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Yamaguchi T, Hoshizaki M, Imai Y, Yamamoto T, Kuba K. Cnot4 heterozygosity attenuates high fat diet-induced obesity in mice and impairs PPARγ-mediated adipocyte differentiation. PLoS One 2025; 20:e0316417. [PMID: 40424271 DOI: 10.1371/journal.pone.0316417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2024] [Accepted: 04/24/2025] [Indexed: 05/29/2025] Open
Abstract
Adipocyte differentiation is crucial for formation and expansion of white adipose tissue and is also associated with the pathologies of obesity. CNOT4 is an E3 ubiquitin ligase and also contains RNA binding domain. In mammals CNOT4 has been suggested to interact with CCR4-NOT complex, a major executor of mRNA poly(A) shortening. While several subunits within the CCR4-NOT complex were shown to be involved in obesity and energy metabolism, the roles of CNOT4 in obesity remain unexplored. In this study, we generated and analyzed Cnot4 knockout mice and found that Cnot4 heterozygous (Cnot4 Het) mice exhibit resistance to high fat diet-induced obesity, including significant reduction in adipose tissue mass and hepatic lipid depots. However, Cnot4 Het did not affect mRNA expression of metabolic genes as well as serum lipid levels or glucose tolerance. On the other hand, Cnot4 Het fibroblasts significantly reduced the capability of differentiation into adipocytes and down-regulated adipogenic gene expression compared to wild type fibroblasts. Mechanistically, heterozygous deletion of Cnot4 down-regulated the transcriptional activity through decreased binding of PPARγ to promoter region of the target gene, thereby suppressing up-regulation of adipocyte marker gene expression in response to rosiglitazone, a PPARγ agonist. These results suggest that CNOT4 mediates adipocyte differentiation during formation and growth of adipose tissue partly through positively regulating transcriptional activity of PPARγ.
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Affiliation(s)
- Tomokazu Yamaguchi
- Department of Pharmacology, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Midori Hoshizaki
- Department of Pharmacology, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
| | - Yumiko Imai
- Department of Medical Infection System, Research Institute Nozaki Tokushukai Hospital, Osaka, Japan
| | - Tadashi Yamamoto
- Cell Signal Unit, Okinawa Institute of Science and Technology, Okinawa, Japan
| | - Keiji Kuba
- Department of Pharmacology, Kyushu University Graduate School of Medical Sciences, Fukuoka, Japan
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2
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Meng Y, Wang X, Liu K, Tang X, Li H, Chen J, Zhong Z. A novel KDM5C mutation associated with intellectual disability: molecular mechanisms and clinical implications. Ital J Pediatr 2025; 51:47. [PMID: 39948613 PMCID: PMC11827480 DOI: 10.1186/s13052-025-01887-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2024] [Accepted: 01/12/2025] [Indexed: 02/16/2025] Open
Abstract
BACKGROUND Among the disease-causing genes associated with X-linked intellectual disability (XLID), KDM5C is one of the most frequently mutated ones. KDM5C is a widely expressed gene that is most highly expressed in the brain. KDM5C modulates the transcriptional activity of genes through demethylation of H3K4, thereby regulating neural development and normal function. We identified a gene from a Chinese family and found that a nonsense mutation of KDM5C was co-segregated with the intellectual disability (ID). METHODS The candidate mutant genes of patients with ID phenotype were screened by Whole Exome Sequencing (WES), and DNA Sanger sequencing was performed for genetic analysis. Pathogenicity prediction tools were used to evaluate the pathogenicity of new mutations. The fusion plasmid was constructed and transfected into the cells, and the changes of mRNA and protein levels of the mutants were detected by semi-qRT-PCR and Western Blot, and the subcellular localization changes of mutant proteins were detected by Immunofluorescence technique. RESULT The nonsense mutation in KDM5C (c.2785 C > T, p. R929X) was identified by whole exome sequencing (WES) and confirmed by Sanger sequencing, resulting in a truncated protein. The mutation was determined by pathogenicity prediction tool able to find non-sense mediated mRNA decay (NMD). Semi-qRT-PCR and Western Blot showed that the mRNA levels of the mutant gene were down-regulated, while the protein level was up-regulated. Additionally, the subcellular localization of the mutant protein changed. CONCLUSIONS The KDM5C mutation found in our study leads to changes in protein levels through NMD and/or protein degradation, and produces residues lacking nuclear localization, thus altering the subcellular localization of the protein. These results may lead to changes in the expression of KDM5C target genes, ultimately contributing to the clinical phenotype observed in the patients.
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Affiliation(s)
- Yunlong Meng
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Department of Pediatrics, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
- Institute of Medical Genetics, Department of Child, Adolescent and Maternal Health, School of Public Health and General Medicine, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Xinyao Wang
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Department of Pediatrics, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
- Institute of Medical Genetics, Department of Child, Adolescent and Maternal Health, School of Public Health and General Medicine, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Kangyu Liu
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Department of Pediatrics, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
- Institute of Medical Genetics, Department of Child, Adolescent and Maternal Health, School of Public Health and General Medicine, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Xingkun Tang
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Department of Pediatrics, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
- Institute of Medical Genetics, Department of Child, Adolescent and Maternal Health, School of Public Health and General Medicine, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Haining Li
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Department of Pediatrics, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China
- Institute of Medical Genetics, Department of Child, Adolescent and Maternal Health, School of Public Health and General Medicine, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Jianjun Chen
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Department of Pediatrics, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China.
- Institute of Medical Genetics, Department of Child, Adolescent and Maternal Health, School of Public Health and General Medicine, School of Medicine, Tongji University, Shanghai, 200092, China.
- Tongji University School of Medicine, 500 Zhennan Road Putuo District, Shanghai, 200331, China.
| | - Zilin Zhong
- Shanghai Key Laboratory of Anesthesiology and Brain Functional Modulation, Clinical Research Center for Anesthesiology and Perioperative Medicine, Translational Research Institute of Brain and Brain-Like Intelligence, Department of Pediatrics, Shanghai Fourth People's Hospital, School of Medicine, Tongji University, Shanghai, 200434, China.
- Institute of Medical Genetics, Department of Child, Adolescent and Maternal Health, School of Public Health and General Medicine, School of Medicine, Tongji University, Shanghai, 200092, China.
- Tongji University School of Medicine, 500 Zhennan Road Putuo District, Shanghai, 200331, China.
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3
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Collart MA, Audebert L, Bushell M. Roles of the CCR4-Not complex in translation and dynamics of co-translation events. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1827. [PMID: 38009591 PMCID: PMC10909573 DOI: 10.1002/wrna.1827] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 10/06/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023]
Abstract
The Ccr4-Not complex is a global regulator of mRNA metabolism in eukaryotic cells that is most well-known to repress gene expression. Delivery of the complex to mRNAs through a multitude of distinct mechanisms accelerates their decay, yet Ccr4-Not also plays an important role in co-translational processes, such as co-translational association of proteins and delivery of translating mRNAs to organelles. The recent structure of Not5 interacting with the translated ribosome has brought to light that embedded information within the codon sequence can be monitored by recruitment of the Ccr4-Not complex to elongating ribosomes. Thereby, the Ccr4-Not complex is empowered with regulatory decisions determining the fate of proteins being synthesized and their encoding mRNAs. This review will focus on the roles of the complex in translation and dynamics of co-translation events. This article is categorized under: Translation > Mechanisms Translation > Regulation.
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Affiliation(s)
- Martine A. Collart
- Department of Microbiology and Molecular MedicineInstitute of Genetics and Genomics Geneva, University of Geneva, Faculty of MedicineGenèveSwitzerland
| | - Léna Audebert
- Department of Microbiology and Molecular MedicineInstitute of Genetics and Genomics Geneva, University of Geneva, Faculty of MedicineGenèveSwitzerland
| | - Martin Bushell
- Cancer Research UK Beatson InstituteGlasgowUK
- School of Cancer Sciences, University of GlasgowGlasgowUK
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Roy A, Niharika, Chakraborty S, Mishra J, Singh SP, Patra SK. Mechanistic aspects of reversible methylation modifications of arginine and lysine of nuclear histones and their roles in human colon cancer. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:261-302. [PMID: 37019596 DOI: 10.1016/bs.pmbts.2023.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
Developmental proceedings and maintenance of cellular homeostasis are regulated by the precise orchestration of a series of epigenetic events that eventually control gene expression. DNA methylation and post-translational modifications (PTMs) of histones are well-characterized epigenetic events responsible for fine-tuning gene expression. PTMs of histones bear molecular logic of gene expression at chromosomal territory and have become a fascinating field of epigenetics. Nowadays, reversible methylation on histone arginine and lysine is gaining increasing attention as a significant PTM related to reorganizing local nucleosomal structure, chromatin dynamics, and transcriptional regulation. It is now well-accepted and reported that histone marks play crucial roles in colon cancer initiation and progression by encouraging abnormal epigenomic reprogramming. It is becoming increasingly clear that multiple PTM marks at the N-terminal tails of the core histones cross-talk with one another to intricately regulate DNA-templated biological processes such as replication, transcription, recombination, and damage repair in several malignancies, including colon cancer. These functional cross-talks provide an additional layer of message, which spatiotemporally fine-tunes the overall gene expression regulation. Nowadays, it is evident that several PTMs instigate colon cancer development. How colon cancer-specific PTM patterns or codes are generated and how they affect downstream molecular events are uncovered to some extent. Future studies would address more about epigenetic communication, and the relationship between histone modification marks to define cellular functions in depth. This chapter will comprehensively highlight the importance of histone arginine and lysine-based methylation modifications and their functional cross-talk with other histone marks from the perspective of colon cancer development.
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Chou KY, Lee JY, Kim KB, Kim E, Lee HS, Ryu HY. Histone modification in Saccharomyces cerevisiae: A review of the current status. Comput Struct Biotechnol J 2023; 21:1843-1850. [PMID: 36915383 PMCID: PMC10006725 DOI: 10.1016/j.csbj.2023.02.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 02/21/2023] [Accepted: 02/22/2023] [Indexed: 02/26/2023] Open
Abstract
The budding yeast Saccharomyces cerevisiae is a well-characterized and popular model system for investigating histone modifications and the inheritance of chromatin states. The data obtained from this model organism have provided essential and critical information for understanding the complexity of epigenetic interactions and regulation in eukaryotes. Recent advances in biotechnology have facilitated the detection and quantitation of protein post-translational modification (PTM), including acetylation, methylation, phosphorylation, ubiquitylation, sumoylation, and acylation, and led to the identification of several novel modification sites in histones. Determining the cellular function of these new histone markers is essential for understanding epigenetic mechanisms and their impact on various biological processes. In this review, we describe recent advances and current views on histone modifications and their effects on chromatin dynamics in S. cerevisiae.
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Key Words
- AdoMet, S-adenosylmethionine
- CAF-1, chromatin assembly factor-1
- CTD, C-terminal domain
- DSB, double-strand break
- E Glu, glutamic acid
- HAT, histone acetyltransferase
- HDAC, histone deacetylase
- Histone acetylation
- Histone acylation
- Histone methylation
- Histone phosphorylation
- Histone sumoylation
- Histone ubiquitylation
- JMJC, Jumonji C
- K Lys, lysine
- PTM, post-translational modification
- R Arg, arginine
- S, serine
- SAGA, Spt-Ada-Gcn5 acetyltransferase
- STUbL, SUMO-targeted ubiquitin ligase
- SUMO, small ubiquitin-like modifier
- T, threonine
- Y, tyrosine
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Affiliation(s)
- Kwon Young Chou
- School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jun-Yeong Lee
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kee-Beom Kim
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Eunjeong Kim
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hyun-Shik Lee
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Hong-Yeoul Ryu
- BK21 Plus KNU Creative BioResearch Group, School of Life Sciences, College of National Sciences, Kyungpook National University, Daegu 41566, Republic of Korea
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Yu Q, Gong X, Tong Y, Wang M, Duan K, Zhang X, Ge F, Yu X, Li S. Phosphorylation of Jhd2 by the Ras-cAMP-PKA(Tpk2) pathway regulates histone modifications and autophagy. Nat Commun 2022; 13:5675. [PMID: 36167807 PMCID: PMC9515143 DOI: 10.1038/s41467-022-33423-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 09/16/2022] [Indexed: 11/12/2022] Open
Abstract
Cells need to coordinate gene expression with their metabolic states to maintain cell homeostasis and growth. How cells transduce nutrient availability to appropriate gene expression remains poorly understood. Here we show that glycolysis regulates histone modifications and gene expression by activating protein kinase A (PKA) via the Ras-cyclic AMP pathway. The catalytic subunit of PKA, Tpk2 antagonizes Jhd2-catalyzed H3K4 demethylation by phosphorylating Jhd2 at Ser321 and Ser340 in response to glucose availability. Tpk2-catalyzed Jhd2 phosphorylation impairs its nuclear localization, reduces its binding to chromatin, and promotes its polyubiquitination and degradation by the proteasome. Tpk2-catalyzed Jhd2 phosphorylation also maintains H3K14 acetylation by preventing the binding of histone deacetylase Rpd3 to chromatin. By phosphorylating Jhd2, Tpk2 regulates gene expression, maintains normal chronological life span and promotes autophagy. These results provide a direct connection between metabolism and histone modifications and shed lights on how cells rewire their biological responses to nutrient signals.
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Affiliation(s)
- Qi Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Xuanyunjing Gong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Yue Tong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Min Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Kai Duan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Xinyu Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China
| | - Feng Ge
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, China
| | - Xilan Yu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China.
| | - Shanshan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, Hubei, 430062, China.
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7
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Zhou M, Yao Z, Zhao M, Fang Q, Ji X, Chen H, Zhao Y. Molecular Cloning and Expression Responses of Jarid2b to High-Temperature Treatment in Nile Tilapia ( Oreochromis niloticus). Genes (Basel) 2022; 13:1719. [PMID: 36292604 PMCID: PMC9602145 DOI: 10.3390/genes13101719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/12/2022] [Accepted: 09/20/2022] [Indexed: 10/27/2023] Open
Abstract
Nile tilapia is a GSD + TE (Genetic Sex Determination + Temperature Effect) fish, and high-temperature treatment during critical thermosensitive periods (TSP) can induce the sex reversal of Nile tilapia genetic females, and brain transcriptomes have revealed the upregulation of Jarid2 (Jumonji and AT-rich domain containing 2) expression after 36 °C high-temperature treatment for 12 days during TSP. It was shown that JARID2 forms a complex with polycomb repressive complex 2 (PRC2) that catalyzed H3K27me3, which was strongly associated with transcriptional repression. In this study, Jarid2b was cloned and characterized in Nile tilapia, which was highly conserved among the analyzed fish species. The expression of Jarid2b was upregulated in the gonad of 21 dpf XX genetic females after 12-day high-temperature treatment and reached a similar level to that of males. Similar responses to high-temperature treatment also appeared in the brain, heart, liver, muscle, eye, and skin tissues. Interestingly, Jarid2b expression was only in response to high-temperature treatment, and not to 17α-methyltestosterone (MT) or letrozole treatments; although, these treatments can also induce the sex reversal of genetic Nile tilapia females. Further studies revealed that Jarid2b responded rapidly at the 8th hour after high-temperature treatment. Considering that JARID2 can recruit PRC2 and establish H3K27me3, we speculated that it might be an upstream gene participating in the regulation of Nile tilapia GSD + TE through regulating the H3K27 methylation level at the locus of many sex differentiation-related genes.
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Affiliation(s)
| | | | | | | | | | | | - Yan Zhao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian 271000, China
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8
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Wu Q, Young B, Wang Y, Davidoff AM, Rankovic Z, Yang J. Recent Advances with KDM4 Inhibitors and Potential Applications. J Med Chem 2022; 65:9564-9579. [PMID: 35838529 PMCID: PMC9531573 DOI: 10.1021/acs.jmedchem.2c00680] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The histone lysine demethylase 4 (KDM4) family plays an important role in regulating gene transcription, DNA repair, and metabolism. The dysregulation of KDM4 functions is associated with many human disorders, including cancer, obesity, and cardiovascular diseases. Selective and potent KDM4 inhibitors may help not only to understand the role of KDM4 in these disorders but also to provide potential therapeutic opportunities. Here, we provide an overview of the field and discuss current status, challenges, and opportunities lying ahead in the development of KDM4-based anticancer therapeutics.
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Affiliation(s)
- Qiong Wu
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Brandon Young
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Yan Wang
- Department of Geriatrics and Occupational Disease, Qingdao Central Hospital, Qingdao 266044, China
| | - Andrew M Davidoff
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Jun Yang
- Department of Surgery, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.,Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science Center, 930 Madison Avenue, Suite 500, Memphis, Tennessee 38163, United States
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9
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Pavlenko E, Ruengeler T, Engel P, Poepsel S. Functions and Interactions of Mammalian KDM5 Demethylases. Front Genet 2022; 13:906662. [PMID: 35899196 PMCID: PMC9309374 DOI: 10.3389/fgene.2022.906662] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/06/2022] [Indexed: 12/26/2022] Open
Abstract
Mammalian histone demethylases of the KDM5 family are mediators of gene expression dynamics during developmental, cellular differentiation, and other nuclear processes. They belong to the large group of JmjC domain containing, 2-oxoglutarate (2-OG) dependent oxygenases and target methylated lysine 4 of histone H3 (H3K4me1/2/3), an epigenetic mark associated with active transcription. In recent years, KDM5 demethylases have gained increasing attention due to their misregulation in many cancer entities and are intensively explored as therapeutic targets. Despite these implications, the molecular basis of KDM5 function has so far remained only poorly understood. Little is known about mechanisms of nucleosome recognition, the recruitment to genomic targets, as well as the local regulation of demethylase activity. Experimental evidence suggests close physical and functional interactions with epigenetic regulators such as histone deacetylase (HDAC) containing complexes, as well as the retinoblastoma protein (RB). To understand the regulation of KDM5 proteins in the context of chromatin, these interactions have to be taken into account. Here, we review the current state of knowledge on KDM5 function, with a particular emphasis on molecular interactions and their potential implications. We will discuss and outline open questions that need to be addressed to better understand histone demethylation and potential demethylation-independent functions of KDM5s. Addressing these questions will increase our understanding of histone demethylation and allow us to develop strategies to target individual KDM5 enzymes in specific biological and disease contexts.
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Affiliation(s)
- Egor Pavlenko
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
| | - Till Ruengeler
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
| | - Paulina Engel
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
| | - Simon Poepsel
- University of Cologne, Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital, Cologne, Germany
- Cologne Excellence Cluster for Cellular Stress Responses in Ageing-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
- *Correspondence: Simon Poepsel,
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10
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The Lysine Demethylases KdmA and KdmB Differently Regulate Asexual Development, Stress Response, and Virulence in Aspergillus fumigatus. J Fungi (Basel) 2022; 8:jof8060590. [PMID: 35736073 PMCID: PMC9225160 DOI: 10.3390/jof8060590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/17/2022] [Accepted: 05/30/2022] [Indexed: 12/04/2022] Open
Abstract
Histone demethylases govern diverse cellular processes, including growth, development, and secondary metabolism. In the present study, we investigated the functions of two lysine demethylases, KdmA and KdmB, in the opportunistic human pathogenic fungus Aspergillus fumigatus. Experiments with mutants harboring deletions of genes encoding KdmA (ΔkdmA) and KdmB (ΔkdmB) showed that KdmA is necessary for normal growth and proper conidiation, whereas KdmB negatively regulates vegetative growth and conidiation. In both mutant strains, tolerance to H2O2 was significantly decreased, and the activities of both conidia-specific catalase (CatA) and mycelia-specific catalase (Cat1) were decreased. Both mutants had significantly increased sensitivity to the guanine nucleotide synthesis inhibitor 6-azauracil (6AU). The ΔkdmA mutant produced more gliotoxin (GT), but the virulence was not changed significantly in immunocompromised mice. In contrast, the production of GT and virulence were markedly reduced by the loss of kdmB. Comparative transcriptomic analyses revealed that the expression levels of developmental process-related genes and antioxidant activity-related genes were downregulated in both mutants. Taken together, we concluded that KdmA and KdmB have opposite roles in vegetative growth, asexual sporulation, and GT production. However, the two proteins were equally important for the development of resistance to 6AU.
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Separovich RJ, Wong MW, Bartolec TK, Hamey JJ, Wilkins MR. Site-specific phosphorylation of histone H3K36 methyltransferase Set2p and demethylase Jhd1p is required for stress responses in Saccharomyces cerevisiae. J Mol Biol 2022; 434:167500. [DOI: 10.1016/j.jmb.2022.167500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 01/17/2022] [Accepted: 02/09/2022] [Indexed: 10/19/2022]
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12
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Yang GJ, Wu J, Miao L, Zhu MH, Zhou QJ, Lu XJ, Lu JF, Leung CH, Ma DL, Chen J. Pharmacological inhibition of KDM5A for cancer treatment. Eur J Med Chem 2021; 226:113855. [PMID: 34555614 DOI: 10.1016/j.ejmech.2021.113855] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/02/2021] [Accepted: 09/02/2021] [Indexed: 12/15/2022]
Abstract
Lysine-specific demethylase 5A (KDM5A, also named RBP2 or JARID1A) is a demethylase that can remove methyl groups from histones H3K4me1/2/3. It is aberrantly expressed in many cancers, where it impedes differentiation and contributes to cancer cell proliferation, cell metastasis and invasiveness, drug resistance, and is associated with poor prognosis. Pharmacological inhibition of KDM5A has been reported to significantly attenuate tumor progression in vitro and in vivo in a range of solid tumors and acute myeloid leukemia. This review will present the structural aspects of KDM5A, its role in carcinogenesis, a comparison of currently available approaches for screening KDM5A inhibitors, a classification of KDM5A inhibitors, and its potential as a drug target in cancer therapy.
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Affiliation(s)
- Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Jia Wu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China; Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macao SAR, 999078, China
| | - Liang Miao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Ming-Hui Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Qian-Jin Zhou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Xin-Jiang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Jian-Fei Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao SAR, 999078, China; Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Macao SAR, 999078, China.
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong, 999077, China.
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, Zhejiang, China; Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, China; Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, China.
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13
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Varghese B, Del Gaudio N, Cobellis G, Altucci L, Nebbioso A. KDM4 Involvement in Breast Cancer and Possible Therapeutic Approaches. Front Oncol 2021; 11:750315. [PMID: 34778065 PMCID: PMC8581295 DOI: 10.3389/fonc.2021.750315] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/13/2021] [Indexed: 12/24/2022] Open
Abstract
Breast cancer (BC) is the second leading cause of cancer death in women, although recent scientific and technological achievements have led to significant improvements in progression-free disease and overall survival of patients. Genetic mutations and epigenetic modifications play a critical role in deregulating gene expression, leading to uncontrolled cell proliferation and cancer progression. Aberrant histone modifications are one of the most frequent epigenetic mechanisms occurring in cancer. In particular, methylation and demethylation of specific lysine residues alter gene accessibility via histone lysine methyltransferases (KMTs) and histone lysine demethylases (KDMs). The KDM family includes more than 30 members, grouped into six subfamilies and two classes based on their sequency homology and catalytic mechanisms, respectively. Specifically, the KDM4 gene family comprises six members, KDM4A-F, which are associated with oncogene activation, tumor suppressor silencing, alteration of hormone receptor downstream signaling, and chromosomal instability. Blocking the activity of KDM4 enzymes renders them "druggable" targets with therapeutic effects. Several KDM4 inhibitors have already been identified as anticancer drugs in vitro in BC cells. However, no KDM4 inhibitors have as yet entered clinical trials due to a number of issues, including structural similarities between KDM4 members and conservation of the active domain, which makes the discovery of selective inhibitors challenging. Here, we summarize our current knowledge of the molecular functions of KDM4 members in BC, describe currently available KDM4 inhibitors, and discuss their potential use in BC therapy.
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Affiliation(s)
- Benluvankar Varghese
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy
| | - Nunzio Del Gaudio
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy
| | - Gilda Cobellis
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy
| | - Lucia Altucci
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy.,Biogem Institute of Molecular Biology and Genetics, Ariano Irpino, Italy
| | - Angela Nebbioso
- Department of Precision Medicine, University of Campania Luigi Vanvitelli, Napoli, Italy.,Saint Camillus International University of Health and Medical Sciences, Rome, Italy
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14
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Lippa NC, Barua S, Aggarwal V, Pereira E, Bain JM. A novel de novo KDM5C variant in a female with global developmental delay and ataxia: a case report. BMC Neurol 2021; 21:358. [PMID: 34530748 PMCID: PMC8447699 DOI: 10.1186/s12883-021-02380-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 09/02/2021] [Indexed: 11/29/2022] Open
Abstract
Background Pathogenic variants in KDM5C are a cause of X-linked intellectual disability in males. Other features in males include short stature, dysmorphic features, seizures and spasticity. In some instances, female relatives were noted to have learning difficulties and mild intellectual disabilities, but full phenotypic descriptions were often incomplete. Recently, detailed phenotypic features of five affected females with de novo variants were described. (Clin Genet 98:43–55, 2020) Four individuals had a protein truncating variant and 1 individual had a missense variant. All five individuals had developmental delay/intellectual disability and three neurological features. Case presentation Here we report a three-year-old female with global developmental delay, hypotonia and ataxia. Through whole exome sequencing, a de novo c.1516A > G (p.Met506Val) variant in KDM5C was identified. This missense variant is in the jumonji-C domain of this multi domain protein where other missense variants have been previously reported in KDM5C related disorder. The KDM5C gene is highly intolerant to functional variation which suggests its pathogenicity. The probands motor delays and language impairment is consistent with other reported female patients with de novo variants in KDM5C. However, other features reported in females (distinctive facial features, skeletal abnormalities, short stature and endocrine features) were absent. To the best of our knowledge, our proband is the first female patient reported with a diagnosis of ataxia. Conclusions This case report provides evidence for an emerging and phenotypic variability that adds to the literature of the role of KDM5C in females with neurodevelopmental disorders as well as movement disorders.
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Affiliation(s)
- Natalie C Lippa
- Institute for Genomic Medicine, Columbia University Irving Medical Center, New York, NY, USA
| | - Subit Barua
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Vimla Aggarwal
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - Elaine Pereira
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
| | - Jennifer M Bain
- Department of Neurology, Columbia University Irving Medical Center, New York, NY, USA.
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15
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Separovich RJ, Wilkins MR. Ready, SET, Go: Post-translational regulation of the histone lysine methylation network in budding yeast. J Biol Chem 2021; 297:100939. [PMID: 34224729 PMCID: PMC8329514 DOI: 10.1016/j.jbc.2021.100939] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/25/2021] [Accepted: 07/01/2021] [Indexed: 11/21/2022] Open
Abstract
Histone lysine methylation is a key epigenetic modification that regulates eukaryotic transcription. Here, we comprehensively review the function and regulation of the histone methylation network in the budding yeast and model eukaryote, Saccharomyces cerevisiae. First, we outline the lysine methylation sites that are found on histone proteins in yeast (H3K4me1/2/3, H3K36me1/2/3, H3K79me1/2/3, and H4K5/8/12me1) and discuss their biological and cellular roles. Next, we detail the reduced but evolutionarily conserved suite of methyltransferase (Set1p, Set2p, Dot1p, and Set5p) and demethylase (Jhd1p, Jhd2p, Rph1p, and Gis1p) enzymes that are known to control histone lysine methylation in budding yeast cells. Specifically, we illustrate the domain architecture of the methylation enzymes and highlight the structural features that are required for their respective functions and molecular interactions. Finally, we discuss the prevalence of post-translational modifications on yeast histone methylation enzymes and how phosphorylation, acetylation, and ubiquitination in particular are emerging as key regulators of enzyme function. We note that it will be possible to completely connect the histone methylation network to the cell's signaling system, given that all methylation sites and cognate enzymes are known, most phosphosites on the enzymes are known, and the mapping of kinases to phosphosites is tractable owing to the modest set of protein kinases in yeast. Moving forward, we expect that the rich variety of post-translational modifications that decorates the histone methylation machinery will explain many of the unresolved questions surrounding the function and dynamics of this intricate epigenetic network.
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Affiliation(s)
- Ryan J Separovich
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Marc R Wilkins
- Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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16
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Islam MT, Wang LC, Chen IJ, Lo KL, Lo WS. Arabidopsis JMJ17 promotes cotyledon greening during de-etiolation by repressing genes involved in tetrapyrrole biosynthesis in etiolated seedlings. THE NEW PHYTOLOGIST 2021; 231:1023-1039. [PMID: 33666236 DOI: 10.1111/nph.17327] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
Arabidopsis histone H3 lysine 4 (H3K4) demethylases play crucial roles in several developmental processes, but their involvement in seedling establishment remain unexplored. Here, we show that Arabidopsis JUMONJI DOMAIN-CONTAINING PROTEIN17 (JMJ17), an H3K4me3 demethylase, is involved in cotyledon greening during seedling establishment. Dark-grown seedlings of jmj17 accumulated a high concentration of protochlorophyllide, an intermediate metabolite in the tetrapyrrole biosynthesis (TPB) pathway that generates chlorophyll (Chl) during photomorphogenesis. Upon light irradiation, jmj17 mutants displayed decreased cotyledon greening and reduced Chl level compared with the wild-type; overexpression of JMJ17 completely rescued the jmj17-5 phenotype. Transcriptomics analysis uncovered that several genes encoding key enzymes involved in TPB were upregulated in etiolated jmj17 seedlings. Consistently, chromatin immunoprecipitation-quantitative PCR revealed elevated H3K4me3 level at the promoters of target genes. Chromatin association of JMJ17 was diminished upon light exposure. Furthermore, JMJ17 interacted with PHYTOCHROME INTERACTING FACTOR1 in the yeast two-hybrid assay. JMJ17 binds directly to gene promoters to demethylate H3K4me3 to suppress PROTOCHLOROPHYLLIDE OXIDOREDUCTASE C expression and TPB in the dark. Light results in de-repression of gene expression to modulate seedling greening during de-etiolation. Our study reveals a new role for histone demethylase JMJ17 in controlling cotyledon greening in etiolated seedlings during the dark-to-light transition.
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Affiliation(s)
- Md Torikul Islam
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, 11529, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, 40227, Taiwan
| | - Long-Chi Wang
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, 11529, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung, 40227, Taiwan
| | - I-Ju Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Kuan-Lin Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
| | - Wan-Sheng Lo
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 11529, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, Academia Sinica and National Chung Hsing University, Taipei, 11529, Taiwan
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17
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He X, Wang Q, Pan J, Liu B, Ruan Y, Huang Y. Systematic analysis of JmjC gene family and stress--response expression of KDM5 subfamily genes in Brassica napus. PeerJ 2021; 9:e11137. [PMID: 33850662 PMCID: PMC8019318 DOI: 10.7717/peerj.11137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 03/01/2021] [Indexed: 12/21/2022] Open
Abstract
Background Jumonji C (JmjC) proteins exert critical roles in plant development and stress response through the removal of lysine methylation from histones. Brassica napus, which originated from spontaneous hybridization by Brassica rapa and Brassica oleracea, is the most important oilseed crop after soybean. In JmjC proteins of Brassica species, the structure and function and its relationship with the parents and model plant Arabidopsis thaliana remain uncharacterized. Systematic identification and analysis for JmjC family in Brassica crops can facilitate the future functional characterization and oilseed crops improvement. Methods Basing on the conserved JmjC domain, JmjC homologs from the three Brassica species, B. rapa (AA), B. oleracea (CC) and B. napus, were identified from the Brassica database. Some methods, such as phylogenic analysis, chromosomal mapping, HMMER searching, gene structure display and Logos analysis, were used to characterize relationships of the JmjC homologs. Synonymous and nonsynonymous nucleotide substitutions were used to infer the information of gene duplication among homologs. Then, the expression levels of BnKDM5 subfamily genes were checked under abiotic stress by qRT-PCR. Results Sixty-five JmjC genes were identified from B. napus genome, 29 from B. rapa, and 23 from B. oleracea. These genes were grouped into seven clades based on the phylogenetic analysis, and their catalytic activities of demethylation were predicted. The average retention rate of B. napus JmjC genes (B. napus JmjC gene from B. rapa (93.1%) and B. oleracea (82.6%)) exceeded whole genome level. JmjC sequences demonstrated high conservation in domain origination, chromosomal location, intron/exon number and catalytic sites. The gene duplication events were confirmed among the homologs. Many of the BrKDM5 subfamily genes showed higher expression under drought and NaCl treatments, but only a few genes were involved in high temperature stress. Conclusions This study provides the first genome-wide characterization of JmjC genes in Brassica species. The BnJmjC exhibits higher conservation during the formation process of allotetraploid than the average retention rates of the whole B. napus genome. Furthermore, expression profiles of many genes indicated that BnKDM5 subfamily genes are involved in stress response to salt, drought and high temperature.
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Affiliation(s)
- Xinghui He
- Key Laboratory of Crop Epigenetic Regulation and Development, Hunan Province, Changsha, China.,Key Laboratory of Plant Genetics and Molecular Biology of Education Department, Changsha, Hunan Province, China.,College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Qianwen Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Jiao Pan
- Key Laboratory of Crop Epigenetic Regulation and Development, Hunan Province, Changsha, China.,Key Laboratory of Plant Genetics and Molecular Biology of Education Department, Changsha, Hunan Province, China.,College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Boyu Liu
- Key Laboratory of Crop Epigenetic Regulation and Development, Hunan Province, Changsha, China.,Key Laboratory of Plant Genetics and Molecular Biology of Education Department, Changsha, Hunan Province, China.,College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Ying Ruan
- Key Laboratory of Crop Epigenetic Regulation and Development, Hunan Province, Changsha, China.,Key Laboratory of Plant Genetics and Molecular Biology of Education Department, Changsha, Hunan Province, China.,College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Yong Huang
- Key Laboratory of Crop Epigenetic Regulation and Development, Hunan Province, Changsha, China.,Key Laboratory of Plant Genetics and Molecular Biology of Education Department, Changsha, Hunan Province, China.,College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan Province, China
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18
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Yang GJ, Zhu MH, Lu XJ, Liu YJ, Lu JF, Leung CH, Ma DL, Chen J. The emerging role of KDM5A in human cancer. J Hematol Oncol 2021; 14:30. [PMID: 33596982 PMCID: PMC7888121 DOI: 10.1186/s13045-021-01041-1] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/01/2021] [Indexed: 12/11/2022] Open
Abstract
Histone methylation is a key posttranslational modification of chromatin, and its dysregulation affects a wide array of nuclear activities including the maintenance of genome integrity, transcriptional regulation, and epigenetic inheritance. Variations in the pattern of histone methylation influence both physiological and pathological events. Lysine-specific demethylase 5A (KDM5A, also known as JARID1A or RBP2) is a KDM5 Jumonji histone demethylase subfamily member that erases di- and tri-methyl groups from lysine 4 of histone H3. Emerging studies indicate that KDM5A is responsible for driving multiple human diseases, particularly cancers. In this review, we summarize the roles of KDM5A in human cancers, survey the field of KDM5A inhibitors including their anticancer activity and modes of action, and the current challenges and potential opportunities of this field.
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Affiliation(s)
- Guan-Jun Yang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China.,Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao SAR, People's Republic of China
| | - Ming-Hui Zhu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Xin-Jiang Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Yan-Jun Liu
- Department of Immunology and Medical Microbiology, Nanjing University of Chinese Medicine, Nanjing, 210046, People's Republic of China
| | - Jian-Fei Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China.,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China.,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China
| | - Chung-Hang Leung
- Institute of Chinese Medical Sciences, State Key Laboratory of Quality Research in Chinese Medicine, University of Macau, Macao SAR, People's Republic of China.
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon, Hong Kong, 999077, People's Republic of China.
| | - Jiong Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Ningbo University, Ningbo, 315211, Zhejiang, People's Republic of China. .,Laboratory of Biochemistry and Molecular Biology, School of Marine Sciences, Ningbo University, Ningbo, 315211, People's Republic of China. .,Key Laboratory of Applied Marine Biotechnology of Ministry of Education, Ningbo University, Ningbo, 315211, People's Republic of China.
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19
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Dong Y, Lu J, Liu J, Jalal A, Wang C. Genome-wide identification and functional analysis of JmjC domain-containing genes in flower development of Rosa chinensis. PLANT MOLECULAR BIOLOGY 2020; 102:417-430. [PMID: 31898146 DOI: 10.1007/s11103-019-00955-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 12/23/2019] [Indexed: 05/18/2023]
Abstract
We genome-wide identified 28 JmjC domain-containing genes, further spatio-temporal expression profiling and genetic analysis defined them as epigenetic regulators in flowering initiation of Rosa chinensis. The JmjC domain-containing histone demethylases play critical roles in maintaining homeostasis of histone methylations, thus are vital for plant growth and development. Genome-wide identification of the JmjC domain-containing genes have been reported in several species, however, no systematic study has been performed in rose plants. In this paper, we identified 28 JmjC domain-containing genes from the newly published genome database of Rosa chinensis. The JmjC domain-containing proteins in R. chinensis were divided into seven groups, KDM3 was the largest group with 13 members, and JmjC domain-only A and KDM5B were the smallest clades both with only one member. Although all the JmjC domain proteins having a conserved JmjC domain, the gene and protein structure experienced differentiation and specification during the evolution, especially in KDM3 clade, one gene (RcJMJ40) was found carrying site deletions for cofactors Fe (II) and α-KG binding which were crucial for demethylase activities, three genes (RcJMJ41, RcJMJ43 and RcJMJ44) had no intron while two of them had tandem JmjC domains. Spatial expression pattern analysis of these JmjC domain-containing genes in different tissues showed most of them were highly expressed in reproductive tissues such as floral meristem and closed flowers than vegetative tissues, demonstrating their important functions in developmental switch from vegetative to reproductive growth of roses. Temporal expression profiling indicated majority of JmjC domain-containing genes from R. chinensis fluctuated along with floral bud differentiation and development, further proving their essential roles in flower organogenesis. VIGS induced silencing of RcJMJ12 led to delayed flowering time, and decreased the expression levels of flowering integrator such as RcFT, RcSOC1, RcFUL, RcLFY and RcAP1, therefore providing the genetic evidence of RcJMJ12 in flowering initiation. Collectively, spatio-temporal expression profiling and genetic analysis defined the JmjC domain-containing genes as important epigenetic regulators in flower development of R. chinensis.
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Affiliation(s)
- Yuwei Dong
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jun Lu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Jinyi Liu
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Abdul Jalal
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China
| | - Changquan Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu, China.
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20
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Hou J, Feng HQ, Chang HW, Liu Y, Li GH, Yang S, Sun CH, Zhang MZ, Yuan Y, Sun J, Zhu-Salzman K, Zhang H, Qin QM. The H3K4 demethylase Jar1 orchestrates ROS production and expression of pathogenesis-related genes to facilitate Botrytis cinerea virulence. THE NEW PHYTOLOGIST 2020; 225:930-947. [PMID: 31529514 DOI: 10.1111/nph.16200] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 09/04/2019] [Indexed: 06/10/2023]
Abstract
Histone 3 Lysine 4 (H3K4) demethylation is ubiquitous in organisms, however the roles of H3K4 demethylase JARID1(Jar1)/KDM5 in fungal development and pathogenesis remain largely unexplored. Here, we demonstrate that Jar1/KDM5 in Botrytis cinerea, the grey mould fungus, plays a crucial role in these processes. The BcJAR1 gene was deleted and its roles in fungal development and pathogenesis were investigated using approaches including genetics, molecular/cell biology, pathogenicity and transcriptomic profiling. BcJar1 regulates H3K4me3 and both H3K4me2 and H3K4me3 methylation levels during vegetative and pathogenic development, respectively. Loss of BcJAR1 impairs conidiation, appressorium formation and stress adaptation; abolishes infection cushion (IC) formation and virulence, but promotes sclerotium production in the ΔBcjar1 mutants. BcJar1 controls reactive oxygen species (ROS) production and proper assembly of Sep4, a core septin protein and virulence determinant, to initiate infection structure (IFS) formation and host penetration. Exogenous cAMP partially restored the mutant appressorium, but not IC, formation. BcJar1 orchestrates global expression of genes for ROS production, stress response, carbohydrate transmembrane transport, secondary metabolites, etc., which may be required for conidiation, IFS formation, host penetration and virulence of the pathogen. Our work systematically elucidates BcJar1 functions and provides novel insights into Jar1/KDM5-mediated H3K4 demethylation in regulating fungal development and pathogenesis.
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Affiliation(s)
- Jie Hou
- College of Plant Sciences, Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
- College of Forestry, BeiHua University, Jilin, 132013, China
| | - Hui-Qiang Feng
- College of Plant Sciences, Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
| | - Hao-Wu Chang
- Key Laboratory of Symbolic Computation and Knowledge Engineering, Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, 130012, China
| | - Yue Liu
- College of Plant Sciences, Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
| | - Gui-Hua Li
- College of Plant Sciences, Jilin University, Changchun, 130062, China
| | - Song Yang
- College of Plant Sciences, Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
| | - Chen-Hao Sun
- College of Plant Sciences, Jilin University, Changchun, 130062, China
| | - Ming-Zhe Zhang
- College of Plant Sciences, Jilin University, Changchun, 130062, China
| | - Ye Yuan
- College of Plant Sciences, Jilin University, Changchun, 130062, China
| | - Jiao Sun
- College of Plant Sciences, Jilin University, Changchun, 130062, China
| | - Keyan Zhu-Salzman
- Department of Entomology, Texas A&M University, College Station, TX, 77843, USA
| | - Hao Zhang
- Key Laboratory of Symbolic Computation and Knowledge Engineering, Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, 130012, China
| | - Qing-Ming Qin
- College of Plant Sciences, Key Laboratory of Zoonosis Research, Ministry of Education, Jilin University, Changchun, China
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21
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Choudhury R, Singh S, Arumugam S, Roguev A, Stewart AF. The Set1 complex is dimeric and acts with Jhd2 demethylation to convey symmetrical H3K4 trimethylation. Genes Dev 2019; 33:550-564. [PMID: 30842216 PMCID: PMC6499330 DOI: 10.1101/gad.322222.118] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 02/15/2019] [Indexed: 12/19/2022]
Abstract
In this study, Choudhury et al. report that yeast Set1C/COMPASS is dimeric and, consequently, symmetrically trimethylates histone 3 Lys4 (H3K4me3) on promoter nucleosomes. This presents a new paradigm for the establishment of epigenetic detail, in which dimeric methyltransferase and monomeric demethylase cooperate to eliminate asymmetry and focus symmetrical H3K4me3 onto selected nucleosomes. Epigenetic modifications can maintain or alter the inherent symmetry of the nucleosome. However, the mechanisms that deposit and/or propagate symmetry or asymmetry are not understood. Here we report that yeast Set1C/COMPASS (complex of proteins associated with Set1) is dimeric and, consequently, symmetrically trimethylates histone 3 Lys4 (H3K4me3) on promoter nucleosomes. Mutation of the dimer interface to make Set1C monomeric abolished H3K4me3 on most promoters. The most active promoters, particularly those involved in the oxidative phase of the yeast metabolic cycle, displayed H3K4me2, which is normally excluded from active promoters, and a subset of these also displayed H3K4me3. In wild-type yeast, deletion of the sole H3K4 demethylase, Jhd2, has no effect. However, in monomeric Set1C yeast, Jhd2 deletion increased H3K4me3 levels on the H3K4me2 promoters. Notably, the association of Set1C with the elongating polymerase was not perturbed by monomerization. These results imply that symmetrical H3K4 methylation is an embedded consequence of Set1C dimerism and that Jhd2 demethylates asymmetric H3K4me3. Consequently, rather than methylation and demethylation acting in opposition as logic would suggest, a dimeric methyltransferase and monomeric demethylase cooperate to eliminate asymmetry and focus symmetrical H3K4me3 onto selected nucleosomes. This presents a new paradigm for the establishment of epigenetic detail.
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Affiliation(s)
- Rupam Choudhury
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
| | - Sukhdeep Singh
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
| | - Senthil Arumugam
- European Molecular Biology Laboratory Australia Node for Single Molecule Science, ARC Centre of Excellence in Advanced Molecular Imaging, School of Medical Sciences, University of New South Wales, Sydney 2052, Australia
| | - Assen Roguev
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany.,Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, California 94518, USA
| | - A Francis Stewart
- Genomics, Biotechnology Center, Center for Molecular and Cellular Bioengineering, University of Technology Dresden, 01307 Dresden, Germany
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22
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Wilson C, Krieg AJ. KDM4B: A Nail for Every Hammer? Genes (Basel) 2019; 10:E134. [PMID: 30759871 PMCID: PMC6410163 DOI: 10.3390/genes10020134] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/05/2019] [Accepted: 02/07/2019] [Indexed: 01/01/2023] Open
Abstract
Epigenetic changes are well-established contributors to cancer progression and normal developmental processes. The reversible modification of histones plays a central role in regulating the nuclear processes of gene transcription, DNA replication, and DNA repair. The KDM4 family of Jumonj domain histone demethylases specifically target di- and tri-methylated lysine 9 on histone H3 (H3K9me3), removing a modification central to defining heterochromatin and gene repression. KDM4 enzymes are generally over-expressed in cancers, making them compelling targets for study and therapeutic inhibition. One of these family members, KDM4B, is especially interesting due to its regulation by multiple cellular stimuli, including DNA damage, steroid hormones, and hypoxia. In this review, we discuss what is known about the regulation of KDM4B in response to the cellular environment, and how this context-dependent expression may be translated into specific biological consequences in cancer and reproductive biology.
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Affiliation(s)
- Cailin Wilson
- Department of Pathology, University of Kansas Medical Center, Kansas City, KS 66160, USA.
| | - Adam J Krieg
- Department of Obstetrics and Gynecology, Oregon Health and Science University, Portland, OR 97239, USA.
- Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Beaverton, OR 97006, USA.
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23
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Fan D, Wang X, Tang X, Ye X, Ren S, Wang D, Luo K. Histone H3K9 demethylase JMJ25 epigenetically modulates anthocyanin biosynthesis in poplar. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 96:1121-1136. [PMID: 30218582 DOI: 10.1111/tpj.14092] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 07/26/2018] [Accepted: 09/06/2018] [Indexed: 05/20/2023]
Abstract
Anthocyanins are involved in several aspects of development and defence in poplar (Populus spp.). Although, over the past decades, significant progress has been made in uncovering these anthocyanin biosynthetic and regulatory mechanisms, the fundamental understanding of the epigenetic regulation in this pathway is still largely unclear. Here, we isolated a histone H3K9 demethylase gene JMJ25 from Populus and characterized its role in anthocyanin biosynthesis by genetic and biochemical approaches. JMJ25 was induced by continuous dark treatment. Overexpression of JMJ25 led to downregulated expression of anthocyanin biosynthetic genes in transgenic poplar, resulting in a significant reduction in anthocyanin content. ChIP-qPCR assays showed that JMJ25 could directly associate with MYB182 chromatin and dynamically demethylate at H3K9me2. Furthermore, JMJ25 also affected the DNA methylation levels of MYB182. By contrast, knockout of JMJ25 by CRISPR/Cas9 resulted in ectopic anthocyanin accumulation under dark condition and increased expression of anthocyanin biosynthetic genes. Our results support a model in which JMJ25 directly affects MYB182 expression by altering the histone methylation status of its chromatin and DNA methylation, resulting in repression of anthocyanin accumulation. This study uncovered an epigenetic mechanism that modulates anthocyanin biosynthesis in poplar.
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Affiliation(s)
- Di Fan
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xianqiang Wang
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xiaofeng Tang
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Xiao Ye
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Sha Ren
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Denghui Wang
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China
| | - Keming Luo
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, Chongqing Key Laboratory of Transgenic Plant and Safety Control, Institute of Resources Botany, School of Life Sciences, Southwest University, Chongqing, 400715, China
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24
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Varma P, Mishra RK. Little imaginal discs, a Trithorax group member, is a constituent of nuclear matrix of Drosophila melanogaster embryos. J Biosci 2018; 43:621-633. [PMID: 30207309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nuclear Matrix (NuMat) is the structural and functional framework of the nucleus. It has been shown that attachment of chromatin to NuMat brings significant regulation of the transcriptional activity of particular genes; however, key components of NuMat involved in this process remain elusive. We have identified Lid (Little imaginal discs) as one of the components of NuMat. It belongs to the TrxG group of proteins involved in activation of important developmental genes. However, unlike other activator proteins of TrxG, Lid is a Jumonji protein involved in H3K4me3 demethylation. Here, we report the association of Lid and its various domains with NuMat which implicates its structural role in chromatin organization and epigenetic basis of cellular memory. We have found that both N and C terminal regions of this protein are capable of associating with NuMat. We have further mapped the association of individual domains and found that, PHD, ARID and JmjC domains can associate with NuMat individually. Moreover, deletion of N-terminal PHD finger does not alter Lid's NuMat association implying that although it is sufficient, yet, it is not necessary for Lid's structural role in NuMat. Based on our findings, we hypothesize that C terminal region of Lid which contains PHD fingers might be responsible for its NuMat association via protein-DNA interactions. However, for the N terminal region harboring both a PHD and an ARID finger, Lid anchors to the NuMat via both protein-protein and protein-DNA interactions. The association of JmjC domain with NuMat is the first report of the association of a demethylase domain with NuMat suggesting that Lid, a demethylase, being part of NuMat might be involved in regulating the chromatin dynamics via its NuMat association.
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Affiliation(s)
- Parul Varma
- CSIR - Center for Cellular and Molecular Biology, Hyderabad 500 007, India
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25
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Little imaginal discs, a Trithorax group member, is a constituent of nuclear matrix of Drosophila melanogaster embryos. J Biosci 2018. [DOI: 10.1007/s12038-018-9773-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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26
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Lin H, Li Q, Li Q, Zhu J, Gu K, Jiang X, Hu Q, Feng F, Qu W, Chen Y, Sun H. Small molecule KDM4s inhibitors as anti-cancer agents. J Enzyme Inhib Med Chem 2018; 33:777-793. [PMID: 29651880 PMCID: PMC6010108 DOI: 10.1080/14756366.2018.1455676] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Histone demethylation is a vital process in epigenetic regulation of gene expression. A number of histone demethylases are present to control the methylated states of histone. Among these enzymes, KDM4s are one subfamily of JmjC KDMs and play important roles in both normal and cancer cells. The discovery of KDM4s inhibitors is a potential therapeutic strategy against different diseases including cancer. Here, we summarize the development of KDM4s inhibitors and some related pharmaceutical information to provide an update of recent progress in KDM4s inhibitors.
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Affiliation(s)
- Hongzhi Lin
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Qihang Li
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Qi Li
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Jie Zhu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Kai Gu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Xueyang Jiang
- b Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Qianqian Hu
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Feng Feng
- b Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Wei Qu
- b Department of Natural Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
| | - Yao Chen
- c School of Pharmacy , Nanjing University of Chinese Medicine , Nanjing , China
| | - Haopeng Sun
- a Department of Medicinal Chemistry , China Pharmaceutical University , Nanjing , China
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27
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Zucconi BE, Cole PA. Allosteric regulation of epigenetic modifying enzymes. Curr Opin Chem Biol 2017; 39:109-115. [PMID: 28689145 DOI: 10.1016/j.cbpa.2017.05.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 05/29/2017] [Indexed: 12/14/2022]
Abstract
Epigenetic enzymes including histone modifying enzymes are key regulators of gene expression in normal and disease processes. Many drug development strategies to target histone modifying enzymes have focused on ligands that bind to enzyme active sites, but allosteric pockets offer potentially attractive opportunities for therapeutic development. Recent biochemical studies have revealed roles for small molecule and peptide ligands binding outside of the active sites in modulating the catalytic activities of histone modifying enzymes. Here we highlight several examples of allosteric regulation of epigenetic enzymes and discuss the biological significance of these findings.
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Affiliation(s)
- Beth E Zucconi
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA.
| | - Philip A Cole
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA.
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28
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Han Y, Li X, Cheng L, Liu Y, Wang H, Ke D, Yuan H, Zhang L, Wang L. Genome-Wide Analysis of Soybean JmjC Domain-Containing Proteins Suggests Evolutionary Conservation Following Whole-Genome Duplication. FRONTIERS IN PLANT SCIENCE 2016; 7:1800. [PMID: 27994610 PMCID: PMC5136575 DOI: 10.3389/fpls.2016.01800] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2016] [Accepted: 11/15/2016] [Indexed: 05/24/2023]
Abstract
Histone modifications, such as methylation and demethylation, play an important role in regulating chromatin structure and gene expression. The JmjC domain-containing proteins, an important family of histone lysine demethylases (KDMs), play a key role in maintaining homeostasis of histone methylation in vivo. In this study, we performed a comprehensive analysis of the jumonji C (JmjC) gene family in the soybean genome and identified 48 JmjC genes (GmJMJs) distributed unevenly across 18 chromosomes. Phylogenetic analysis showed that these JmjC domain-containing genes can be divided into eight groups. GmJMJs within the same phylogenetic group share similar exon/intron organization and domain composition. In addition, 16 duplicated gene pairs were formed by a Glycine-specific whole-genome duplication (WGD) event approximately 13 million years ago (Mya). By investigating the expression profiles of these gene pairs in various tissues, we showed that the expression pattern is conserved in the polyploidy-derived JmjC duplicates, demonstrating that the majority of GmJMJs were preferentially retained after the most recent WGD event and suggesting important roles for demethylase duplications in soybean evolution. These results shed light on the evolutionary history of this family in soybean and provide insights into the JmjCs which will be helpful to reveal their functions in controlling soybean development.
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Affiliation(s)
- Yapeng Han
- College of Life Sciences, Xinyang Normal UniversityXinyang, China
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal UniversityXinyang, China
| | - Xiangyong Li
- College of Life Sciences, Xinyang Normal UniversityXinyang, China
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal UniversityXinyang, China
| | - Lin Cheng
- College of Life Sciences, Xinyang Normal UniversityXinyang, China
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal UniversityXinyang, China
| | - Yanchun Liu
- College of Life Sciences, Xinyang Normal UniversityXinyang, China
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal UniversityXinyang, China
| | - Hui Wang
- College of Life Sciences, Xinyang Normal UniversityXinyang, China
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal UniversityXinyang, China
| | - Danxia Ke
- College of Life Sciences, Xinyang Normal UniversityXinyang, China
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal UniversityXinyang, China
| | - Hongyu Yuan
- College of Life Sciences, Xinyang Normal UniversityXinyang, China
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal UniversityXinyang, China
| | - Liangsheng Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityFuzhou, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps (Fujian Agriculture and Forestry University), Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Lei Wang
- College of Life Sciences, Xinyang Normal UniversityXinyang, China
- Institute for Conservation and Utilization of Agro-bioresources in Dabie Mountains, Xinyang Normal UniversityXinyang, China
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29
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30
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Blair LP, Liu Z, Labitigan RLD, Wu L, Zheng D, Xia Z, Pearson EL, Nazeer FI, Cao J, Lang SM, Rines RJ, Mackintosh SG, Moore CL, Li W, Tian B, Tackett AJ, Yan Q. KDM5 lysine demethylases are involved in maintenance of 3'UTR length. SCIENCE ADVANCES 2016; 2:e1501662. [PMID: 28138513 PMCID: PMC5262454 DOI: 10.1126/sciadv.1501662] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 10/20/2016] [Indexed: 06/06/2023]
Abstract
The complexity by which cells regulate gene and protein expression is multifaceted and intricate. Regulation of 3' untranslated region (UTR) processing of mRNA has been shown to play a critical role in development and disease. However, the process by which cells select alternative mRNA forms is not well understood. We discovered that the Saccharomyces cerevisiae lysine demethylase, Jhd2 (also known as KDM5), recruits 3'UTR processing machinery and promotes alteration of 3'UTR length for some genes in a demethylase-dependent manner. Interaction of Jhd2 with both chromatin and RNA suggests that Jhd2 affects selection of polyadenylation sites through a transcription-coupled mechanism. Furthermore, its mammalian homolog KDM5B (also known as JARID1B or PLU1), but not KDM5A (also known as JARID1A or RBP2), promotes shortening of CCND1 transcript in breast cancer cells. Consistent with these results, KDM5B expression correlates with shortened CCND1 in human breast tumor tissues. In contrast, both KDM5A and KDM5B are involved in the lengthening of DICER1. Our findings suggest both a novel role for this family of demethylases and a novel targetable mechanism for 3'UTR processing.
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Affiliation(s)
- Lauren P. Blair
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Zongzhi Liu
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | | | - Lizhen Wu
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Dinghai Zheng
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Zheng Xia
- Division of Biostatistics, Dan L Duncan Comprehensive Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Erica L. Pearson
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Fathima I. Nazeer
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Jian Cao
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Sabine M. Lang
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Rachel J. Rines
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Samuel G. Mackintosh
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72032, USA
| | - Claire L. Moore
- Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, MA 02111, USA
| | - Wei Li
- Division of Biostatistics, Dan L Duncan Comprehensive Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bin Tian
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ 07103, USA
| | - Alan J. Tackett
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72032, USA
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
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31
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Peng Y, Alexov E. Cofactors-loaded quaternary structure of lysine-specific demethylase 5C (KDM5C) protein: Computational model. Proteins 2016; 84:1797-1809. [PMID: 27696497 DOI: 10.1002/prot.25162] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 09/02/2016] [Accepted: 09/06/2016] [Indexed: 12/13/2022]
Abstract
The KDM5C gene (also known as JARID1C and SMCX) is located on the X chromosome and encodes a ubiquitously expressed 1560-aa protein, which plays an important role in lysine methylation (specifically reverses tri- and di-methylation of Lys4 of histone H3). Currently, 13 missense mutations in KDM5C have been linked to X-linked mental retardation. However, the molecular mechanism of disease is currently unknown due to the experimental difficulties in expressing such large protein and the lack of experimental 3D structure. In this work, we utilize homology modeling, docking, and experimental data to predict 3D structures of KDM5C domains and their mutual arrangement. The resulting quaternary structure includes KDM5C JmjN, ARID, PHD1, JmjC, ZF domains, substrate histone peptide, enzymatic cofactors, and DNA. The predicted quaternary structure was investigated with molecular dynamic simulation for its stability, and further analysis was carried out to identify features measured experimentally. The predicted structure of KDM5C was used to investigate the effects of disease-causing mutations and it was shown that the mutations alter domain stability and inter-domain interactions. The structural model reported in this work could prompt experimental investigations of KDM5C domain-domain interaction and exploration of undiscovered functionalities. Proteins 2016; 84:1797-1809. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Yunhui Peng
- Department of Physics and Astronomy, Computational Biophysics and Bioinformatics, Clemson University, Clemson, South Carolina, 29634
| | - Emil Alexov
- Department of Physics and Astronomy, Computational Biophysics and Bioinformatics, Clemson University, Clemson, South Carolina, 29634
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32
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Ramakrishnan S, Pokhrel S, Palani S, Pflueger C, Parnell TJ, Cairns BR, Bhaskara S, Chandrasekharan MB. Counteracting H3K4 methylation modulators Set1 and Jhd2 co-regulate chromatin dynamics and gene transcription. Nat Commun 2016; 7:11949. [PMID: 27325136 PMCID: PMC4919544 DOI: 10.1038/ncomms11949] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 05/17/2016] [Indexed: 02/03/2023] Open
Abstract
Histone H3K4 methylation is connected to gene transcription from yeast to humans, but its mechanistic roles in transcription and chromatin dynamics remain poorly understood. We investigated the functions for Set1 and Jhd2, the sole H3K4 methyltransferase and H3K4 demethylase, respectively, in S. cerevisiae. Here, we show that Set1 and Jhd2 predominantly co-regulate genome-wide transcription. We find combined activities of Set1 and Jhd2 via H3K4 methylation contribute to positive or negative transcriptional regulation. Providing mechanistic insights, our data reveal that Set1 and Jhd2 together control nucleosomal turnover and occupancy during transcriptional co-regulation. Moreover, we find a genome-wide co-regulation of chromatin structure by Set1 and Jhd2 at different groups of transcriptionally active or inactive genes and at different regions within yeast genes. Overall, our study puts forth a model wherein combined actions of Set1 and Jhd2 via modulating H3K4 methylation-demethylation together control chromatin dynamics during various facets of transcriptional regulation.
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Affiliation(s)
- Saravanan Ramakrishnan
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Srijana Pokhrel
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Sowmiya Palani
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Christian Pflueger
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.,Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Timothy J Parnell
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.,Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Bradley R Cairns
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.,Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Srividya Bhaskara
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.,Department of Oncological Sciences, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Mahesh B Chandrasekharan
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA.,Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
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33
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Slama P. Identification of family determining residues in Jumonji-C lysine demethylases: A sequence-based, family wide classification. Proteins 2016; 84:397-407. [PMID: 26757344 PMCID: PMC4755873 DOI: 10.1002/prot.24986] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/31/2015] [Accepted: 01/04/2016] [Indexed: 12/12/2022]
Abstract
Histone post-translational modifications play a critical role in the regulation of gene expression. Methylation of lysines at N-terminal tails of histones has been shown to be involved in such regulation. While this modification was long considered to be irreversible, two different classes of enzymes capable of carrying out the demethylation of histone lysines were recently identified: the oxidases, such as LSD1, and the oxygenases (JmjC-containing). Here, a family-wide analysis of the second of these classes is proposed, with over 300 proteins studied at the sequence level. We show that a correlated evolution analysis yields some position/residue pairs which are critical at comparing JmjC sequences and enables the classification of JmjC domains into five families. A few positions appear more frequently among conditions, such as positions 23 (directly C-terminal to the second iron ligand), 24, 252 and 253 (directly N-terminal to a conserved Asn). Implications of family conditions are studied in detail on PHF2, revealing the meaningfulness of the sequence-derived conditions at the structural level. These results should help obtain insights on the diversity of JmjC-containing proteins solely by considering some of the amino acids present in their JmjC domain.
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Affiliation(s)
- Patrick Slama
- Center for Imaging Science, Institute for Computational Medicine, The Johns Hopkins University, Baltimore, Maryland
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Mutations in the KDM5C ARID Domain and Their Plausible Association with Syndromic Claes-Jensen-Type Disease. Int J Mol Sci 2015; 16:27270-87. [PMID: 26580603 PMCID: PMC4661880 DOI: 10.3390/ijms161126022] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Revised: 11/01/2015] [Accepted: 11/04/2015] [Indexed: 11/30/2022] Open
Abstract
Mutations in KDM5C gene are linked to X-linked mental retardation, the syndromic Claes-Jensen-type disease. This study focuses on non-synonymous mutations in the KDM5C ARID domain and evaluates the effects of two disease-associated missense mutations (A77T and D87G) and three not-yet-classified missense mutations (R108W, N142S, and R179H). We predict the ARID domain’s folding and binding free energy changes due to mutations, and also study the effects of mutations on protein dynamics. Our computational results indicate that A77T and D87G mutants have minimal effect on the KDM5C ARID domain stability and DNA binding. In parallel, the change in the free energy unfolding caused by the mutants A77T and D87G were experimentally measured by urea-induced unfolding experiments and were shown to be similar to the in silico predictions. The evolutionary conservation analysis shows that the disease-associated mutations are located in a highly-conserved part of the ARID structure (N-terminal domain), indicating their importance for the KDM5C function. N-terminal residues’ high conservation suggests that either the ARID domain utilizes the N-terminal to interact with other KDM5C domains or the N-terminal is involved in some yet unknown function. The analysis indicates that, among the non-classified mutations, R108W is possibly a disease-associated mutation, while N142S and R179H are probably harmless.
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Huang F, Ramakrishnan S, Pokhrel S, Pflueger C, Parnell TJ, Kasten MM, Currie SL, Bhachech N, Horikoshi M, Graves BJ, Cairns BR, Bhaskara S, Chandrasekharan MB. Interaction of the Jhd2 Histone H3 Lys-4 Demethylase with Chromatin Is Controlled by Histone H2A Surfaces and Restricted by H2B Ubiquitination. J Biol Chem 2015; 290:28760-77. [PMID: 26451043 DOI: 10.1074/jbc.m115.693085] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Indexed: 11/06/2022] Open
Abstract
Histone H3 lysine 4 (H3K4) methylation is a dynamic modification. In budding yeast, H3K4 methylation is catalyzed by the Set1-COMPASS methyltransferase complex and is removed by Jhd2, a JMJC domain family demethylase. The catalytic JmjC and JmjN domains of Jhd2 have the ability to remove all three degrees (mono-, di-, and tri-) of H3K4 methylation. Jhd2 also contains a plant homeodomain (PHD) finger required for its chromatin association and H3K4 demethylase functions. The Jhd2 PHD finger associates with chromatin independent of H3K4 methylation and the H3 N-terminal tail. Therefore, how Jhd2 associates with chromatin to perform H3K4 demethylation has remained unknown. We report a novel interaction between the Jhd2 PHD finger and histone H2A. Two residues in H2A (Phe-26 and Glu-57) serve as a binding site for Jhd2 in vitro and mediate its chromatin association and H3K4 demethylase functions in vivo. Using RNA sequencing, we have identified the functional target genes for Jhd2 and the H2A Phe-26 and Glu-57 residues. We demonstrate that H2A Phe-26 and Glu-57 residues control chromatin association and H3K4 demethylase functions of Jhd2 during positive or negative regulation of transcription at target genes. Importantly, we show that H2B Lys-123 ubiquitination blocks Jhd2 from accessing its binding site on chromatin, and thereby, we have uncovered a second mechanism by which H2B ubiquitination contributes to the trans-histone regulation of H3K4 methylation. Overall, our study provides novel insights into the chromatin binding dynamics and H3K4 demethylase functions of Jhd2.
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Affiliation(s)
- Fu Huang
- the Stowers Institute for Medical Research, Kansas City, Missouri 64110, and
| | - Saravanan Ramakrishnan
- From the Departments of Radiation Oncology and the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112
| | - Srijana Pokhrel
- From the Departments of Radiation Oncology and the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112
| | - Christian Pflueger
- the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, Oncological Sciences and
| | - Timothy J Parnell
- the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112
| | - Margaret M Kasten
- the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, Oncological Sciences and
| | - Simon L Currie
- the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, Oncological Sciences and
| | - Niraja Bhachech
- the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, Oncological Sciences and
| | - Masami Horikoshi
- the Laboratory of Developmental Biology, Institute of Molecular and Cellular Biosciences, University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Barbara J Graves
- the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, Oncological Sciences and
| | - Bradley R Cairns
- the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, Oncological Sciences and
| | - Srividya Bhaskara
- From the Departments of Radiation Oncology and the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, Oncological Sciences and
| | - Mahesh B Chandrasekharan
- From the Departments of Radiation Oncology and the Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112,
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Huang Y, Chen D, Liu C, Shen W, Ruan Y. Evolution and conservation of JmjC domain proteins in the green lineage. Mol Genet Genomics 2015; 291:33-49. [PMID: 26152513 DOI: 10.1007/s00438-015-1089-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/29/2015] [Indexed: 10/25/2022]
Abstract
Histone modification regulates plant development events by epigenetically silencing or activating gene expression, and histone methylation is regulated by histone lysine methyltransferases (KMTs) and histone lysine demethylases (KDMs). The JmjC domain proteins, an important KDM family, erase methyl marks (CH3-) from histones and play key roles in maintaining homeostasis of histone methylation in vivo. Here, we analyzed 169 JmjC domain proteins from whole genomes of plants ranging from green alga to higher plants together with 36 from two animals (fruit fly and human). The plant JmjC domain proteins were divided into seven groups. Group-I KDM4/JHDM3 and Group-V JMJD6 were found in all the plant species and the other groups were detected mainly in vascular or seed plants. Group-I KDM4/JHDM3 was potentially associated with demethylation of H3K9me2/3, H3K27me2/3, and H3K36me1/2/3, Group-II KDM5A with H3K4me1/2/3, Group-III KDM5B with H3K4me1/2/3 and H3K9me1/2/3, Group-V JMJD6 with H3R2, H4R3, and hydroxylation of H4, and Group-VII KDM3/JHDM2 with H3K9me1/2/3. Group-IV/Group-VI JmjC domain-only A/B proteins were involved in hydroxylation and demethylation of unknown substrate sites. The binding sites for the cofactors Fe(II) and α-ketoglutarate in the JmjC domains also were analyzed. In the α-ketoglutarate binding sites, Thr/Phe/Ser and Lys were conserved and in the Fe(II) binding sites, two His and Glu/Asp were conserved. The results show that JmjC domain proteins are a conserved family in which domain organization and cofactor binding sites have been modified in some species. Our results provide insights into KDM evolution and lay a foundation for functional characterization of KDMs.
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Affiliation(s)
- Yong Huang
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, 410128, Changsha, China. .,Key Laboratory of Education, Department of Hunan Province On Plant Genetics and Molecular Biology, Hunan Agricultural University, 410128, Changsha, China.
| | - Donghong Chen
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, 410128, Changsha, China.,Key Laboratory of Education, Department of Hunan Province On Plant Genetics and Molecular Biology, Hunan Agricultural University, 410128, Changsha, China
| | - Chunlin Liu
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, 410128, Changsha, China
| | - Wenhui Shen
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, 410128, Changsha, China.,Institut de Biologie Moléculaire Des Plantes Du CNRS, Université de Strasbourg, 12 Rue Du Général Zimmer, 67084, Strasbourg Cedex, France
| | - Ying Ruan
- College of Bioscience and Biotechnology, International Associated Laboratory of CNRS-FU-HAU On Plant Epigenome Research, Hunan Agricultural University, 410128, Changsha, China. .,Key Laboratory of Education, Department of Hunan Province On Plant Genetics and Molecular Biology, Hunan Agricultural University, 410128, Changsha, China. .,Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Agricultural University, 410128, Changsha, China.
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Torres IO, Kuchenbecker KM, Nnadi CI, Fletterick RJ, Kelly MJS, Fujimori DG. Histone demethylase KDM5A is regulated by its reader domain through a positive-feedback mechanism. Nat Commun 2015; 6:6204. [PMID: 25686748 DOI: 10.1038/ncomms7204] [Citation(s) in RCA: 90] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Accepted: 01/05/2015] [Indexed: 12/13/2022] Open
Abstract
The retinoblastoma binding protein KDM5A removes methyl marks from lysine 4 of histone H3 (H3K4). Misregulation of KDM5A contributes to the pathogenesis of lung and gastric cancers. In addition to its catalytic jumonji C domain, KDM5A contains three PHD reader domains, commonly recognized as chromatin recruitment modules. It is unknown whether any of these domains in KDM5A have functions beyond recruitment and whether they regulate the catalytic activity of the demethylase. Here using biochemical and nuclear magnetic resonance (NMR)-based structural studies, we show that the PHD1 preferentially recognizes unmethylated H3K4 histone tail, product of KDM5A-mediated demethylation of tri-methylated H3K4 (H3K4me3). Binding of unmodified H3 peptide to the PHD1 stimulates catalytic domain-mediated removal of methyl marks from H3K4me3 peptide and nucleosome substrates. This positive-feedback mechanism--enabled by the functional coupling between a reader and a catalytic domain in KDM5A--suggests a model for the spread of demethylation on chromatin.
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Affiliation(s)
- Idelisse Ortiz Torres
- 1] Department of Cellular and Molecular Pharmacology, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA [2] Chemistry and Chemical Biology Graduate Program, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA
| | - Kristopher M Kuchenbecker
- 1] Department of Biochemistry and Biophysics, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA [2] Biophysics Graduate Program, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA
| | - Chimno I Nnadi
- 1] Department of Cellular and Molecular Pharmacology, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA [2] Chemistry and Chemical Biology Graduate Program, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA [3] UCSF Medical Scientist Training Program, University of California, 513 Parnassus Avenue, San Francisco, California 94143, USA
| | - Robert J Fletterick
- Department of Biochemistry and Biophysics, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA
| | - Mark J S Kelly
- Department of Pharmaceutical Chemistry, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA
| | - Danica Galonić Fujimori
- 1] Department of Cellular and Molecular Pharmacology, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA [2] Department of Pharmaceutical Chemistry, University of California, 600 16th Street, Genentech Hall, San Francisco, California 94158, USA
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38
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Brookes E, Laurent B, Õunap K, Carroll R, Moeschler JB, Field M, Schwartz CE, Gecz J, Shi Y. Mutations in the intellectual disability gene KDM5C reduce protein stability and demethylase activity. Hum Mol Genet 2015; 24:2861-72. [PMID: 25666439 DOI: 10.1093/hmg/ddv046] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 02/02/2015] [Indexed: 01/03/2023] Open
Abstract
Mutations in KDM5C are an important cause of X-linked intellectual disability in males. KDM5C encodes a histone demethylase, suggesting that alterations in chromatin landscape may contribute to disease. We used primary patient cells and biochemical approaches to investigate the effects of patient mutations on KDM5C expression, stability and catalytic activity. We report and characterize a novel nonsense mutation, c.3223delG (p.V1075Yfs*2), which leads to loss of KDM5C protein. We also characterize two KDM5C missense mutations, c.1439C>T (p.P480L) and c.1204G>T (p.D402Y) that are compatible with protein production, but compromise stability and enzymatic activity. Finally, we demonstrate that a c.2T>C mutation in the translation initiation codon of KDM5C results in translation re-start and production of a N-terminally truncated protein (p.M1_E165del) that is unstable and lacks detectable demethylase activity. Patient fibroblasts do not show global changes in histone methylation but we identify several up-regulated genes, suggesting local changes in chromatin conformation and gene expression. This thorough examination of KDM5C patient mutations demonstrates the utility of examining the molecular consequences of patient mutations on several levels, ranging from enzyme production to catalytic activity, when assessing the functional outcomes of intellectual disability mutations.
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Affiliation(s)
- Emily Brookes
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA, Division of Newborn Medicine, Boston Children's Hospital, MA 02115, USA
| | - Benoit Laurent
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA, Division of Newborn Medicine, Boston Children's Hospital, MA 02115, USA
| | - Katrin Õunap
- Department of Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia, Department of Pediatrics, University of Tartu, Tartu, Estonia
| | - Renee Carroll
- School of Paediatrics and Reproductive Health and Robinson Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - John B Moeschler
- Department of Pediatrics, Geisel School of Medicine, Lebanon, NH 03756, USA
| | | | - Charles E Schwartz
- JC Self Research Institute, Greenwood Genetic Center, Greenwood, SC 29646, USA
| | - Jozef Gecz
- School of Paediatrics and Reproductive Health and Robinson Institute, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Yang Shi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA, Division of Newborn Medicine, Boston Children's Hospital, MA 02115, USA,
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39
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Harmeyer KM, South PF, Bishop B, Ogas J, Briggs SD. Immediate chromatin immunoprecipitation and on-bead quantitative PCR analysis: a versatile and rapid ChIP procedure. Nucleic Acids Res 2014; 43:e38. [PMID: 25539918 PMCID: PMC4381045 DOI: 10.1093/nar/gku1347] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 12/15/2014] [Indexed: 12/12/2022] Open
Abstract
Genome-wide chromatin immunoprecipitation (ChIP) studies have brought significant insight into the genomic localization of chromatin-associated proteins and histone modifications. The large amount of data generated by these analyses, however, require approaches that enable rapid validation and analysis of biological relevance. Furthermore, there are still protein and modification targets that are difficult to detect using standard ChIP methods. To address these issues, we developed an immediate chromatin immunoprecipitation procedure which we call ZipChip. ZipChip significantly reduces the time and increases sensitivity allowing for rapid screening of multiple loci. Here we describe how ZipChIP enables detection of histone modifications (H3K4 mono- and trimethylation) and two yeast histone demethylases, Jhd2 and Rph1, which were previously difficult to detect using standard methods. Furthermore, we demonstrate the versatility of ZipChIP by analyzing the enrichment of the histone deacetylase Sir2 at heterochromatin in yeast and enrichment of the chromatin remodeler, PICKLE, at euchromatin in Arabidopsis thaliana.
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Affiliation(s)
- Kayla M Harmeyer
- Department of Biochemistry and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Paul F South
- Department of Biochemistry and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Brett Bishop
- Department of Biochemistry and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Joe Ogas
- Department of Biochemistry and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Scott D Briggs
- Department of Biochemistry and Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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40
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Ryu HY, Ahn S. Yeast histone H3 lysine 4 demethylase Jhd2 regulates mitotic rDNA condensation. BMC Biol 2014; 12:75. [PMID: 25248920 PMCID: PMC4201760 DOI: 10.1186/s12915-014-0075-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Indexed: 11/24/2022] Open
Abstract
Background Nucleolar ribosomal DNA is tightly associated with silent heterochromatin, which is important for rDNA stability, nucleolar integration and cellular senescence. Two pathways have been described that lead to rDNA silencing in yeast: 1) the RENT (regulator of nucleolar silencing and telophase exit) complex, which is composed of Net1, Sir2 and Cdc14 and is required for Sir2-dependent rDNA silencing; and 2) the Sir2-independent silencing mechanism, which involves the Tof2 and Tof2-copurified complex, made up of Lrs4 and Csm1. Here, we present evidence that changes in histone H3 lysine methylation levels distinctly regulate rDNA silencing by recruiting different silencing proteins to rDNA, thereby contributing to rDNA silencing and nucleolar organization in yeast. Results We found that Lys4, Lys79 and Lys36 methylation within histone H3 acts as a bivalent marker for the regulation of rDNA recombination and RENT complex-mediated rDNA silencing, both of which are Sir2-dependent pathways. By contrast, we found that Jhd2, an evolutionarily conserved JARID1 family H3 Lys4 demethylase, affects all states of methylated H3K4 within the nontranscribed spacer (NTS) regions of rDNA and that its activity is required for the regulation of rDNA silencing in a Sir2-independent manner. In this context, Jhd2 regulates rDNA recombination through the Tof2/Csm1/Lrs4 pathway and prevents excessive recruitment of Tof2, Csm1/Lrs4 and condensin subunits to the replication fork barrier site within the NTS1 region. Our FISH analyses further demonstrate that the demethylase activity of Jhd2 regulates mitotic rDNA condensation and that JHD2-deficient cells contain the mostly hypercondensed rDNA mislocalized away from the nuclear periphery. Conclusions Our results show that yeast Jhd2, which demethylates histone H3 Lys4 near the rDNA locus, regulates rDNA repeat stability and rDNA silencing in a Sir2-independent manner by maintaining Csm1/Lrs4 and condensin association with rDNA regions during mitosis. These data suggest that Jhd2-mediated alleviation of excessive Csm1/Lrs4 or condensin at the NTS1 region of rDNA is required for the integrity of rDNA repeats and proper rDNA silencing during mitosis. Electronic supplementary material The online version of this article (doi:10.1186/s12915-014-0075-3) contains supplementary material, which is available to authorized users.
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The histone demethylase activity of Rph1 is not essential for its role in the transcriptional response to nutrient signaling. PLoS One 2014; 9:e95078. [PMID: 24999627 PMCID: PMC4085034 DOI: 10.1371/journal.pone.0095078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 03/21/2014] [Indexed: 12/22/2022] Open
Abstract
Rph1 and Gis1 are two related yeast zinc finger proteins that function as downstream effectors in the Ras/PKA, TOR and Sch9 nutrient signaling pathways. Both proteins also contain JmjC histone demethylase domains, but only Rph1 is known to be an active enzyme, demethylating lysine 36 of histone H3. We have studied to what extent the demethylase activity of Rph1 contributes to its role in nutrient signaling by performing gene expression microarray experiments on a yeast strain containing a catalytically inactive allele of RPH1. We find that the enzymatic activity of Rph1 is not essential for its role in growth phase dependent gene regulation. However, the ability of Rph1 to both activate and repress transcription is partially impaired in the active site mutant, indicating that the demethylase activity may enhance its function in vivo. Consistent with this, we find that the Rph1 mutation and a deletion of the histone H3 methylase Set2 affect the same target genes in opposite directions. Genes that are differentially expressed in the Rph1 mutant are also enriched for binding of Rpd3, a downstream effector in silencing, to their promoters. The expression of some subtelomeric genes and genes involved in sporulation and meiosis are also affected by the mutation, suggesting a role for Rph1-dependent demethylation in regulating these genes. A small set of genes are more strongly affected by the active site mutation, indicating a more pronounced role for the demethylase activity in their regulation by Rph1.
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Abstract
Histone modifiers like acetyltransferases, methyltransferases, and demethylases are critical regulators of most DNA-based nuclear processes, de facto controlling cell cycle progression and cell fate. These enzymes perform very precise post-translational modifications on specific histone residues, which in turn are recognized by different effector modules/proteins. We now have a better understanding of how these enzymes exhibit such specificity. As they often reside in multisubunit complexes, they use associated factors to target their substrates within chromatin structure and select specific histone mark-bearing nucleosomes. In this review, we cover the current understanding of how histone modifiers select their histone targets. We also explain how different experimental approaches can lead to conflicting results about the histone specificity and function of these enzymes.
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Affiliation(s)
- Marie-Eve Lalonde
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Hôtel-Dieu de Québec, Quebec City, Quebec G1R 2J6, Canada
| | - Xue Cheng
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Hôtel-Dieu de Québec, Quebec City, Quebec G1R 2J6, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Centre de Recherche du CHU de Québec-Axe Oncologie, Hôtel-Dieu de Québec, Quebec City, Quebec G1R 2J6, Canada
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KDM5C mutational screening among males with intellectual disability suggestive of X-Linked inheritance and review of the literature. Eur J Med Genet 2014; 57:138-44. [PMID: 24583395 DOI: 10.1016/j.ejmg.2014.02.011] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2013] [Accepted: 02/17/2014] [Indexed: 01/18/2023]
Abstract
An increasing number of neurodevelopmental diseases have been associated with disruption of chromatin remodeling in eukaryotes. Lysine(K)-specific demethylase 5C (KDM5C) is a versatile epigenetic regulator that removes di- and tri-methyl groups of lysine 4 on histone H3 (H3K4) from transcriptional targets and is essential for neuronal survival and dendritic growth. Mutations in KDM5C gene, located at Xp11.22, have been reported as an important cause of both syndromic and non-syndromic X-linked intellectual disability (XLID) in males. The aim of this study was to evaluate the prevalence and spectrum of KDM5C mutations among Brazilian patients with XLID. To access the impact of KDM5C variants on XLID, a cohort of 143 males with a family history of intellectual disability (ID) suggestive of X-linked inheritance were enrolled. Common genetic causes of XLID were previously excluded and the entire coding and flanking intronic sequences of KDM5C gene were screened by direct Sanger sequencing. Seven nucleotide changes were observed: one pathogenic mutation (c.2172C>A, p.Cys724*), one novel variant with unknown value (c.633G>C, p.Arg211Arg) and five apparently benign sequence changes. In silico analysis of the variants revealed a putative creation of an Exonic Splicing Enhancer sequence by the silent c.633G>C mutation, which co-segregates with the ID phenotype. Our results point out to a KDM5C pathogenic mutational frequency of 0.7% among males with probable XLID. This is the first KDM5C screening among ID males from a country in Latin America and provides new clues about the significance of KDM5C mutations for genetic counseling.
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Lin C, Song W, Bi X, Zhao J, Huang Z, Li Z, Zhou J, Cai J, Zhao H. Recent advances in the ARID family: focusing on roles in human cancer. Onco Targets Ther 2014; 7:315-24. [PMID: 24570593 PMCID: PMC3933769 DOI: 10.2147/ott.s57023] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The human AT-rich interaction domain (ARID) family contains seven subfamilies and 15 members characterized by having an ARID. Members of the ARID family have the ability to regulate transcription and are involved in cell differentiation and proliferation. Accumulating evidence suggests that ARID family members are involved in cancer-related signaling pathways, highly mutated or differentially expressed in tumor tissues, and act as predictive factors for cancer prognosis or therapeutic outcome. Here we review the molecular biology and clinical studies concerned with the role played by the ARID family in cancer. This may contribute to our understanding of the initiation and progression of cancer from a novel point of view, as well as providing potential targets for cancer therapy.
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Affiliation(s)
- Chen Lin
- Department of Abdominal Surgical Oncology, Cancer Hospital, Beijing, People's Republic of China
| | - Wei Song
- National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Xinyu Bi
- Department of Abdominal Surgical Oncology, Cancer Hospital, Beijing, People's Republic of China
| | - Jianjun Zhao
- Department of Abdominal Surgical Oncology, Cancer Hospital, Beijing, People's Republic of China
| | - Zhen Huang
- Department of Abdominal Surgical Oncology, Cancer Hospital, Beijing, People's Republic of China
| | - Zhiyu Li
- Department of Abdominal Surgical Oncology, Cancer Hospital, Beijing, People's Republic of China
| | - Jianguo Zhou
- Department of Abdominal Surgical Oncology, Cancer Hospital, Beijing, People's Republic of China
| | - Jianqiang Cai
- Department of Abdominal Surgical Oncology, Cancer Hospital, Beijing, People's Republic of China
| | - Hong Zhao
- Department of Abdominal Surgical Oncology, Cancer Hospital, Beijing, People's Republic of China
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45
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Liang CY, Wang LC, Lo WS. Dissociation of the H3K36 demethylase Rph1 from chromatin mediates derepression of environmental stress-response genes under genotoxic stress in Saccharomyces cerevisiae. Mol Biol Cell 2013; 24:3251-62. [PMID: 23985319 PMCID: PMC3806659 DOI: 10.1091/mbc.e12-11-0820] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The H3K36 demethylase Rph1 is a transcriptional repressor for stress-responsive genes in yeast. Rph1-mediated transcriptional repression is relieved by phosphorylation of Rph1, reduced Rph1 level, and dissociation of Rph1 from chromatin with genotoxic stress. Rph1 may function as a regulatory node in different stress-signaling pathways. Cells respond to environmental signals by altering gene expression through transcription factors. Rph1 is a histone demethylase containing a Jumonji C (JmjC) domain and belongs to the C2H2 zinc-finger protein family. Here we investigate the regulatory network of Rph1 in yeast by expression microarray analysis. More than 75% of Rph1-regulated genes showed increased expression in the rph1-deletion mutant, suggesting that Rph1 is mainly a transcriptional repressor. The binding motif 5′-CCCCTWA-3′, which resembles the stress response element, is overrepresented in the promoters of Rph1-repressed genes. A significant proportion of Rph1-regulated genes respond to DNA damage and environmental stress. Rph1 is a labile protein, and Rad53 negatively modulates Rph1 protein level. We find that the JmjN domain is important in maintaining protein stability and the repressive effect of Rph1. Rph1 is directly associated with the promoter region of targeted genes and dissociated from chromatin before transcriptional derepression on DNA damage and oxidative stress. Of interest, the master stress-activated regulator Msn2 also regulates a subset of Rph1-repressed genes under oxidative stress. Our findings confirm the regulatory role of Rph1 as a transcriptional repressor and reveal that Rph1 might be a regulatory node connecting different signaling pathways responding to environmental stresses.
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Affiliation(s)
- Chung-Yi Liang
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan Institute of Biochemistry and Molecular Biology, College of Medicine, National Taiwan University, Taipei 10051, Taiwan
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Black JC, Van Rechem C, Whetstine JR. Histone lysine methylation dynamics: establishment, regulation, and biological impact. Mol Cell 2013. [PMID: 23200123 DOI: 10.1016/j.molcel.2012.11.006] [Citation(s) in RCA: 911] [Impact Index Per Article: 75.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Histone lysine methylation has emerged as a critical player in the regulation of gene expression, cell cycle, genome stability, and nuclear architecture. Over the past decade, a tremendous amount of progress has led to the characterization of methyl modifications and the lysine methyltransferases (KMTs) and lysine demethylases (KDMs) that regulate them. Here, we review the discovery and characterization of the KMTs and KDMs and the methyl modifications they regulate. We discuss the localization of the KMTs and KDMs as well as the distribution of lysine methylation throughout the genome. We highlight how these data have shaped our view of lysine methylation as a key determinant of complex chromatin states. Finally, we discuss the regulation of KMTs and KDMs by proteasomal degradation, posttranscriptional mechanisms, and metabolic status. We propose key questions for the field and highlight areas that we predict will yield exciting discoveries in the years to come.
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Affiliation(s)
- Joshua C Black
- Massachusetts General Hospital Cancer Center and Department of Medicine, Harvard Medical School, 13(th) Street, Charlestown, MA 02129, USA
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Grafodatskaya D, Chung BHY, Butcher DT, Turinsky AL, Goodman SJ, Choufani S, Chen YA, Lou Y, Zhao C, Rajendram R, Abidi FE, Skinner C, Stavropoulos J, Bondy CA, Hamilton J, Wodak S, Scherer SW, Schwartz CE, Weksberg R. Multilocus loss of DNA methylation in individuals with mutations in the histone H3 lysine 4 demethylase KDM5C. BMC Med Genomics 2013; 6:1. [PMID: 23356856 PMCID: PMC3573947 DOI: 10.1186/1755-8794-6-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 01/14/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND A number of neurodevelopmental syndromes are caused by mutations in genes encoding proteins that normally function in epigenetic regulation. Identification of epigenetic alterations occurring in these disorders could shed light on molecular pathways relevant to neurodevelopment. RESULTS Using a genome-wide approach, we identified genes with significant loss of DNA methylation in blood of males with intellectual disability and mutations in the X-linked KDM5C gene, encoding a histone H3 lysine 4 demethylase, in comparison to age/sex matched controls. Loss of DNA methylation in such individuals is consistent with known interactions between DNA methylation and H3 lysine 4 methylation. Further, loss of DNA methylation at the promoters of the three top candidate genes FBXL5, SCMH1, CACYBP was not observed in more than 900 population controls. We also found that DNA methylation at these three genes in blood correlated with dosage of KDM5C and its Y-linked homologue KDM5D. In addition, parallel sex-specific DNA methylation profiles in brain samples from control males and females were observed at FBXL5 and CACYBP. CONCLUSIONS We have, for the first time, identified epigenetic alterations in patient samples carrying a mutation in a gene involved in the regulation of histone modifications. These data support the concept that DNA methylation and H3 lysine 4 methylation are functionally interdependent. The data provide new insights into the molecular pathogenesis of intellectual disability. Further, our data suggest that some DNA methylation marks identified in blood can serve as biomarkers of epigenetic status in the brain.
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Affiliation(s)
- Daria Grafodatskaya
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Barian HY Chung
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, ON, Canada
- Centre of Reproduction, Growth & Development, Department of Pediatrics & Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Darci T Butcher
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Andrei L Turinsky
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada
| | - Sarah J Goodman
- Centre of Reproduction, Growth & Development, Department of Pediatrics & Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Sana Choufani
- Centre of Reproduction, Growth & Development, Department of Pediatrics & Adolescent Medicine, The University of Hong Kong, Hong Kong, Hong Kong
| | - Yi-An Chen
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Youliang Lou
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Chunhua Zhao
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Rageen Rajendram
- Genetics and Genome Biology Program, Hospital for Sick Children, Toronto, ON, Canada
| | - Fatima E Abidi
- J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC, USA
| | - Cindy Skinner
- J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC, USA
| | - James Stavropoulos
- Department of Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Carolyn A Bondy
- Developmental Endocrinology Branch, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jill Hamilton
- Division of Endocrinology, Department of Pediatrics, Hospital for Sick Children, Toronto, ON, Canada
- Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Shoshana Wodak
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, ON, Canada
| | - Stephen W Scherer
- Department of Molecular and Medical Genetics, University of Toronto, Toronto, ON, Canada
- The Centre for Applied Genomics, Hospital for Sick Children, Toronto, ON, Canada
| | - Charles E Schwartz
- J.C. Self Research Institute, Greenwood Genetic Center, Greenwood, SC, USA
| | - Rosanna Weksberg
- Division of Clinical and Metabolic Genetics, Hospital for Sick Children, Toronto, ON, Canada
- Department of Pediatrics, University of Toronto, Toronto, ON, Canada
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Reese JC. The control of elongation by the yeast Ccr4-not complex. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1829:127-33. [PMID: 22975735 PMCID: PMC3545033 DOI: 10.1016/j.bbagrm.2012.09.001] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2012] [Revised: 08/30/2012] [Accepted: 09/03/2012] [Indexed: 12/12/2022]
Abstract
The Ccr4-Not complex is a highly conserved nine-subunit protein complex that has been implicated in virtually all aspects of gene control, including transcription, mRNA decay and quality control, RNA export, translational repression and protein ubiquitylation. Understanding its mechanisms of action has been difficult due to the size of the complex and the fact that it regulates mRNAs and proteins at many levels in both the cytoplasm and the nucleus. Recently, biochemical and genetic studies on the yeast Ccr4-Not complex have revealed insights into its role in promoting elongation by RNA polymerase II. This review will describe what is known about the Ccr4-Not complex in regulating transcription elongation and its possible collaboration with other factors traveling with RNAPII across genes. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.
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Affiliation(s)
- Joseph C Reese
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA 16802, USA.
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Histone H3K4 demethylation is negatively regulated by histone H3 acetylation in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2012; 109:18505-10. [PMID: 23091032 DOI: 10.1073/pnas.1202070109] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Histone H3 lysine 4 trimethylation (H3K4me3) is a hallmark of transcription initiation, but how H3K4me3 is demethylated during gene repression is poorly understood. Jhd2, a JmjC domain protein, was recently identified as the major H3K4me3 histone demethylase (HDM) in Saccharomyces cerevisiae. Although JHD2 is required for removal of methylation upon gene repression, deletion of JHD2 does not result in increased levels of H3K4me3 in bulk histones, indicating that this HDM is unable to demethylate histones during steady-state conditions. In this study, we showed that this was due to the negative regulation of Jhd2 activity by histone H3 lysine 14 acetylation (H3K14ac), which colocalizes with H3K4me3 across the yeast genome. We demonstrated that loss of the histone H3-specific acetyltransferases (HATs) resulted in genome-wide depletion of H3K4me3, and this was not due to a transcription defect. Moreover, H3K4me3 levels were reestablished in HAT mutants following loss of JHD2, which suggested that H3-specific HATs and Jhd2 serve opposing functions in regulating H3K4me3 levels. We revealed the molecular basis for this suppression by demonstrating that H3K14ac negatively regulated Jhd2 demethylase activity on an acetylated peptide in vitro. These results revealed the existence of a general mechanism for removal of H3K4me3 following gene repression.
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50
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Koturbash I, Simpson NE, Beland FA, Pogribny IP. Alterations in histone H4 lysine 20 methylation: implications for cancer detection and prevention. Antioxid Redox Signal 2012; 17:365-74. [PMID: 22035019 DOI: 10.1089/ars.2011.4370] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
SIGNIFICANCE Cancer development and progression are associated with numerous genetic, epigenetic, and metabolic changes. RECENT ADVANCES A number of epigenetic aberrations have been characterized in cancer, including DNA methylation and various histone modification changes. One of the most unique and enigmatic epigenetic marks that is noticeably altered in several major human cancers is methylation of histone H4 lysine 20; however, there is insufficient knowledge of the underlying molecular mechanisms associated with this abberation. CRITICAL ISSUES This review presents current evidence of the role of histone H4 lysine 20 methylation in normal and cancer cells and during tumorigenesis induced by genotoxic and nongenotoxic carcinogens. Additionally, it describes molecular mechanisms that may cause this alteration and highlights the significance of this epigenetic mark as an early indicator of carcinogenesis. FUTURE DIRECTIONS Accumulating evidence suggests that dietary components may be significant regulators of the cellular epigenome, including histone methylation, by providing and maintaining the adequate levels of S-adenosyl-L-methionine, flavin adenine dinucleotide, α-ketoglutarate, and iron. Future research should elucidate the potential for modifying cellular metabolism through dietary intervention for timely regulation of the epigenome as means for the prevention of cancer development.
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Affiliation(s)
- Igor Koturbash
- Division of Biochemical Toxicology, National Center for Toxicological Research, Jefferson, Arkansas 72079, USA
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