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Brocato ER, Easter R, Morgan A, Kakani M, Lee G, Wolstenholme JT. Adolescent binge ethanol impacts H3K9me3-occupancy at synaptic genes and the regulation of oligodendrocyte development. Front Mol Neurosci 2024; 17:1389100. [PMID: 38840776 PMCID: PMC11150558 DOI: 10.3389/fnmol.2024.1389100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Accepted: 05/06/2024] [Indexed: 06/07/2024] Open
Abstract
Introduction Binge drinking in adolescence can disrupt myelination and cause brain structural changes that persist into adulthood. Alcohol consumption at a younger age increases the susceptibility of these changes. Animal models to understand ethanol's actions on myelin and white matter show that adolescent binge ethanol can alter the developmental trajectory of oligodendrocytes, myelin structure, and myelin fiber density. Oligodendrocyte differentiation is epigenetically regulated by H3K9 trimethylation (H3K9me3). Prior studies have shown that adolescent binge ethanol dysregulates H3K9 methylation and decreases H3K9-related gene expression in the PFC. Methods Here, we assessed ethanol-induced changes to H3K9me3 occupancy at genomic loci in the developing adolescent PFC. We further assessed ethanol-induced changes at the transcription level with qPCR time course approaches in oligodendrocyte-enriched cells to assess changes in oligodendrocyte progenitor and oligodendrocytes specifically. Results Adolescent binge ethanol altered H3K9me3 regulation of synaptic-related genes and genes specific for glutamate and potassium channels in a sex-specific manner. In PFC tissue, we found an early change in gene expression in transcription factors associated with oligodendrocyte differentiation that may lead to the later significant decrease in myelin-related gene expression. This effect appeared stronger in males. Conclusion Further exploration in oligodendrocyte cell enrichment time course and dose response studies could suggest lasting dysregulation of oligodendrocyte maturation at the transcriptional level. Overall, these studies suggest that binge ethanol may impede oligodendrocyte differentiation required for ongoing myelin development in the PFC by altering H3K9me3 occupancy at synaptic-related genes. We identify potential genes that may be contributing to adolescent binge ethanol-related myelin loss.
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Affiliation(s)
- Emily R. Brocato
- Pharmacology and Toxicology Department, Virginia Commonwealth University, Richmond, VA, United States
| | - Rachel Easter
- Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Alanna Morgan
- Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Meenakshi Kakani
- Pharmacology and Toxicology Department, Virginia Commonwealth University, Richmond, VA, United States
| | - Grace Lee
- Pharmacology and Toxicology Department, Virginia Commonwealth University, Richmond, VA, United States
| | - Jennifer T. Wolstenholme
- Pharmacology and Toxicology Department, Virginia Commonwealth University, Richmond, VA, United States
- Alcohol Research Center, Virginia Commonwealth University, Richmond, VA, United States
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2
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Zhou HY, Wang BQ, Chen MX, Wang YF, Jiang YF, Ma J. KDM4C represses liver fibrosis by regulating H3K9me3 methylation of ALKBH5 and m6A methylation of snail1 mRNA. J Dig Dis 2024; 25:298-309. [PMID: 38938016 DOI: 10.1111/1751-2980.13291] [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: 11/13/2023] [Revised: 05/22/2024] [Accepted: 05/24/2024] [Indexed: 06/29/2024]
Abstract
OBJECTIVE We aimed to disclose the molecular mechanism of snail1 in liver fibrosis. METHODS Carbon tetrachloride (CCl4) was used to induce a liver fibrosis model in mice whereby serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) levels were evaluated, and liver pathological alternations were assessed. Rat hepatic stellate cells (HSC-T6) were irritated with transforming growth factor (TGF)-β1, followed by assessment of cell viability and migration. The levels of snail1, ALKBH5, and lysine specific demethylase 4C (KDM4C) were quantified by immunohistochemistry, western blot, or reverse transcription-quantitative polymerase chain reaction, in addition to α-smooth muscle actin (SMA), anti-collagen type I α1 (COL1A1), vimentin, and E-cadherin. Photoactivatable ribonucleoside-enhanced crosslinking and immunoprecipitation and RNA stability were evaluated to determine the relationship between ALKBH5 and snail1. Changes in KDM4C-bound ALKBH5 promoter and enrichment of histone H3 lysine 9 trimethylation (H3K9me3) at the ALKBH5 promoter were determined using chromatin immunoprecipitation. RESULTS In fibrosis mice, snail1 was upregulated while ALKBH5 and KDM4C were downregulated. KDM4C overexpression reduced serum ALT and AST levels, liver injury, and α-SMA, COL1A1 and VIMENTIN expressions but increased E-cadherin expression. However, the aforementioned trends were reversed by concurrent overexpression of snail1. In HSC-T6 cells exposed to TGF-β1, ALKBH5 overexpression weakened cell viability and migration, downregulated α-SMA, COL1A1 and VIMENTIN, upregulated E-CADHERIN, and decreased m6A modification of snail1 and its mRNA stability. KDM4C increased ALKBH5 expression by lowering H3K9me3 level, but inhibited HSC-T6 cell activation by regulating the ALKBH5/snail1 axis. CONCLUSION KDM4C decreases H3K9me3 methylation to upregulate ALKBH5 and subsequently inhibits snail1, ultimately impeding liver fibrosis.
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Affiliation(s)
- Hua Ying Zhou
- Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Bing Qing Wang
- Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Meng Xuan Chen
- Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Yi Fan Wang
- Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Yong Fang Jiang
- Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
| | - Jing Ma
- Department of Infectious Diseases, The Second Xiangya Hospital, Central South University, Changsha, Hunan Province, China
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3
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Li Y, Huang J, Bao L, Zhu J, Duan W, Zheng H, Wang H, Jiang Y, Liu W, Zhang M, Yu Y, Yi C, Ji X. RNA Pol II preferentially regulates ribosomal protein expression by trapping disassociated subunits. Mol Cell 2023; 83:1280-1297.e11. [PMID: 36924766 DOI: 10.1016/j.molcel.2023.02.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 12/12/2022] [Accepted: 02/23/2023] [Indexed: 03/17/2023]
Abstract
RNA polymerase II (RNA Pol II) has been recognized as a passively regulated multi-subunit holoenzyme. However, the extent to which RNA Pol II subunits might be important beyond the RNA Pol II complex remains unclear. Here, fractions containing disassociated RPB3 (dRPB3) were identified by size exclusion chromatography in various cells. Through a unique strategy, i.e., "specific degradation of disassociated subunits (SDDS)," we demonstrated that dRPB3 functions as a regulatory component of RNA Pol II to enable the preferential control of 3' end processing of ribosomal protein genes directly through its N-terminal domain. Machine learning analysis of large-scale genomic features revealed that the little elongation complex (LEC) helps to specialize the functions of dRPB3. Mechanistically, dRPB3 facilitates CBC-PCF11 axis activity to increase the efficiency of 3' end processing. Furthermore, RPB3 is dynamically regulated during development and diseases. These findings suggest that RNA Pol II gains specific regulatory functions by trapping disassociated subunits in mammalian cells.
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Affiliation(s)
- Yuanjun Li
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jie Huang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Lijun Bao
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Junyi Zhu
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Wenjia Duan
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Haonan Zheng
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Hui Wang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yongpeng Jiang
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Weiwei Liu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Meiling Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yang Yu
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiong Ji
- Key Laboratory of Cell Proliferation and Differentiation of the Ministry of Education, School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
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4
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Jiang Y, Liu L, Yang ZQ. KDM4 Demethylases: Structure, Function, and Inhibitors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1433:87-111. [PMID: 37751137 DOI: 10.1007/978-3-031-38176-8_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/27/2023]
Abstract
KDM4 histone demethylases mainly catalyze the removal of methyl marks from H3K9 and H3K36 to epigenetically regulate chromatin structure and gene expression. KDM4 expression is strictly regulated to ensure proper function in a myriad of biological processes, including transcription, cellular proliferation and differentiation, DNA damage repair, immune response, and stem cell self-renewal. Aberrant expression of KDM4 demethylase has been documented in many types of blood and solid tumors, and thus, KDM4s represent promising therapeutic targets. In this chapter, we summarize the current knowledge of the structures and regulatory mechanisms of KDM4 proteins and our understanding of their alterations in human pathological processes with a focus on development and cancer. We also review the reported KDM4 inhibitors and discuss their potential as therapeutic agents.
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Affiliation(s)
- Yuanyuan Jiang
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, 4100 John R Street, HWCRC 815, Detroit, MI, 48201, USA
| | - Lanxin Liu
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, 4100 John R Street, HWCRC 815, Detroit, MI, 48201, USA
| | - Zeng-Quan Yang
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, 4100 John R Street, HWCRC 815, Detroit, MI, 48201, USA.
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5
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Scott V, Dey D, Kuwik J, Hinkelman K, Waldman M, Islam K. Allele-Specific Chemical Rescue of Histone Demethylases Using Abiotic Cofactors. ACS Chem Biol 2022; 17:3321-3330. [PMID: 34496208 DOI: 10.1021/acschembio.1c00335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Closely related protein families evolved from common ancestral genes present a significant hurdle in developing member- and isoform-specific chemical probes, owing to their similarity in fold and function. In this piece of work, we explore an allele-specific chemical rescue strategy to activate a "dead" variant of a wildtype protein using synthetic cofactors and demonstrate its successful application to the members of the alpha-ketoglutarate (αKG)-dependent histone demethylase 4 (KDM4) family. We show that a mutation at a specific residue in the catalytic site renders the variant inactive toward the natural cosubstrate. In contrast, αKG derivatives bearing appropriate stereoelectronic features endowed the mutant with native-like demethylase activity while remaining refractory to a set of wild type dioxygenases. The orthogonal enzyme-cofactor pairs demonstrated site- and degree-specific lysine demethylation on a full-length chromosomal histone in the cellular milieu. Our work offers a strategy to modulate a specific histone demethylase by identifying and engineering a conserved phenylalanine residue, which acts as a gatekeeper in the KDM4 subfamily, to sensitize the enzyme toward a novel set of αKG derivatives. The orthogonal pairs developed herein will serve as probes to study the role of degree-specific lysine demethylation in mammalian gene expression. Furthermore, this approach to overcome active site degeneracy is expected to have general application among all human αKG-dependent dioxygenases.
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Affiliation(s)
- Valerie Scott
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Debasis Dey
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Jordan Kuwik
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Kathryn Hinkelman
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Megan Waldman
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Kabirul Islam
- Department of Chemistry, University of Pittsburgh, 219 Parkman Avenue, Pittsburgh, Pennsylvania 15260, United States
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6
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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: 5] [Impact Index Per Article: 2.5] [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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7
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Sehrawat P, Shobhawat R, Kumar A. Catching Nucleosome by Its Decorated Tails Determines Its Functional States. Front Genet 2022; 13:903923. [PMID: 35910215 PMCID: PMC9329655 DOI: 10.3389/fgene.2022.903923] [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: 03/24/2022] [Accepted: 06/07/2022] [Indexed: 11/13/2022] Open
Abstract
The fundamental packaging unit of chromatin, i.e., nucleosome, consists of ∼147 bp of DNA wrapped around a histone octamer composed of the core histones, H2A, H2B, H3, and H4, in two copies each. DNA packaged in nucleosomes must be accessible to various machineries, including replication, transcription, and DNA damage repair, implicating the dynamic nature of chromatin even in its compact state. As the tails protrude out of the nucleosome, they are easily accessible to various chromatin-modifying machineries and undergo post-translational modifications (PTMs), thus playing a critical role in epigenetic regulation. PTMs can regulate chromatin states via charge modulation on histones, affecting interaction with various chromatin-associated proteins (CAPs) and DNA. With technological advancement, the list of PTMs is ever-growing along with their writers, readers, and erasers, expanding the complexity of an already intricate epigenetic field. In this review, we discuss how some of the specific PTMs on flexible histone tails affect the nucleosomal structure and regulate the accessibility of chromatin from a mechanistic standpoint and provide structural insights into some newly identified PTM–reader interaction.
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8
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Structural mechanism of bivalent histone H3K4me3K9me3 recognition by the Spindlin1/C11orf84 complex in rRNA transcription activation. Nat Commun 2021; 12:949. [PMID: 33574238 PMCID: PMC7878818 DOI: 10.1038/s41467-021-21236-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 01/18/2021] [Indexed: 12/11/2022] Open
Abstract
Spindlin1 is a unique multivalent epigenetic reader that facilitates ribosomal RNA transcription. In this study, we provide molecular and structural basis by which Spindlin1 acts in complex with C11orf84 to preferentially recognize non-canonical bivalent mark of trimethylated lysine 4 and lysine 9 present on the same histone H3 tail (H3K4me3K9me3). We demonstrate that C11orf84 binding stabilizes Spindlin1 and enhances its association with bivalent H3K4me3K9me3 mark. The functional analysis suggests that Spindlin1/C11orf84 complex can displace HP1 proteins from H3K4me3K9me3-enriched rDNA loci, thereby facilitating the conversion of these poised rDNA repeats from the repressed state to the active conformation, and the consequent recruitment of RNA Polymerase I for rRNA transcription. Our study uncovers a previously unappreciated mechanism of bivalent H3K4me3K9me3 recognition by Spindlin1/C11orf84 complex required for activation of rRNA transcription. Spindlin1 is an epigenetic reader that facilitates ribosomal RNA transcription. Here the authors reveal in vitro and structural evidence suggesting that Spindlin1 acts together with C11orf84 to recognize noncanonical bivalent mark of trimethylated lysine 4 and lysine 9 present on histone H3 tail (H3K4me3K9me3).
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9
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Anderson SE, Longbotham JE, O'Kane PT, Ugur FS, Fujimori DG, Mrksich M. Exploring the Ligand Preferences of the PHD1 Domain of Histone Demethylase KDM5A Reveals Tolerance for Modifications of the Q5 Residue of Histone 3. ACS Chem Biol 2021; 16:205-213. [PMID: 33314922 PMCID: PMC8168426 DOI: 10.1021/acschembio.0c00891] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Understanding the ligand preferences of epigenetic reader domains enables identification of modification states of chromatin with which these domains associate and can yield insight into recruitment and catalysis of chromatin-acting complexes. However, thorough exploration of the ligand preferences of reader domains is hindered by the limitations of traditional protein-ligand binding assays. Here, we evaluate the binding preferences of the PHD1 domain of histone demethylase KDM5A using the protein interaction by SAMDI (PI-SAMDI) assay, which measures protein-ligand binding in a high-throughput and sensitive manner via binding-induced enhancement in the activity of a reporter enzyme, in combination with fluorescence polarization. The PI-SAMDI assay was validated by confirming its ability to accurately profile the relative binding affinity of a set of well-characterized histone 3 (H3) ligands of PHD1. The assay was then used to assess the affinity of PHD1 for 361 H3 mutant ligands, a select number of which were further characterized by fluorescence polarization. Together, these experiments revealed PHD1's tolerance for H3Q5 mutations, including an unexpected tolerance for aromatic residues in this position. Motivated by this finding, we further demonstrate a high-affinity interaction between PHD1 and recently identified Q5-serotonylated H3. This work yields interesting insights into permissible PHD1-H3 interactions and demonstrates the value of interfacing PI-SAMDI and fluorescence polarization in investigations of protein-ligand binding.
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Affiliation(s)
- Sarah E Anderson
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - James E Longbotham
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
| | - Patrick T O'Kane
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
| | - Fatima S Ugur
- Chemistry and Chemical Biology Graduate Program, University of California San Francisco, San Francisco, California 94158, United States
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, California 94158, United States
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California 94158, United States
- Quantitative Biosciences Institute, University of California San Francisco, San Francisco, California 94158, United States
| | - Milan Mrksich
- Department of Chemistry, Northwestern University, Evanston, Illinois 60208, United States
- Department of Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Cell and Developmental Biology, Northwestern University, Evanston, Illinois 60208, United States
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10
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Kato H, Kushima I, Mori D, Yoshimi A, Aleksic B, Nawa Y, Toyama M, Furuta S, Yu Y, Ishizuka K, Kimura H, Arioka Y, Tsujimura K, Morikawa M, Okada T, Inada T, Nakatochi M, Shinjo K, Kondo Y, Kaibuchi K, Funabiki Y, Kimura R, Suzuki T, Yamakawa K, Ikeda M, Iwata N, Takahashi T, Suzuki M, Okahisa Y, Takaki M, Egawa J, Someya T, Ozaki N. Rare genetic variants in the gene encoding histone lysine demethylase 4C (KDM4C) and their contributions to susceptibility to schizophrenia and autism spectrum disorder. Transl Psychiatry 2020; 10:421. [PMID: 33279929 PMCID: PMC7719193 DOI: 10.1038/s41398-020-01107-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 11/08/2020] [Accepted: 11/17/2020] [Indexed: 12/23/2022] Open
Abstract
Dysregulation of epigenetic processes involving histone methylation induces neurodevelopmental impairments and has been implicated in schizophrenia (SCZ) and autism spectrum disorder (ASD). Variants in the gene encoding lysine demethylase 4C (KDM4C) have been suggested to confer a risk for such disorders. However, rare genetic variants in KDM4C have not been fully evaluated, and the functional impact of the variants has not been studied using patient-derived cells. In this study, we conducted copy number variant (CNV) analysis in a Japanese sample set (2605 SCZ and 1141 ASD cases, and 2310 controls). We found evidence for significant associations between CNVs in KDM4C and SCZ (p = 0.003) and ASD (p = 0.04). We also observed a significant association between deletions in KDM4C and SCZ (corrected p = 0.04). Next, to explore the contribution of single nucleotide variants in KDM4C, we sequenced the coding exons in a second sample set (370 SCZ and 192 ASD cases) and detected 18 rare missense variants, including p.D160N within the JmjC domain of KDM4C. We, then, performed association analysis for p.D160N in a third sample set (1751 SCZ and 377 ASD cases, and 2276 controls), but did not find a statistical association with these disorders. Immunoblotting analysis using lymphoblastoid cell lines from a case with KDM4C deletion revealed reduced KDM4C protein expression and altered histone methylation patterns. In conclusion, this study strengthens the evidence for associations between KDM4C CNVs and these two disorders and for their potential functional effect on histone methylation patterns.
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Affiliation(s)
- Hidekazu Kato
- grid.27476.300000 0001 0943 978XDepartment of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan. .,Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan.
| | - Daisuke Mori
- grid.27476.300000 0001 0943 978XDepartment of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan ,grid.27476.300000 0001 0943 978XBrain and Mind Research Center, Nagoya University, Nagoya, Japan
| | - Akira Yoshimi
- grid.259879.80000 0000 9075 4535Division of Clinical Sciences and Neuropsychopharmacology, Faculty and Graduate School of Pharmacy, Meijo University, Nagoya, Japan
| | - Branko Aleksic
- grid.27476.300000 0001 0943 978XDepartment of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshihiro Nawa
- grid.27476.300000 0001 0943 978XDepartment of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Miho Toyama
- grid.27476.300000 0001 0943 978XDepartment of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Sho Furuta
- grid.27476.300000 0001 0943 978XDepartment of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yanjie Yu
- grid.27476.300000 0001 0943 978XDepartment of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kanako Ishizuka
- grid.27476.300000 0001 0943 978XDepartment of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroki Kimura
- grid.27476.300000 0001 0943 978XDepartment of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuko Arioka
- grid.27476.300000 0001 0943 978XDepartment of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan ,grid.437848.40000 0004 0569 8970Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Keita Tsujimura
- grid.27476.300000 0001 0943 978XDepartment of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan ,grid.27476.300000 0001 0943 978XInnovative Research Unit for Developmental Disorders, Institute of Advanced Research, Nagoya University, Nagoya, Japan
| | - Mako Morikawa
- grid.27476.300000 0001 0943 978XDepartment of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takashi Okada
- grid.27476.300000 0001 0943 978XDepartment of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Toshiya Inada
- grid.27476.300000 0001 0943 978XDepartment of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Masahiro Nakatochi
- grid.27476.300000 0001 0943 978XPublic Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keiko Shinjo
- grid.27476.300000 0001 0943 978XDivision of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yutaka Kondo
- grid.27476.300000 0001 0943 978XDivision of Cancer Biology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Kozo Kaibuchi
- grid.27476.300000 0001 0943 978XDepartment of Cell Pharmacology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasuko Funabiki
- grid.258799.80000 0004 0372 2033Department of Cognitive and Behavioral Science, Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Ryo Kimura
- grid.258799.80000 0004 0372 2033Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Toshimitsu Suzuki
- grid.260433.00000 0001 0728 1069Department of Neurodevelopmental Disorder Genetics, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan ,grid.474690.8Laboratory for Neurogenetics, RIKEN Center for Brain Science, Saitama, Japan
| | - Kazuhiro Yamakawa
- grid.260433.00000 0001 0728 1069Department of Neurodevelopmental Disorder Genetics, Institute of Brain Science, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan ,grid.474690.8Laboratory for Neurogenetics, RIKEN Center for Brain Science, Saitama, Japan
| | - Masashi Ikeda
- grid.256115.40000 0004 1761 798XDepartment of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - Nakao Iwata
- grid.256115.40000 0004 1761 798XDepartment of Psychiatry, Fujita Health University School of Medicine, Toyoake, Japan
| | - Tsutomu Takahashi
- grid.267346.20000 0001 2171 836XDepartment of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan ,grid.267346.20000 0001 2171 836XResearch Center for Idling Brain Science, University of Toyama, Toyama, Japan
| | - Michio Suzuki
- grid.267346.20000 0001 2171 836XDepartment of Neuropsychiatry, University of Toyama Graduate School of Medicine and Pharmaceutical Sciences, Toyama, Japan ,grid.267346.20000 0001 2171 836XResearch Center for Idling Brain Science, University of Toyama, Toyama, Japan
| | - Yuko Okahisa
- grid.261356.50000 0001 1302 4472Department of Neuropsychiatry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Manabu Takaki
- grid.261356.50000 0001 1302 4472Department of Neuropsychiatry, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama, Japan
| | - Jun Egawa
- grid.260975.f0000 0001 0671 5144Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Toshiyuki Someya
- grid.260975.f0000 0001 0671 5144Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Norio Ozaki
- grid.27476.300000 0001 0943 978XDepartment of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
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11
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Wang Z, Liu D, Xu B, Tian R, Zuo Y. Modular arrangements of sequence motifs determine the functional diversity of KDM proteins. Brief Bioinform 2020; 22:5912575. [PMID: 32987405 DOI: 10.1093/bib/bbaa215] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Histone lysine demethylases (KDMs) play a vital role in regulating chromatin dynamics and transcription. KDM proteins are given modular activities by its sequence motifs with obvious roles division, which endow the complex and diverse functions. In our review, according to functional features, we classify sequence motifs into four classes: catalytic motifs, targeting motifs, regulatory motifs and potential motifs. JmjC, as the main catalytic motif, combines to Fe2+ and α-ketoglutarate by residues H-D/E-H and S-N-N/Y-K-N/Y-T/S. Targeting motifs make catalytic motifs recognize specific methylated lysines, such as PHD that helps KDM5 to demethylate H3K4me3. Regulatory motifs consist of a functional network. For example, NLS, Ser-rich, TPR and JmjN motifs regulate the nuclear localization. And interactions through the CW-type-C4H2C2-SWIRM are necessary to the demethylase activity of KDM1B. Additionally, many conservative domains that have potential functions but no deep exploration are reviewed for the first time. These conservative domains are usually amino acid-rich regions, which have great research value. The arrangements of four types of sequence motifs generate that KDM proteins diversify toward modular activities and biological functions. Finally, we draw a blueprint of functional mechanisms to discuss the modular activity of KDMs.
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Affiliation(s)
- Zerong Wang
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University
| | - Dongyang Liu
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University. He is now studying for a master's degree at the institute of botany of the Chinese Academy of Sciences. His research interests include bioinformatics and computational genomics
| | - Baofang Xu
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University
| | - Ruixia Tian
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University
| | - Yongchun Zuo
- State key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, College of life sciences, Inner Mongolia University. His research interests include bioinformatics and integration analysis of multiomics in cell reprogramming
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12
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Longbotham JE, Zhang MY, Fujimori DG. Domain cross-talk in regulation of histone modifications: Molecular mechanisms and targeting opportunities. Curr Opin Chem Biol 2020; 57:105-113. [PMID: 32758979 DOI: 10.1016/j.cbpa.2020.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 02/06/2023]
Abstract
Functional cross-talk between the catalytic and reader domains in chromatin-modifying enzymes and protein complexes enable coordinated regulation of chromatin modification status, and consequently impacts chromatin-associated processes. ZZ domains are a recently identified class of chromatin readers that recognize the N-terminal region of histone H3 to direct and regulate acetylation activity of several histone acetylation complexes. Cross-talk between chromatin readers sensitive to methylation, and catalytic domains of methyltransferases and demethylases impacts substrate specificity, catalytic activity, and propagation of chromatin marks. Recently described allosteric ligands that target domain communication highlight the potential of domain cross-talk in the development of the next-generation of chromatin-directed therapeutics.
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Affiliation(s)
- James E Longbotham
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94158, USA
| | - Meng Yao Zhang
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94158, USA
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94158, USA; Department of Pharmaceutical Chemistry, University of California San Francisco, 600 16th Street, Genentech Hall, San Francisco, CA 94158, USA; Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA 94158, USA.
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13
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Understanding the interplay between CpG island-associated gene promoters and H3K4 methylation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1863:194567. [PMID: 32360393 PMCID: PMC7294231 DOI: 10.1016/j.bbagrm.2020.194567] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/24/2020] [Accepted: 04/22/2020] [Indexed: 02/07/2023]
Abstract
The precise regulation of gene transcription is required to establish and maintain cell type-specific gene expression programs during multicellular development. In addition to transcription factors, chromatin, and its chemical modification, play a central role in regulating gene expression. In vertebrates, DNA is pervasively methylated at CG dinucleotides, a modification that is repressive to transcription. However, approximately 70% of vertebrate gene promoters are associated with DNA elements called CpG islands (CGIs) that are refractory to DNA methylation. CGIs integrate the activity of a range of chromatin-regulating factors that can post-translationally modify histones and modulate gene expression. This is exemplified by the trimethylation of histone H3 at lysine 4 (H3K4me3), which is enriched at CGI-associated gene promoters and correlates with transcriptional activity. Through studying H3K4me3 at CGIs it has become clear that CGIs shape the distribution of H3K4me3 and, in turn, H3K4me3 influences the chromatin landscape at CGIs. Here we will discuss our understanding of the emerging relationship between CGIs, H3K4me3, and gene expression.
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14
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Catania S, Dumesic PA, Pimentel H, Nasif A, Stoddard CI, Burke JE, Diedrich JK, Cook S, Shea T, Geinger E, Lintner R, Yates JR, Hajkova P, Narlikar GJ, Cuomo CA, Pritchard JK, Madhani HD. Evolutionary Persistence of DNA Methylation for Millions of Years after Ancient Loss of a De Novo Methyltransferase. Cell 2020; 180:263-277.e20. [PMID: 31955845 PMCID: PMC7197499 DOI: 10.1016/j.cell.2019.12.012] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/09/2019] [Accepted: 12/10/2019] [Indexed: 12/18/2022]
Abstract
Cytosine methylation of DNA is a widespread modification of DNA that plays numerous critical roles. In the yeast Cryptococcus neoformans, CG methylation occurs in transposon-rich repeats and requires the DNA methyltransferase Dnmt5. We show that Dnmt5 displays exquisite maintenance-type specificity in vitro and in vivo and utilizes similar in vivo cofactors as the metazoan maintenance methylase Dnmt1. Remarkably, phylogenetic and functional analysis revealed that the ancestral species lost the gene for a de novo methylase, DnmtX, between 50-150 mya. We examined how methylation has persisted since the ancient loss of DnmtX. Experimental and comparative studies reveal efficient replication of methylation patterns in C. neoformans, rare stochastic methylation loss and gain events, and the action of natural selection. We propose that an epigenome has been propagated for >50 million years through a process analogous to Darwinian evolution of the genome.
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Affiliation(s)
- Sandra Catania
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Phillip A Dumesic
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Harold Pimentel
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Ammar Nasif
- MRC London Institute of Medical Sciences (LMS), Reprogramming and Chromatin Group, Du Cane Road, W12 0NN London, UK; Institute of Clinical Sciences, Imperial College Faculty of Medicine, Du Cane Rd, W12 0NN London, UK
| | - Caitlin I Stoddard
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jordan E Burke
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jolene K Diedrich
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Sophie Cook
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Terrance Shea
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Elizabeth Geinger
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Robert Lintner
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Petra Hajkova
- MRC London Institute of Medical Sciences (LMS), Reprogramming and Chromatin Group, Du Cane Road, W12 0NN London, UK; Institute of Clinical Sciences, Imperial College Faculty of Medicine, Du Cane Rd, W12 0NN London, UK
| | - Geeta J Narlikar
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Christina A Cuomo
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jonathan K Pritchard
- Department of Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Hiten D Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA; Chan-Zuckerberg Biohub, San Francisco, CA 94158, USA.
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15
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Le Bihan YV, Lanigan RM, Atrash B, McLaughlin MG, Velupillai S, Malcolm AG, England KS, Ruda GF, Mok NY, Tumber A, Tomlin K, Saville H, Shehu E, McAndrew C, Carmichael L, Bennett JM, Jeganathan F, Eve P, Donovan A, Hayes A, Wood F, Raynaud FI, Fedorov O, Brennan PE, Burke R, van Montfort RLM, Rossanese OW, Blagg J, Bavetsias V. C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-ones: Studies towards the identification of potent, cell penetrant Jumonji C domain containing histone lysine demethylase 4 subfamily (KDM4) inhibitors, compound profiling in cell-based target engagement assays. Eur J Med Chem 2019; 177:316-337. [PMID: 31158747 PMCID: PMC6580095 DOI: 10.1016/j.ejmech.2019.05.041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 05/14/2019] [Accepted: 05/14/2019] [Indexed: 12/25/2022]
Abstract
Residues in the histone substrate binding sites that differ between the KDM4 and KDM5 subfamilies were identified. Subsequently, a C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-one series was designed to rationally exploit these residue differences between the histone substrate binding sites in order to improve affinity for the KDM4-subfamily over KDM5-subfamily enzymes. In particular, residues E169 and V313 (KDM4A numbering) were targeted. Additionally, conformational restriction of the flexible pyridopyrimidinone C8-substituent was investigated. These approaches yielded potent and cell-penetrant dual KDM4/5-subfamily inhibitors including 19a (KDM4A and KDM5B Ki = 0.004 and 0.007 μM, respectively). Compound cellular profiling in two orthogonal target engagement assays revealed a significant reduction from biochemical to cell-based activity across multiple analogues; this decrease was shown to be consistent with 2OG competition, and suggests that sub-nanomolar biochemical potency will be required with C8-substituted pyrido[3,4-d]pyrimidin-4(3H)-one compounds to achieve sub-micromolar target inhibition in cells.
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Affiliation(s)
- Yann-Vaï Le Bihan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Rachel M Lanigan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Butrus Atrash
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Mark G McLaughlin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Srikannathasan Velupillai
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Andrew G Malcolm
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Katherine S England
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Gian Filippo Ruda
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - N Yi Mok
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Anthony Tumber
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Kathy Tomlin
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Harry Saville
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Erald Shehu
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Craig McAndrew
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - LeAnne Carmichael
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - James M Bennett
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Fiona Jeganathan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Paul Eve
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Adam Donovan
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Angela Hayes
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Francesca Wood
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Florence I Raynaud
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Oleg Fedorov
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Paul E Brennan
- Structural Genomics Consortium (SGC), University of Oxford, ORCRB Roosevelt Drive, Oxford, OX3 7DQ, UK; Target Discovery Institute (TDI), Nuffield Department of Medicine, University of Oxford, NDMRB, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Rosemary Burke
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Rob L M van Montfort
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Olivia W Rossanese
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK
| | - Julian Blagg
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK.
| | - Vassilios Bavetsias
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, UK.
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16
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Nic-Can GI, Rodas-Junco BA, Carrillo-Cocom LM, Zepeda-Pedreguera A, Peñaloza-Cuevas R, Aguilar-Ayala FJ, Rojas-Herrera RA. Epigenetic Regulation of Adipogenic Differentiation by Histone Lysine Demethylation. Int J Mol Sci 2019; 20:E3918. [PMID: 31408999 PMCID: PMC6719019 DOI: 10.3390/ijms20163918] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 07/29/2019] [Indexed: 12/13/2022] Open
Abstract
Obesity is a rising public health problem that contributes to the development of several metabolic diseases and cancer. Adipocyte precursors outside of adipose depots that expand due to overweight and obesity may have a negative impact on human health. Determining how progenitor cells acquire a preadipocyte commitment and become mature adipocytes remains a significant challenge. Over the past several years, we have learned that the establishment of cellular identity is widely influenced by changes in histone marks, which in turn modulate chromatin structure. In this regard, histone lysine demethylases (KDMs) are now emerging as key players that shape chromatin through their ability to demethylate almost all major histone methylation sites. Recent research has shown that KDMs orchestrate the chromatin landscape, which mediates the activation of adipocyte-specific genes. In addition, KDMs have functions in addition to their enzymatic activity, which are beginning to be revealed, and their dysregulation seems to be related to the development of metabolic disorders. In this review, we highlight the biological functions of KDMs that contribute to the establishment of a permissive or repressive chromatin environment during the mesenchymal stem cell transition into adipocytes. Understanding how KDMs regulate adipogenesis might prompt the development of new strategies for fighting obesity-related diseases.
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Affiliation(s)
- Geovanny I Nic-Can
- CONACYT-Facultad de Ingeniería Química, Universidad Autónoma de Yucatán.; Periférico Norte Kilómetro 33.5, Tablaje Catastral 13615, Chuburná de Hidalgo Inn, Mérida 97203, Yucatán, Mexico.
- Laboratorio Translacional de Células Troncales-Facultad de Odontología, Universidad Autónoma de Yucatán, Calle 61-A X Av, Itzaes Costado Sur "Parque de la Paz", Col. Centro, Mérida 97000, Yucatán, Mexico.
| | - Beatriz A Rodas-Junco
- CONACYT-Facultad de Ingeniería Química, Universidad Autónoma de Yucatán.; Periférico Norte Kilómetro 33.5, Tablaje Catastral 13615, Chuburná de Hidalgo Inn, Mérida 97203, Yucatán, Mexico
- Laboratorio Translacional de Células Troncales-Facultad de Odontología, Universidad Autónoma de Yucatán, Calle 61-A X Av, Itzaes Costado Sur "Parque de la Paz", Col. Centro, Mérida 97000, Yucatán, Mexico
| | - Leydi M Carrillo-Cocom
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán.; Periférico Norte Kilómetro 33.5, Tablaje Catastral 13615, Chuburná de Hidalgo Inn, Mérida 97203, Yucatán, Mexico
| | - Alejandro Zepeda-Pedreguera
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán.; Periférico Norte Kilómetro 33.5, Tablaje Catastral 13615, Chuburná de Hidalgo Inn, Mérida 97203, Yucatán, Mexico
| | - Ricardo Peñaloza-Cuevas
- Laboratorio Translacional de Células Troncales-Facultad de Odontología, Universidad Autónoma de Yucatán, Calle 61-A X Av, Itzaes Costado Sur "Parque de la Paz", Col. Centro, Mérida 97000, Yucatán, Mexico
| | - Fernando J Aguilar-Ayala
- Laboratorio Translacional de Células Troncales-Facultad de Odontología, Universidad Autónoma de Yucatán, Calle 61-A X Av, Itzaes Costado Sur "Parque de la Paz", Col. Centro, Mérida 97000, Yucatán, Mexico
| | - Rafael A Rojas-Herrera
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán.; Periférico Norte Kilómetro 33.5, Tablaje Catastral 13615, Chuburná de Hidalgo Inn, Mérida 97203, Yucatán, Mexico
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17
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Monaghan L, Massett ME, Bunschoten RP, Hoose A, Pirvan PA, Liskamp RMJ, Jørgensen HG, Huang X. The Emerging Role of H3K9me3 as a Potential Therapeutic Target in Acute Myeloid Leukemia. Front Oncol 2019; 9:705. [PMID: 31428579 PMCID: PMC6687838 DOI: 10.3389/fonc.2019.00705] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/16/2019] [Indexed: 12/23/2022] Open
Abstract
Growing evidence has demonstrated that epigenetic dysregulation is a common pathological feature in human cancer cells. Global alterations in the epigenetic landscape are prevalent in malignant cells across different solid tumors including, prostate cancer, non-small-cell lung cancer, renal cell carcinoma, and in haemopoietic malignancy. In particular, DNA hypomethylation and histone hypoacetylation have been observed in acute myeloid leukemia (AML) patient blasts, with histone methylation being an emerging area of study. Histone 3 lysine 9 trimethylation (H3K9me3) is a post-translational modification known to be involved in the regulation of a broad range of biological processes, including the formation of transcriptionally silent heterochromatin. Following the observation of its aberrant methylation status in hematological malignancy and several other cancer phenotypes, recent studies have associated H3K9me3 levels with patient outcome and highlighted key molecular mechanisms linking H3K9me3 profile with AML etiology in a number of large-scale meta-analysis. Consequently, the development and application of small molecule inhibitors which target the histone methyltransferases or demethylase enzymes known to participate in the oncogenic regulation of H3K9me3 in AML represents an advancing area of ongoing study. Here, we provide a comprehensive review on how this particular epigenetic mark is regulated within cells and its emerging role as a potential therapeutic target in AML, along with an update on the current research into advancing the generation of more potent and selective inhibitors against known H3K9 methyltransferases and demethylases.
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Affiliation(s)
- Laura Monaghan
- Haemato-Oncology/Systems Medicine Group, Paul O'Gorman Leukemia Research Center, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Matthew E. Massett
- Haemato-Oncology/Systems Medicine Group, Paul O'Gorman Leukemia Research Center, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Alex Hoose
- School of Chemistry, University of Glasgow, Glasgow, United Kingdom
| | | | | | - Heather G. Jørgensen
- Haemato-Oncology/Systems Medicine Group, Paul O'Gorman Leukemia Research Center, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Xu Huang
- Haemato-Oncology/Systems Medicine Group, Paul O'Gorman Leukemia Research Center, Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
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18
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Longbotham JE, Chio CM, Dharmarajan V, Trnka MJ, Torres IO, Goswami D, Ruiz K, Burlingame AL, Griffin PR, Fujimori DG. Histone H3 binding to the PHD1 domain of histone demethylase KDM5A enables active site remodeling. Nat Commun 2019; 10:94. [PMID: 30626866 PMCID: PMC6327041 DOI: 10.1038/s41467-018-07829-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 11/23/2018] [Indexed: 02/06/2023] Open
Abstract
Histone demethylase KDM5A removes methyl marks from lysine 4 of histone H3 and is often overexpressed in cancer. The in vitro demethylase activity of KDM5A is allosterically enhanced by binding of its product, unmodified H3 peptides, to its PHD1 reader domain. However, the molecular basis of this allosteric enhancement is unclear. Here we show that saturation of the PHD1 domain by the H3 N-terminal tail peptides stabilizes binding of the substrate to the catalytic domain and improves the catalytic efficiency of demethylation. When present in saturating concentrations, differently modified H3 N-terminal tail peptides have a similar effect on demethylation. However, they vary greatly in their affinity towards the PHD1 domain, suggesting that H3 modifications can tune KDM5A activity. Furthermore, hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) experiments reveal conformational changes in the allosterically enhanced state. Our findings may enable future development of anti-cancer therapies targeting regions involved in allosteric regulation. The demethylase activity of KDM5A is allosterically enhanced by binding of histone H3 to its PHD1 reader domain, through an unknown mechanism. Here the authors show that the PHD1 domain drives ligand-induced allosteric stimulation by stabilizing the binding of substrate to the catalytic domain.
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Affiliation(s)
- James E Longbotham
- Department of Cellular and Molecular Pharmacology, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | - Cynthia M Chio
- Department of Cellular and Molecular Pharmacology, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | | | - Michael J Trnka
- Department of Pharmaceutical Chemistry, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | - Idelisse Ortiz Torres
- Chemistry and Chemical Biology Graduate Program, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | - Devrishi Goswami
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Karen Ruiz
- TETRAD Graduate Program, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | - Alma L Burlingame
- Department of Pharmaceutical Chemistry, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Danica Galonić Fujimori
- Department of Cellular and Molecular Pharmacology, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA. .,Department of Pharmaceutical Chemistry, University of California, 600 16th Street, Genentech Hall, San Francisco, CA, 94158, USA.
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19
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Sudhamalla B, Wang S, Snyder V, Kavoosi S, Arora S, Islam K. Complementary Steric Engineering at the Protein-Ligand Interface for Analogue-Sensitive TET Oxygenases. J Am Chem Soc 2018; 140:10263-10269. [PMID: 30028600 PMCID: PMC6400064 DOI: 10.1021/jacs.8b05283] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Ten-eleven translocation (TET) enzymes employ O2, earth-abundant iron, and 2-ketoglutarate (2KG) to perform iterative C-H oxidation of 5-methylcytosine in DNA to control expression of the mammalian genome. Given that more than 60 such C-H oxygenases are present in humans, determining context-dependent functions of each of these enzymes is a pivotal challenge. In an effort to tackle the problem, we developed analogue-sensitive TET enzymes to perturb the activity of a specific member. We rationally engineered the TET2-2KG interface to develop TET2 variants with an expanded active site that can be specifically inhibited by the N-oxalylglycine (NOG) derivatives carrying a complementary steric "bump". Herein, we describe the identification and engineering of a bulky gatekeeper residue for TET proteins, characterize the orthogonal mutant-inhibitor pairs, and show generality of the approach. Employing cell-permeable NOG analogues, we show that the TET2 mutant can be specifically inhibited to conditionally modulate cytosine methylation in chromosomal DNA in intact human cells. Finally, we demonstrate application of the orthogonal mutant-inhibitor pair to probe transcriptional activity of a specific TET member in cells. Our work provides a general platform for developing analogue-sensitive 2KG-dependent oxygenases to unravel their functions in diverse signaling processes.
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Affiliation(s)
- Babu Sudhamalla
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Sinan Wang
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | | | | | | | - Kabirul Islam
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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20
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Targeting lysine specific demethylase 4A (KDM4A) tandem TUDOR domain – A fragment based approach. Bioorg Med Chem Lett 2018; 28:1708-1713. [DOI: 10.1016/j.bmcl.2018.04.050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 12/12/2022]
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21
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Dhall A, Weller CE, Chu A, Shelton PMM, Chatterjee C. Chemically Sumoylated Histone H4 Stimulates Intranucleosomal Demethylation by the LSD1-CoREST Complex. ACS Chem Biol 2017; 12:2275-2280. [PMID: 28832116 DOI: 10.1021/acschembio.7b00716] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Lysine-specific demethylase 1 (LSD1) downregulates eukaryotic gene activity by demethylating mono- and dimethylated Lys4 in histone H3. Elucidating the biochemical crosstalk of LSD1 with histone post-translational modifications (PTMs) is essential for developing LSD1-targeted therapeutics in human cancers. We interrogated the small ubiquitin-like modifier (SUMO)-driven regulation of LSD1 activity with semisynthetic nucleosomes containing site-specifically methylated and sumoylated histones. We discovered that nucleosomes containing sumoylated histone H4 (suH4), a modification associated with gene repression, stimulate LSD1 activity by a mechanism dependent upon the SUMO-interaction motif in CoREST. Furthermore, the stimulatory effect of suH4 was spatially limited and did not extend to the demethylation of adjacent nonsumoylated nucleosomes. Thus, we have identified histone modification by SUMO as the first PTM that stimulates intranucleosomal demethylation by the developmentally critical LSD1-CoREST complex.
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Affiliation(s)
- Abhinav Dhall
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Caroline E. Weller
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Aurea Chu
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Patrick M. M. Shelton
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Champak Chatterjee
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
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22
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Abstract
As an important epigenetic mark, lysine methylations play critical roles in the regulation of both chromatin and non-chromatin proteins. There are three levels of lysine methylation, mono-, di-, and trimethylation. Each one has turned out to be biologically distinctive. For the biochemical characterization of proteins with lysine methylation, multiple chemical biology methods have been developed. This concept article will highlight these developments and their applications in epigenetic investigation of protein functions.
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Affiliation(s)
- Zhipeng A. Wang
- Chemistry Department, Texas A&M University, College Station, TX, 77843, USA
| | - Wenshe R. Liu
- Chemistry Department, Texas A&M University, College Station, TX, 77843, USA
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23
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Hancock R, Masson N, Dunne K, Flashman E, Kawamura A. The Activity of JmjC Histone Lysine Demethylase KDM4A is Highly Sensitive to Oxygen Concentrations. ACS Chem Biol 2017; 12:1011-1019. [PMID: 28051298 PMCID: PMC5404277 DOI: 10.1021/acschembio.6b00958] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/04/2017] [Indexed: 01/04/2023]
Abstract
The JmjC histone lysine demethylases (KDMs) are epigenetic regulators involved in the removal of methyl groups from post-translationally modified lysyl residues within histone tails, modulating gene transcription. These enzymes require molecular oxygen for catalytic activity and, as 2-oxoglutarate (2OG)-dependent oxygenases, are related to the cellular oxygen sensing HIF hydroxylases PHD2 and FIH. Recent studies have indicated that the activity of some KDMs, including the pseudogene-encoded KDM4E, may be sensitive to changing oxygen concentrations. Here, we report detailed analysis of the effect of oxygen availability on the activity of the KDM4 subfamily member KDM4A, importantly demonstrating a high level of O2 sensitivity both with isolated protein and in cells. Kinetic analysis of the recombinant enzyme revealed a high KMapp(O2) of 173 ± 23 μM, indicating that the activity of the enzyme is able to respond sensitively to a reduction in oxygen concentration. Furthermore, immunofluorescence experiments in U2OS cells conditionally overexpressing KDM4A showed that the cellular activity of KDM4A against its primary substrate, H3K9me3, displayed a graded response to depleting oxygen concentrations in line with the data obtained using isolated protein. These results suggest that KDM4A possesses the potential to act as an oxygen sensor in the context of chromatin modifications, with possible implications for epigenetic regulation in hypoxic disease states. Importantly, this correlation between the oxygen sensitivity of the catalytic activity of KDM4A in biochemical and cellular assays demonstrates the utility of biochemical studies in understanding the factors contributing to the diverse biological functions and varied activity of the 2OG oxygenases.
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Affiliation(s)
- Rebecca
L Hancock
- Chemistry
Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
- Radcliffe
Department of Medicine, Division of Cardiovascular Medicine, BHF Centre of Research Excellence, Wellcome Trust
Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Norma Masson
- Target Discovery Institute, NDM Research Building, University
of Oxford, Roosevelt
Drive, Oxford OX3 7BN, United Kingdom
| | - Kate Dunne
- Chemistry
Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
- Radcliffe
Department of Medicine, Division of Cardiovascular Medicine, BHF Centre of Research Excellence, Wellcome Trust
Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Emily Flashman
- Chemistry
Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Akane Kawamura
- Chemistry
Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, United Kingdom
- Radcliffe
Department of Medicine, Division of Cardiovascular Medicine, BHF Centre of Research Excellence, Wellcome Trust
Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
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24
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The histone demethylase KDM4B regulates peritoneal seeding of ovarian cancer. Oncogene 2016; 36:2565-2576. [PMID: 27869162 PMCID: PMC5418103 DOI: 10.1038/onc.2016.412] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 09/14/2016] [Accepted: 09/18/2016] [Indexed: 02/06/2023]
Abstract
Epithelial ovarian cancer (EOC) has poor prognosis and rapid recurrence because of widespread dissemination of peritoneal metastases at diagnosis. Multiple pathways contribute to the aggressiveness of ovarian cancer, including hypoxic signaling mechanisms. In this study, we have determined that the hypoxia-inducible histone demethylase KDM4B is expressed in ∼60% of EOC tumors assayed, including primary and matched metastatic tumors. Expression of KDM4B in tumors is positively correlated with expression of the tumor hypoxia marker CA-IX, and is robustly induced in EOC cell lines exposed to hypoxia. KDM4B regulates expression of metastatic genes and pathways, and loss of KDM4B increases H3K9 trimethylation at the promoters of target genes like LOXL2, LCN2 and PDGFB. Suppressing KDM4B inhibits ovarian cancer cell invasion, migration and spheroid formation in vitro. KDM4B also regulates seeding and growth of peritoneal tumors in vivo, where its expression corresponds to hypoxic regions. This is the first demonstration that a Jumonji-domain histone demethylase regulates cellular processes required for peritoneal dissemination of cancer cells, one of the predominant factors affecting prognosis of EOC. The pathways regulated by KDM4B may present novel opportunities to develop combinatorial therapies to improve existing therapies for EOC patients.
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25
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Su Z, Wang F, Lee JH, Stephens KE, Papazyan R, Voronina E, Krautkramer KA, Raman A, Thorpe JJ, Boersma MD, Kuznetsov VI, Miller MD, Taverna SD, Phillips GN, Denu JM. Reader domain specificity and lysine demethylase-4 family function. Nat Commun 2016; 7:13387. [PMID: 27841353 PMCID: PMC5114558 DOI: 10.1038/ncomms13387] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2016] [Accepted: 09/28/2016] [Indexed: 12/14/2022] Open
Abstract
The KDM4 histone demethylases are conserved epigenetic regulators linked to development, spermatogenesis and tumorigenesis. However, how the KDM4 family targets specific chromatin regions is largely unknown. Here, an extensive histone peptide microarray analysis uncovers trimethyl-lysine histone-binding preferences among the closely related KDM4 double tudor domains (DTDs). KDM4A/B DTDs bind strongly to H3K23me3, a poorly understood histone modification recently shown to be enriched in meiotic chromatin of ciliates and nematodes. The 2.28 Å co-crystal structure of KDM4A-DTD in complex with H3K23me3 peptide reveals key intermolecular interactions for H3K23me3 recognition. Furthermore, analysis of the 2.56 Å KDM4B-DTD crystal structure pinpoints the underlying residues required for exclusive H3K23me3 specificity, an interaction supported by in vivo co-localization of KDM4B and H3K23me3 at heterochromatin in mammalian meiotic and newly postmeiotic spermatocytes. In vitro demethylation assays suggest H3K23me3 binding by KDM4B stimulates H3K36 demethylation. Together, these results provide a possible mechanism whereby H3K23me3-binding by KDM4B directs localized H3K36 demethylation during meiosis and spermatogenesis.
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Affiliation(s)
- Zhangli Su
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | - Fengbin Wang
- Biosciences at Rice, Rice University, Houston, Texas 77005, USA
| | - Jin-Hee Lee
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | - Kimberly E. Stephens
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Romeo Papazyan
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Ekaterina Voronina
- Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA
| | - Kimberly A. Krautkramer
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | - Ana Raman
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Jeremy J. Thorpe
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - Melissa D. Boersma
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | - Vyacheslav I. Kuznetsov
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
| | | | - Sean D. Taverna
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
- Center for Epigenetics, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
| | - George N. Phillips
- Biosciences at Rice, Rice University, Houston, Texas 77005, USA
- Department of Chemistry, Rice University, Houston, Texas 77005, USA
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
| | - John M. Denu
- Wisconsin Institute for Discovery, Morgridge Institute for Research, University of Wisconsin–Madison, Madison, Wisconsin 53715, USA
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin–Madison, 330 North Orchard Street, Madison, Wisconsin 53715, USA
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26
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Breski M, Dey D, Obringer S, Sudhamalla B, Islam K. Engineering Biological C-H Functionalization Leads to Allele-Specific Regulation of Histone Demethylases. J Am Chem Soc 2016; 138:13505-13508. [PMID: 27709909 DOI: 10.1021/jacs.6b08653] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oxidative C-H hydroxylation of methyl groups, followed by their removal from DNA, RNA, or histones, is an epigenetic process critical to transcriptional reprogramming and cell fate determination. This reaction is catalyzed by Fe(II)-dependent dioxygenases using the essential metabolite 2-ketoglutarate (2KG) as a cofactor. Given that the human genome encodes for more than 60 2KG-dependent dioxygenases, assigning their individual functions remains a significant challenge. Here we describe a protein-ligand interface engineering approach to break the biochemical degeneracy of these enzymes. Using histone lysine demethylase 4 as a proof-of-concept, we show that the enzyme active site can be expanded to employ bulky 2KG analogues that do not sensitize wild-type demethylases. We establish the orthogonality, substrate specificity, and catalytic competency of the engineered demethylation apparatus in biochemical assays. We further demonstrate demethylation of cognate substrates in physiologically relevant settings. Our results provide a paradigm for rapid and conditional manipulation of histone demethylases to uncloak their isoform-specific functions.
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Affiliation(s)
- Megan Breski
- Department of Chemistry and ∥Department of Human Genetics, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Debasis Dey
- Department of Chemistry and ∥Department of Human Genetics, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Sara Obringer
- Department of Chemistry and ∥Department of Human Genetics, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Babu Sudhamalla
- Department of Chemistry and ∥Department of Human Genetics, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Kabirul Islam
- Department of Chemistry and ∥Department of Human Genetics, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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