequently co-lost in other evolutionary clades. The presence-absence patterns of these genes are not random; almost all CDCA7 harboring eukaryote species also have HELLS and DNMT1 (or another maintenance methyltransferase, DNMT5). Coevolution of presence-absence patterns (CoPAP) analysis in Ecdysozoa further indicates coevolutionary linkages among CDCA7, HELLS, DNMT1 and its activator UHRF1. We hypothesize that CDCA7 becomes dispensable in species that lost HELLS or DNA methylation, and/or the loss of CDCA7 triggers the replacement of DNA methylation by other chromatin regulation mechanisms. Our study suggests that a unique specialized role of CDCA7 in HELLS-dependent DNA methylation maintenance is broadly inherited from the last eukaryotic common ancestor.
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Affiliation(s)
- Hironori Funabiki
- Laboratory of Chromosome and Cell Biology, The Rockefeller UniversityNew YorkUnited States
| | - Isabel E Wassing
- Laboratory of Chromosome and Cell Biology, The Rockefeller UniversityNew YorkUnited States
| | - Qingyuan Jia
- Laboratory of Chromosome and Cell Biology, The Rockefeller UniversityNew YorkUnited States
| | - Ji-Dung Luo
- Bioinformatics Resource Center, The Rockefeller UniversityNew YorkUnited States
| | - Thomas Carroll
- Bioinformatics Resource Center, The Rockefeller UniversityNew YorkUnited States
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2
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Lee SC, Adams DW, Ipsaro JJ, Cahn J, Lynn J, Kim HS, Berube B, Major V, Calarco JP, LeBlanc C, Bhattacharjee S, Ramu U, Grimanelli D, Jacob Y, Voigt P, Joshua-Tor L, Martienssen RA. Chromatin remodeling of histone H3 variants by DDM1 underlies epigenetic inheritance of DNA methylation. Cell 2023; 186:4100-4116.e15. [PMID: 37643610 PMCID: PMC10529913 DOI: 10.1016/j.cell.2023.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/19/2023] [Accepted: 08/01/2023] [Indexed: 08/31/2023]
Abstract
Nucleosomes block access to DNA methyltransferase, unless they are remodeled by DECREASE in DNA METHYLATION 1 (DDM1LSH/HELLS), a Snf2-like master regulator of epigenetic inheritance. We show that DDM1 promotes replacement of histone variant H3.3 by H3.1. In ddm1 mutants, DNA methylation is partly restored by loss of the H3.3 chaperone HIRA, while the H3.1 chaperone CAF-1 becomes essential. The single-particle cryo-EM structure at 3.2 Å of DDM1 with a variant nucleosome reveals engagement with histone H3.3 near residues required for assembly and with the unmodified H4 tail. An N-terminal autoinhibitory domain inhibits activity, while a disulfide bond in the helicase domain supports activity. DDM1 co-localizes with H3.1 and H3.3 during the cell cycle, and with the DNA methyltransferase MET1Dnmt1, but is blocked by H4K16 acetylation. The male germline H3.3 variant MGH3/HTR10 is resistant to remodeling by DDM1 and acts as a placeholder nucleosome in sperm cells for epigenetic inheritance.
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Affiliation(s)
- Seung Cho Lee
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Dexter W Adams
- W. M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA; Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jonathan J Ipsaro
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; W. M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA
| | - Jonathan Cahn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Jason Lynn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Hyun-Soo Kim
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Benjamin Berube
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; Cold Spring Harbor Laboratory School of Biological Sciences, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Viktoria Major
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Joseph P Calarco
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; Cold Spring Harbor Laboratory School of Biological Sciences, 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Chantal LeBlanc
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Sonali Bhattacharjee
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Umamaheswari Ramu
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Daniel Grimanelli
- Institut de Recherche pour le Développement, 911Avenue Agropolis, 34394 Montpelier, France
| | - Yannick Jacob
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Philipp Voigt
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Leemor Joshua-Tor
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA; W. M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute, Cold Spring Harbor, NY 11724, USA.
| | - Robert A Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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Lee SC, Adams DW, Ipsaro JJ, Cahn J, Lynn J, Kim HS, Berube B, Major V, Calarco JP, LeBlanc C, Bhattacharjee S, Ramu U, Grimanelli D, Jacob Y, Voigt P, Joshua-Tor L, Martienssen RA. Chromatin remodeling of histone H3 variants underlies epigenetic inheritance of DNA methylation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.11.548598. [PMID: 37503143 PMCID: PMC10369972 DOI: 10.1101/2023.07.11.548598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Epigenetic inheritance refers to the faithful replication of DNA methylation and histone modification independent of DNA sequence. Nucleosomes block access to DNA methyltransferases, unless they are remodeled by DECREASE IN DNA METHYLATION1 (DDM1 Lsh/HELLS ), a Snf2-like master regulator of epigenetic inheritance. We show that DDM1 activity results in replacement of the transcriptional histone variant H3.3 for the replicative variant H3.1 during the cell cycle. In ddm1 mutants, DNA methylation can be restored by loss of the H3.3 chaperone HIRA, while the H3.1 chaperone CAF-1 becomes essential. The single-particle cryo-EM structure at 3.2 Å of DDM1 with a variant nucleosome reveals direct engagement at SHL2 with histone H3.3 at or near variant residues required for assembly, as well as with the deacetylated H4 tail. An N-terminal autoinhibitory domain binds H2A variants to allow remodeling, while a disulfide bond in the helicase domain is essential for activity in vivo and in vitro . We show that differential remodeling of H3 and H2A variants in vitro reflects preferential deposition in vivo . DDM1 co-localizes with H3.1 and H3.3 during the cell cycle, and with the DNA methyltransferase MET1 Dnmt1 . DDM1 localization to the chromosome is blocked by H4K16 acetylation, which accumulates at DDM1 targets in ddm1 mutants, as does the sperm cell specific H3.3 variant MGH3 in pollen, which acts as a placeholder nucleosome in the germline and contributes to epigenetic inheritance.
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Affiliation(s)
- Seung Cho Lee
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Dexter W. Adams
- W. M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute; Cold Spring Harbor, NY 11724, USA
- Graduate Program in Genetics, Stony Brook University; Stony Brook, NY 11794, USA
| | - Jonathan J. Ipsaro
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- W. M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute; Cold Spring Harbor, NY 11724, USA
| | - Jonathan Cahn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Jason Lynn
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Hyun-Soo Kim
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Benjamin Berube
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Cold Spring Harbor Laboratory School of Biological Sciences; 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Viktoria Major
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh; Edinburgh EH9 3BF, United Kingdom
| | - Joseph P. Calarco
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Cold Spring Harbor Laboratory School of Biological Sciences; 1 Bungtown Rd, Cold Spring Harbor, NY 11724, USA
| | - Chantal LeBlanc
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Present address: Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University; 260 Whitney Ave., New Haven, CT, 06511, USA
| | - Sonali Bhattacharjee
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Umamaheswari Ramu
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
| | - Daniel Grimanelli
- Institut de Recherche pour le Développement; 911 Avenue Agropolis, 34394 Montpellier, France
| | - Yannick Jacob
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- Present address: Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University; 260 Whitney Ave., New Haven, CT, 06511, USA
| | - Philipp Voigt
- Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh; Edinburgh EH9 3BF, United Kingdom
- Present address: Epigenetics Programme, Babraham Institute; Cambridge CB22 3AT, United Kingdom
| | - Leemor Joshua-Tor
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
- W. M. Keck Structural Biology Laboratory, Howard Hughes Medical Institute; Cold Spring Harbor, NY 11724, USA
| | - Robert A. Martienssen
- Howard Hughes Medical Institute, Cold Spring Harbor Laboratory; 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA
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Fu MP, Merrill SM, Sharma M, Gibson WT, Turvey SE, Kobor MS. Rare diseases of epigenetic origin: Challenges and opportunities. Front Genet 2023; 14:1113086. [PMID: 36814905 PMCID: PMC9939656 DOI: 10.3389/fgene.2023.1113086] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 01/24/2023] [Indexed: 02/09/2023] Open
Abstract
Rare diseases (RDs), more than 80% of which have a genetic origin, collectively affect approximately 350 million people worldwide. Progress in next-generation sequencing technology has both greatly accelerated the pace of discovery of novel RDs and provided more accurate means for their diagnosis. RDs that are driven by altered epigenetic regulation with an underlying genetic basis are referred to as rare diseases of epigenetic origin (RDEOs). These diseases pose unique challenges in research, as they often show complex genetic and clinical heterogeneity arising from unknown gene-disease mechanisms. Furthermore, multiple other factors, including cell type and developmental time point, can confound attempts to deconvolute the pathophysiology of these disorders. These challenges are further exacerbated by factors that contribute to epigenetic variability and the difficulty of collecting sufficient participant numbers in human studies. However, new molecular and bioinformatics techniques will provide insight into how these disorders manifest over time. This review highlights recent studies addressing these challenges with innovative solutions. Further research will elucidate the mechanisms of action underlying unique RDEOs and facilitate the discovery of treatments and diagnostic biomarkers for screening, thereby improving health trajectories and clinical outcomes of affected patients.
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Affiliation(s)
- Maggie P. Fu
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Sarah M. Merrill
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Mehul Sharma
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada,Department of Pediatrics, Faculty of Medicine, BC Children’s Hospital, University of British Columbia, Vancouver, BC, Canada
| | - William T. Gibson
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada
| | - Stuart E. Turvey
- BC Children’s Hospital Research Institute, Vancouver, BC, Canada,Department of Pediatrics, Faculty of Medicine, BC Children’s Hospital, University of British Columbia, Vancouver, BC, Canada
| | - Michael S. Kobor
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, BC, Canada,Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, BC, Canada,BC Children’s Hospital Research Institute, Vancouver, BC, Canada,*Correspondence: Michael S. Kobor,
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5
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De Dieuleveult M, Bizet M, Colin L, Calonne E, Bachman M, Li C, Stancheva I, Miotto B, Fuks F, Deplus R. The chromatin remodelling protein LSH/HELLS regulates the amount and distribution of DNA hydroxymethylation in the genome. Epigenetics 2021; 17:422-443. [PMID: 33960278 DOI: 10.1080/15592294.2021.1917152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Ten-Eleven Translocation (TET) proteins convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) leading to a dynamic epigenetic state of DNA that can influence transcription and chromatin organization. While TET proteins interact with complexes involved in transcriptional repression and activation, the overall understanding of the molecular mechanisms involved in TET-mediated regulation of gene expression still remains limited. Here, we show that TET proteins interact with the chromatin remodelling protein lymphoid-specific helicase (LSH/HELLS) in vivo and in vitro. In mouse embryonic fibroblasts (MEFs) and embryonic stem cells (ESCs) knock out of Lsh leads to a significant reduction of 5-hydroxymethylation amount in the DNA. Whole genome sequencing of 5hmC in wild-type versus Lsh knock-out MEFs and ESCs showed that in absence of Lsh, some regions of the genome gain 5hmC while others lose it, with mild correlation with gene expression changes. We further show that differentially hydroxymethylated regions did not completely overlap with differentially methylated regions indicating that changes in 5hmC distribution upon Lsh knock-out are not a direct consequence of 5mC decrease. Altogether, our results suggest that LSH, which interacts with TET proteins, contributes to the regulation of 5hmC levels and distribution in MEFs and ESCs.
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Affiliation(s)
- Maud De Dieuleveult
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium.,Université De Paris, Institut Cochin, Inserm, Cnrs, PARIS, France
| | - Martin Bizet
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Laurence Colin
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Emilie Calonne
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Martin Bachman
- Medicines Discovery Catapult, Alderley Park, Macclesfield, UK
| | - Chao Li
- , Max Born Crescent, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Irina Stancheva
- , Max Born Crescent, Institute of Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Benoit Miotto
- Université De Paris, Institut Cochin, Inserm, Cnrs, PARIS, France
| | - François Fuks
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
| | - Rachel Deplus
- Laboratory of Cancer Epigenetics, Faculty of Medicine, ULB-Cancer Research Centre (U-CRC), Université Libre De Bruxelles, Brussels, Belgium
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6
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Vukic M, Daxinger L. DNA methylation in disease: Immunodeficiency, Centromeric instability, Facial anomalies syndrome. Essays Biochem 2019; 63:773-783. [PMID: 31724723 PMCID: PMC6923317 DOI: 10.1042/ebc20190035] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/01/2019] [Accepted: 10/02/2019] [Indexed: 12/19/2022]
Abstract
DNA methylation is an epigenetic modification essential for normal mammalian development. Initially associated with gene silencing, more diverse roles for DNA methylation in the regulation of gene expression patterns are increasingly being recognized. Some of these insights come from studying the function of genes that are mutated in human diseases characterized by abnormal DNA methylation landscapes. The first disorder to be associated with congenital defects in DNA methylation was Immunodeficiency, Centromeric instability, Facial anomalies syndrome (ICF). The hallmark of this syndrome is hypomethylation of pericentromeric satellite repeats, with mutations in four genes: DNMT3B, ZBTB24, CDCA7 and HELLS, being linked to the disease. Here, we discuss recent progress in understanding the molecular interactions between these genes and consider current evidence for how aberrant DNA methylation may contribute to the abnormal phenotype present in ICF syndrome patients.
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Affiliation(s)
- Maja Vukic
- Department of Human Genetics, Leiden University Medical Centre (LUMC), Leiden 2300, RC, The Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Centre (LUMC), Leiden 2300, RC, The Netherlands
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7
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Chen L, Shi Y, Liu N, Wang Z, Yang R, Yan B, Liu X, Lai W, Liu Y, Xiao D, Zhou H, Cheng Y, Cao Y, Liu S, Xia Z, Tao Y. DNA methylation modifier LSH inhibits p53 ubiquitination and transactivates p53 to promote lipid metabolism. Epigenetics Chromatin 2019; 12:59. [PMID: 31594538 PMCID: PMC6781351 DOI: 10.1186/s13072-019-0302-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 09/03/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The stability of p53 is mainly controlled by ubiquitin-dependent degradation, which is triggered by the E3 ubiquitin ligase MDM2. The chromatin modifier lymphoid-specific helicase (LSH) is essential for DNA methylation and cancer progression as a transcriptional repressor. The potential interplay between chromatin modifiers and transcription factors remains largely unknown. RESULTS Here, we present data suggesting that LSH regulates p53 in cis through two pathways: prevention proteasomal degradation through its deubiquitination, which is achieved by reducing the lysine 11-linked, lysine 48-linked polyubiquitin chains (K11 and K48) on p53; and revival of the transcriptional activity of p53 by forming a complex with PKM2 (pyruvate kinase 2). Furthermore, we confirmed that the LSH-PKM2 interaction occurred at the intersubunit interface region of the PKM2 C-terminal region and the coiled-coil domains (CC) and ATP-binding domains of LSH, and this interaction regulated p53-mediated transactivation in cis in lipid metabolism, especially lipid catabolism. CONCLUSION These findings suggest that LSH is a novel regulator of p53 through the proteasomal pathway, thereby providing an alternative mechanism of p53 involvement in lipid metabolism in cancer.
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Affiliation(s)
- Ling Chen
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, 410078, Hunan, China
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, China
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Ying Shi
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, 410078, Hunan, China
| | - Na Liu
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, 410078, Hunan, China
| | - Zuli Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, 410078, Hunan, China
| | - Rui Yang
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, 410078, Hunan, China
| | - Bin Yan
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, 410078, Hunan, China
- Department of Oncology, Institute of Medical Sciences, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Xiaoli Liu
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, 410078, Hunan, China
| | - Weiwei Lai
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, 410078, Hunan, China
| | - Yating Liu
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, 410078, Hunan, China
| | - Desheng Xiao
- Department of Pathology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Hu Zhou
- Shanghai Institute of Material Medica, Chinese Academy of Sciences (CAS), 555 Zu Chongzhi Road, Zhangjiang Hi-Tech Park, Shanghai, 201203, China
| | - Yan Cheng
- Department of Pharmacology, School of Pharmaceutical Sciences, Central South University, Changsha, 410078, Hunan, China
| | - Ya Cao
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, 410078, Hunan, China
| | - Shuang Liu
- Department of Oncology, Institute of Medical Sciences, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China
| | - Zanxian Xia
- Department of Cell Biology, School of Life Sciences, Central South University, Changsha, Hunan, China.
- Hunan Key Laboratory of Animal Models for Human Diseases, School of Life Sciences, Central South University, Changsha, Hunan, China.
| | - Yongguang Tao
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Department of Pathology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China.
- NHC Key Laboratory of Carcinogenesis (Central South University), Cancer Research Institute and School of Basic Medicine, Central South University, 110 Xiangya Road, Changsha, 410078, Hunan, China.
- Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, China.
- Department of Oncology, Institute of Medical Sciences, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China.
- Department of Pathology, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, 410008, Hunan, China.
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8
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Parihar V, Dangwal M, Arya D, Kapoor S, Kapoor M. Decrease in DNA methylation 1 interacts with chromomethylase and like heterochromatin protein 1 in
Physcomitrella patens. FEBS Lett 2019; 593:2686-2697. [DOI: 10.1002/1873-3468.13524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 06/22/2019] [Accepted: 06/26/2019] [Indexed: 12/14/2022]
Affiliation(s)
- Vimala Parihar
- University School of Biotechnology Guru Gobind Singh Indraprastha University New Delhi India
| | - Meenakshi Dangwal
- University School of Biotechnology Guru Gobind Singh Indraprastha University New Delhi India
| | - Deepshikha Arya
- University School of Biotechnology Guru Gobind Singh Indraprastha University New Delhi India
| | - Sanjay Kapoor
- University School of Biotechnology Guru Gobind Singh Indraprastha University New Delhi India
- Interdisciplinary Centre for Plant Genomics, Department of Plant Molecular Biology University of Delhi South Campus New Delhi India
| | - Meenu Kapoor
- University School of Biotechnology Guru Gobind Singh Indraprastha University New Delhi India
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9
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Pennings S, Revuelta A, McLaughlin KA, Abd Hadi NA, Petchreing P, Ottaviano R, Meehan RR. Dynamics and Mechanisms of DNA Methylation Reprogramming. EPIGENETICS AND REGENERATION 2019:19-45. [DOI: 10.1016/b978-0-12-814879-2.00002-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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