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Honer MA, Ferman BI, Gray ZH, Bondarenko EA, Whetstine JR. Epigenetic modulators provide a path to understanding disease and therapeutic opportunity. Genes Dev 2024; 38:473-503. [PMID: 38914477 PMCID: PMC11293403 DOI: 10.1101/gad.351444.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The discovery of epigenetic modulators (writers, erasers, readers, and remodelers) has shed light on previously underappreciated biological mechanisms that promote diseases. With these insights, novel biomarkers and innovative combination therapies can be used to address challenging and difficult to treat disease states. This review highlights key mechanisms that epigenetic writers, erasers, readers, and remodelers control, as well as their connection with disease states and recent advances in associated epigenetic therapies.
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Affiliation(s)
- Madison A Honer
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Benjamin I Ferman
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Zach H Gray
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Biomedical Sciences Program, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania 19140, USA
| | - Elena A Bondarenko
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
| | - Johnathan R Whetstine
- Cancer Epigenetics Institute, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA;
- Nuclear Dynamics and Cancer Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA
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2
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Becht DC, Kanai A, Biswas S, Halawa M, Zeng L, Cox KL, Poirier MG, Zhou MM, Shi X, Yokoyama A, Kutateladze TG. The winged helix domain of MORF binds CpG islands and the TAZ2 domain of p300. iScience 2024; 27:109367. [PMID: 38500836 PMCID: PMC10946326 DOI: 10.1016/j.isci.2024.109367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/19/2024] [Accepted: 02/26/2024] [Indexed: 03/20/2024] Open
Abstract
Acetylation of histones by lysine acetyltransferases (KATs) provides a fundamental mechanism by which chromatin structure and transcriptional programs are regulated. Here, we describe a dual binding activity of the first winged helix domain of human MORF KAT (MORFWH1) that recognizes the TAZ2 domain of p300 KAT (p300TAZ2) and CpG rich DNA sequences. Structural and biochemical studies identified distinct DNA and p300TAZ2 binding sites, allowing MORFWH1 to independently engage either ligand. Genomic data show that MORF/MOZWH1 colocalizes with H3K18ac, a product of enzymatic activity of p300, on CpG rich promoters of target genes. Our findings suggest a functional cooperation of MORF and p300 KATs in transcriptional regulation.
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Affiliation(s)
- Dustin C. Becht
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Akinori Kanai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba 277-0882, Japan
| | - Soumi Biswas
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Mohamed Halawa
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Lei Zeng
- Bethune Institute of Epigenetic Medicine, First Hospital of Jilin University, Changchun 130061, China
- International Center of Future Science, Jilin University, Changchun 130012, China
| | - Khan L. Cox
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | | | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xiaobing Shi
- Department of Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata 997-0052, Japan
| | - Tatiana G. Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
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3
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Sharma S, Chung CY, Uryu S, Petrovic J, Cao J, Rickard A, Nady N, Greasley S, Johnson E, Brodsky O, Khan S, Wang H, Wang Z, Zhang Y, Tsaparikos K, Chen L, Mazurek A, Lapek J, Kung PP, Sutton S, Richardson PF, Greenwald EC, Yamazaki S, Jones R, Maegley KA, Bingham P, Lam H, Stupple AE, Kamal A, Chueh A, Cuzzupe A, Morrow BJ, Ren B, Carrasco-Pozo C, Tan CW, Bhuva DD, Allan E, Surgenor E, Vaillant F, Pehlivanoglu H, Falk H, Whittle JR, Newman J, Cursons J, Doherty JP, White KL, MacPherson L, Devlin M, Dennis ML, Hattarki MK, De Silva M, Camerino MA, Butler MS, Dolezal O, Pilling P, Foitzik R, Stupple PA, Lagiakos HR, Walker SR, Hediyeh-Zadeh S, Nuttall S, Spall SK, Charman SA, Connor T, Peat TS, Avery VM, Bozikis YE, Yang Y, Zhang M, Monahan BJ, Voss AK, Thomas T, Street IP, Dawson SJ, Dawson MA, Lindeman GJ, Davis MJ, Visvader JE, Paul TA. Discovery of a highly potent, selective, orally bioavailable inhibitor of KAT6A/B histone acetyltransferases with efficacy against KAT6A-high ER+ breast cancer. Cell Chem Biol 2023; 30:1191-1210.e20. [PMID: 37557181 DOI: 10.1016/j.chembiol.2023.07.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 02/07/2023] [Accepted: 07/16/2023] [Indexed: 08/11/2023]
Abstract
KAT6A, and its paralog KAT6B, are histone lysine acetyltransferases (HAT) that acetylate histone H3K23 and exert an oncogenic role in several tumor types including breast cancer where KAT6A is frequently amplified/overexpressed. However, pharmacologic targeting of KAT6A to achieve therapeutic benefit has been a challenge. Here we describe identification of a highly potent, selective, and orally bioavailable KAT6A/KAT6B inhibitor CTx-648 (PF-9363), derived from a benzisoxazole series, which demonstrates anti-tumor activity in correlation with H3K23Ac inhibition in KAT6A over-expressing breast cancer. Transcriptional and epigenetic profiling studies show reduced RNA Pol II binding and downregulation of genes involved in estrogen signaling, cell cycle, Myc and stem cell pathways associated with CTx-648 anti-tumor activity in ER-positive (ER+) breast cancer. CTx-648 treatment leads to potent tumor growth inhibition in ER+ breast cancer in vivo models, including models refractory to endocrine therapy, highlighting the potential for targeting KAT6A in ER+ breast cancer.
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Affiliation(s)
- Shikhar Sharma
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA.
| | - Chi-Yeh Chung
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Sean Uryu
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Jelena Petrovic
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Joan Cao
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Amanda Rickard
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Nataliya Nady
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | | | - Eric Johnson
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Oleg Brodsky
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Showkhin Khan
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Hui Wang
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Zhenxiong Wang
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Yong Zhang
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | | | - Lei Chen
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Anthony Mazurek
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - John Lapek
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Pei-Pei Kung
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Scott Sutton
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | | | - Eric C Greenwald
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Shinji Yamazaki
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Rhys Jones
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Karen A Maegley
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Patrick Bingham
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Hieu Lam
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA
| | - Alexandra E Stupple
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Medicinal Chemistry and Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia; CANThera Discovery, Melbourne, VIC 3000, Australia
| | - Aileen Kamal
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Anderly Chueh
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Anthony Cuzzupe
- SYNthesis Med Chem (Australia) Pty Ltd, Bio21 Institute, 30 Flemington Road, Parkville, VIC 3052, Australia
| | - Benjamin J Morrow
- Medicinal Chemistry and Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia; Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia
| | - Bin Ren
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, VIC 3052, Australia
| | - Catalina Carrasco-Pozo
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Discovery Biology, Centre for Cellular Phenomics, Griffith University, Brisbane QLD 4111, Australia
| | - Chin Wee Tan
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Dharmesh D Bhuva
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Elizabeth Allan
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Elliot Surgenor
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - François Vaillant
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Havva Pehlivanoglu
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Hendrik Falk
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia; Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, VIC 3052, Australia
| | - James R Whittle
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Janet Newman
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, VIC 3052, Australia
| | - Joseph Cursons
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Judy P Doherty
- Peter MacCallum Cancer Centre, Melbourne VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Karen L White
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Medicinal Chemistry and Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Laura MacPherson
- Peter MacCallum Cancer Centre, Melbourne VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Mark Devlin
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Peter MacCallum Cancer Centre, Melbourne VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Matthew L Dennis
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, VIC 3052, Australia
| | - Meghan K Hattarki
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, VIC 3052, Australia
| | - Melanie De Silva
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Michelle A Camerino
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Medicinal Chemistry and Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Miriam S Butler
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Peter MacCallum Cancer Centre, Melbourne VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Olan Dolezal
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, VIC 3052, Australia
| | - Patricia Pilling
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, VIC 3052, Australia
| | - Richard Foitzik
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Medicinal Chemistry and Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia; OncologyOne Pty Ltd, Melbourne, VIC 3000, Australia
| | - Paul A Stupple
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Medicinal Chemistry and Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia; CANThera Discovery, Melbourne, VIC 3000, Australia
| | - H Rachel Lagiakos
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Medicinal Chemistry and Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Scott R Walker
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Medicinal Chemistry and Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia; Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, VIC 3052, Australia
| | - Soroor Hediyeh-Zadeh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Stewart Nuttall
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, VIC 3052, Australia
| | - Sukhdeep K Spall
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Susan A Charman
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Medicinal Chemistry and Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Theresa Connor
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Peter MacCallum Cancer Centre, Melbourne VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Thomas S Peat
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Commonwealth Scientific and Industrial Research Organisation (CSIRO), Parkville, VIC 3052, Australia
| | - Vicky M Avery
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Discovery Biology, Centre for Cellular Phenomics, Griffith University, Brisbane QLD 4111, Australia
| | - Ylva E Bozikis
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; Medicinal Chemistry and Centre for Drug Candidate Optimisation, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia
| | - Yuqing Yang
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Ming Zhang
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia
| | - Brendon J Monahan
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia; CANThera Discovery, Melbourne, VIC 3000, Australia
| | - Anne K Voss
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Tim Thomas
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Ian P Street
- Cancer Therapeutics CRC, Melbourne, VIC 3000, Australia; The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia; OncologyOne Pty Ltd, Melbourne, VIC 3000, Australia; Children's Cancer Institute, Randwick, NSW 2031, Australia; University of New South Wales, Randwick, NSW 2021, Australia
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Melbourne VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Mark A Dawson
- Peter MacCallum Cancer Centre, Melbourne VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Geoffrey J Lindeman
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medicine, Royal Melbourne Hospital, The University of Melbourne, Parkville, VIC 3010, Australia; Parkville Familial Cancer Centre and Department of Medical Oncology, The Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Parkville, VIC 3050, Australia
| | - Melissa J Davis
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia; Department of Clinical Pathology, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Jane E Visvader
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC 3052, Australia
| | - Thomas A Paul
- Pfizer, Oncology Research & Development, San Diego, CA 92121, USA.
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Komata Y, Kanai A, Maeda T, Inaba T, Yokoyama A. MOZ/ENL complex is a recruiting factor of leukemic AF10 fusion proteins. Nat Commun 2023; 14:1979. [PMID: 37031220 PMCID: PMC10082848 DOI: 10.1038/s41467-023-37712-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 03/22/2023] [Indexed: 04/10/2023] Open
Abstract
Changes in the transcriptional machinery cause aberrant self-renewal of non-stem hematopoietic progenitors. AF10 fusions, such as CALM-AF10, are generated via chromosomal translocations, causing malignant leukemia. In this study, we demonstrate that AF10 fusion proteins cause aberrant self-renewal via ENL, which binds to MOZ/MORF lysine acetyltransferases (KATs). The interaction of ENL with MOZ, via its YEATS domain, is critical for CALM-AF10-mediated leukemic transformation. The MOZ/ENL complex recruits DOT1L/AF10 fusion complexes and maintains their chromatin retention via KAT activity. Therefore, inhibitors of MOZ/MORF KATs directly suppress the functions of AF10 fusion proteins, thereby exhibiting strong antitumor effects on AF10 translocation-induced leukemia. Combinatorial inhibition of MOZ/MORF and DOT1L cooperatively induces differentiation of CALM-AF10-leukemia cells. These results reveal roles for the MOZ/ENL complex as an essential recruiting factor of the AF10 fusion/DOT1L complex, providing a rationale for using MOZ/MORF KAT inhibitors in AF10 translocation-induced leukemia.
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Affiliation(s)
- Yosuke Komata
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata, 997-0052, Japan
| | - Akinori Kanai
- Laboratory of Systems Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan
- Department of Molecular Oncology and Leukemia Program Project, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Hiroshima, 734-8553, Japan
| | - Takahiro Maeda
- Division of Precision Medicine, Kyushu University Graduate School of Medical Sciences, Fukuoka, Fukuoka, 812-8582, Japan
| | - Toshiya Inaba
- Department of Molecular Oncology and Leukemia Program Project, Research Institute for Radiation Biology and Medicine, Hiroshima University, Hiroshima, Hiroshima, 734-8553, Japan
| | - Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata, 997-0052, Japan.
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5
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Peng Y, Liu J, Inuzuka H, Wei W. Targeted protein posttranslational modifications by chemically induced proximity for cancer therapy. J Biol Chem 2023; 299:104572. [PMID: 36870680 PMCID: PMC10050664 DOI: 10.1016/j.jbc.2023.104572] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023] Open
Abstract
Post-translational modifications (PTMs) regulate all aspects of protein function. Therefore, upstream regulators of PTMs, such as kinases, acetyltransferases, or methyltransferases, are potential therapeutic targets for human diseases, including cancer. To date, multiple inhibitors and/or agonists of these PTM upstream regulators are in clinical use, while others are still in development. However, these upstream regulators control not only the PTMs of disease-related target proteins but also other disease-irrelevant substrate proteins. Thus, nontargeted perturbing activities may introduce unwanted off-target toxicity issues that limit the use of these drugs in successful clinical applications. Therefore, alternative drugs that solely regulate a specific PTM of the disease-relevant protein target may provide a more precise effect in treating disease with relatively low side effects. To this end, chemically induced proximity has recently emerged as a powerful research tool, and several chemical inducers of proximity (CIPs) have been used to target and regulate protein ubiquitination, phosphorylation, acetylation, and glycosylation. These CIPs have a high potential to be translated into clinical drugs and several examples such as PROTACs and MGDs are now in clinical trials. Hence, more CIPs need to be developed to cover all types of PTMs, such as methylation and palmitoylation, thus providing a full spectrum of tools to regulate protein PTM in basic research and also in clinical application for effective cancer treatment.
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Affiliation(s)
- Yunhua Peng
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA; The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Center for Mitochondrial Biology and Medicine, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.
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6
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Atypical histone targets of PHD fingers. J Biol Chem 2023; 299:104601. [PMID: 36907441 PMCID: PMC10124903 DOI: 10.1016/j.jbc.2023.104601] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/12/2023] Open
Abstract
Plant homeodomain (PHD) fingers are structurally conserved zinc fingers that selectively bind unmodified or methylated at lysine 4 histone H3 tails. This binding stabilizes transcription factors and chromatin-modifying proteins at specific genomic sites, which is required for vital cellular processes, including gene expression and DNA repair. Several PHD fingers have recently been shown to recognize other regions of H3 or histone H4. In this review, we detail molecular mechanisms and structural features of the non-canonical histone recognition, discuss biological implications of the atypical interactions, highlight therapeutic potential of PHD fingers, and compare inhibition strategies.
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7
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Azemin WA, Alias N, Ali AM, Shamsir MS. In silico analysis prediction of HepTH1-5 as a potential therapeutic agent by targeting tumour suppressor protein networks. J Biomol Struct Dyn 2023; 41:1141-1167. [PMID: 34935583 DOI: 10.1080/07391102.2021.2017349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Many studies reported that the activation of tumour suppressor protein, p53 induced the human hepcidin expression. However, its expression decreased when p53 was silenced in human hepatoma cells. Contrary to Tilapia hepcidin TH1-5, HepTH1-5 was previously reported to trigger the p53 activation through the molecular docking approach. The INhibitor of Growth (ING) family members are also shown to directly interact with p53 and promote cell cycle arrest, senescence, apoptosis and participate in DNA replication and DNA damage responses to suppress the tumour initiation and progression. However, the interrelation between INGs and HepTH1-5 remains unknown. Therefore, this study aims to identify the mechanism and their protein interactions using in silico approaches. The finding revealed that HepTH1-5 and its ligands had interacted mostly on hotspot residues of ING proteins which involved in histone modifications via acetylation, phosphorylation, and methylation. This proves that HepTH1-5 might implicate in an apoptosis signalling pathway and preserve the protein structure and function of INGs by reducing the perturbation of histone binding upon oxidative stress response. This study would provide theoretical guidance for the design and experimental studies to decipher the role of HepTH1-5 as a potential therapeutic agent for cancer therapy. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Wan-Atirah Azemin
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia.,Faculty of Science, Bioinformatics Research Group (BIRG), Department of Biosciences, Universiti Teknologi Malaysia, Skudai, Malaysia
| | - Nadiawati Alias
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia
| | - Abdul Manaf Ali
- Faculty of Bioresources and Food Industry, School of Agriculture Science and Biotechnology, Universiti Sultan Zainal Abidin, Besut, Malaysia
| | - Mohd Shahir Shamsir
- Faculty of Science, Bioinformatics Research Group (BIRG), Department of Biosciences, Universiti Teknologi Malaysia, Skudai, Malaysia.,Faculty of Applied Sciences and Technology, Universiti Tun Hussein Onn Malaysia, Pagoh Higher Education Hub, Muar, Malaysia
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8
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Becht DC, Klein BJ, Kanai A, Jang SM, Cox KL, Zhou BR, Phanor SK, Zhang Y, Chen RW, Ebmeier CC, Lachance C, Galloy M, Fradet-Turcotte A, Bulyk ML, Bai Y, Poirier MG, Côté J, Yokoyama A, Kutateladze TG. MORF and MOZ acetyltransferases target unmethylated CpG islands through the winged helix domain. Nat Commun 2023; 14:697. [PMID: 36754959 PMCID: PMC9908889 DOI: 10.1038/s41467-023-36368-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 01/26/2023] [Indexed: 02/10/2023] Open
Abstract
Human acetyltransferases MOZ and MORF are implicated in chromosomal translocations associated with aggressive leukemias. Oncogenic translocations involve the far amino terminus of MOZ/MORF, the function of which remains unclear. Here, we identified and characterized two structured winged helix (WH) domains, WH1 and WH2, in MORF and MOZ. WHs bind DNA in a cooperative manner, with WH1 specifically recognizing unmethylated CpG sequences. Structural and genomic analyses show that the DNA binding function of WHs targets MORF/MOZ to gene promoters, stimulating transcription and H3K23 acetylation, and WH1 recruits oncogenic fusions to HOXA genes that trigger leukemogenesis. Cryo-EM, NMR, mass spectrometry and mutagenesis studies provide mechanistic insight into the DNA-binding mechanism, which includes the association of WH1 with the CpG-containing linker DNA and binding of WH2 to the dyad of the nucleosome. The discovery of WHs in MORF and MOZ and their DNA binding functions could open an avenue in developing therapeutics to treat diseases associated with aberrant MOZ/MORF acetyltransferase activities.
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Affiliation(s)
- Dustin C Becht
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Akinori Kanai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, the University of Tokyo, Kashiwa, Chiba, 277-0882, Japan
| | - Suk Min Jang
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC, G1R 3S3, Canada
| | - Khan L Cox
- Department of Physics, Ohio State University, Columbus, OH, 43210, USA
| | - Bing-Rui Zhou
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Sabrina K Phanor
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Yi Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Ruo-Wen Chen
- Department of Physics, Ohio State University, Columbus, OH, 43210, USA
| | | | - Catherine Lachance
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC, G1R 3S3, Canada
| | - Maxime Galloy
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC, G1R 3S3, Canada
| | - Amelie Fradet-Turcotte
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC, G1R 3S3, Canada
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | - Yawen Bai
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michael G Poirier
- Department of Physics, Ohio State University, Columbus, OH, 43210, USA
| | - Jacques Côté
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC, G1R 3S3, Canada.
| | - Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Yamagata, 997-0052, Japan.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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9
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Weber LM, Jia Y, Stielow B, Gisselbrecht S, Cao Y, Ren Y, Rohner I, King J, Rothman E, Fischer S, Simon C, Forné I, Nist A, Stiewe T, Bulyk M, Wang Z, Liefke R. The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain. Nucleic Acids Res 2023; 51:574-594. [PMID: 36537216 PMCID: PMC9881136 DOI: 10.1093/nar/gkac1188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/04/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
The lysine acetyltransferase KAT6A (MOZ, MYST3) belongs to the MYST family of chromatin regulators, facilitating histone acetylation. Dysregulation of KAT6A has been implicated in developmental syndromes and the onset of acute myeloid leukemia (AML). Previous work suggests that KAT6A is recruited to its genomic targets by a combinatorial function of histone binding PHD fingers, transcription factors and chromatin binding interaction partners. Here, we demonstrate that a winged helix (WH) domain at the very N-terminus of KAT6A specifically interacts with unmethylated CpG motifs. This DNA binding function leads to the association of KAT6A with unmethylated CpG islands (CGIs) genome-wide. Mutation of the essential amino acids for DNA binding completely abrogates the enrichment of KAT6A at CGIs. In contrast, deletion of a second WH domain or the histone tail binding PHD fingers only subtly influences the binding of KAT6A to CGIs. Overexpression of a KAT6A WH1 mutant has a dominant negative effect on H3K9 histone acetylation, which is comparable to the effects upon overexpression of a KAT6A HAT domain mutant. Taken together, our work revealed a previously unrecognized chromatin recruitment mechanism of KAT6A, offering a new perspective on the role of KAT6A in gene regulation and human diseases.
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Affiliation(s)
- Lisa Marie Weber
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Yulin Jia
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Bastian Stielow
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Stephen S Gisselbrecht
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Yinghua Cao
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Yanpeng Ren
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Iris Rohner
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Jessica King
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Elisabeth Rothman
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sabrina Fischer
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Clara Simon
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Ignasi Forné
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-University (LMU) Munich, Martinsried 82152, Germany
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps University of Marburg, Marburg 35043, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps University of Marburg, Marburg 35043, Germany
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Zhanxin Wang
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Robert Liefke
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
- Department of Hematology, Oncology, and Immunology, University Hospital Giessen and Marburg, Marburg 35043, Germany
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10
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Viita T, Côté J. The MOZ-BRPF1 acetyltransferase complex in epigenetic crosstalk linked to gene regulation, development, and human diseases. Front Cell Dev Biol 2023; 10:1115903. [PMID: 36712963 PMCID: PMC9873972 DOI: 10.3389/fcell.2022.1115903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/29/2022] [Indexed: 01/12/2023] Open
Abstract
Acetylation of lysine residues on histone tails is an important post-translational modification (PTM) that regulates chromatin dynamics to allow gene transcription as well as DNA replication and repair. Histone acetyltransferases (HATs) are often found in large multi-subunit complexes and can also modify specific lysine residues in non-histone substrates. Interestingly, the presence of various histone PTM recognizing domains (reader domains) in these complexes ensures their specific localization, enabling the epigenetic crosstalk and context-specific activity. In this review, we will cover the biochemical and functional properties of the MOZ-BRPF1 acetyltransferase complex, underlining its role in normal biological processes as well as in disease progression. We will discuss how epigenetic reader domains within the MOZ-BRPF1 complex affect its chromatin localization and the histone acetyltransferase specificity of the complex. We will also summarize how MOZ-BRPF1 is linked to development via controlling cell stemness and how mutations or changes in expression levels of MOZ/BRPF1 can lead to developmental disorders or cancer. As a last touch, we will review the latest drug candidates for these two proteins and discuss the therapeutic possibilities.
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Affiliation(s)
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Oncology Division of Centre Hospitalier Universitaire de Québec-Université Laval Research Center, Laval University Cancer Research Center, Quebec City, QC, Canada
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11
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Yokoyama A. Role of the MOZ/MLL-mediated transcriptional activation system for self-renewal in normal hematopoiesis and leukemogenesis. FEBS J 2022; 289:7987-8002. [PMID: 34482632 PMCID: PMC10078767 DOI: 10.1111/febs.16180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 07/17/2021] [Accepted: 09/03/2021] [Indexed: 01/14/2023]
Abstract
Homeostasis in the blood system is maintained by the balance between self-renewing stem cells and nonstem cells. To promote self-renewal, transcriptional regulators maintain epigenetic information during multiple rounds of cell division. Mutations in such transcriptional regulators cause aberrant self-renewal, leading to leukemia. MOZ, a histone acetyltransferase, and MLL, a histone methyltransferase, are transcriptional regulators that promote the self-renewal of hematopoietic stem cells. Gene rearrangements of MOZ and MLL generate chimeric genes encoding fusion proteins that function as constitutively active forms. These MOZ and MLL fusion proteins constitutively activate transcription of their target genes and cause aberrant self-renewal in committed hematopoietic progenitors, which normally do not self-renew. Recent progress in the field suggests that MOZ and MLL are part of a transcriptional activation system that activates the transcription of genes with nonmethylated CpG-rich promoters. The nonmethylated state of CpGs is normally maintained during cell divisions from the mother cell to the daughter cells. Thus, the MOZ/MLL-mediated transcriptional activation system replicates the expression profile of mother cells in daughter cells by activating the transcription of genes previously transcribed in the mother cell. This review summarizes the functions of the components of the MOZ/MLL-mediated transcriptional activation system and their roles in the promotion of self-renewal.
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Affiliation(s)
- Akihiko Yokoyama
- Tsuruoka Metabolomics Laboratory, National Cancer Center, Tsuruoka, Japan.,National Cancer Center Research Institute, Tokyo, Japan
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12
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Zeng F, Yang Y, Xu Z, Wang Z, Ke H, Zhang J, Dong T, Yang W, Wang J. Clinical manifestations and genetic analysis of a newborn with Arboleda−Tham syndrome. Front Genet 2022; 13:990098. [PMID: 36386811 PMCID: PMC9641261 DOI: 10.3389/fgene.2022.990098] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/22/2022] [Indexed: 11/27/2022] Open
Abstract
Arboleda−Tham syndrome (ARTHS) is a rare disorder first characterized in 2015 and is caused by mutations in lysine (K) acetyltransferase 6A (KAT6A, a.k.a. MOZ, MYST3). Its clinical symptoms have rarely been reported in newborns from birth up to the first few months after birth. In this study, a newborn was diagnosed with ARTHS based on the clinical symptoms and a mutation c.3937G>A (p.Asp1313Asn) in KAT6A. The clinical manifestations, diagnosis, and treatment of the newborn with ARTHS were recorded during follow-up observations. The main symptoms of the proband at birth were asphyxia, involuntary breathing, low muscle tone, early feeding, movement difficulties, weak crying, weakened muscle tone of the limbs, and embrace reflex, and facial features were not obvious at birth. There was obvious developmental delay, as well as hypotonic and oro-intestinal problems in the first few months after birth. Mouse growth factor was used to nourish the brain nerves, and touching, kneading the back, passive movements of the limbs, and audio−visual stimulation were used for rehabilitation. We hope that this study expands the phenotypic spectrum of this syndrome to newborns and the library of KAT6A mutations that lead to ARTHS. Consequently, the data can be used as a basis for genetic counseling and in clinical and prenatal diagnosis for ARTHS prevention.
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Affiliation(s)
- Feng Zeng
- Department of Neonatology, Xuancheng Central Hospital, Xuancheng, Anhui, China
| | - Yue Yang
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Zhaohui Xu
- Department of Paediatrics, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Ziwen Wang
- Graduate School, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Huan Ke
- Nursing Department, Xuancheng Central Hospital, Xuancheng, Anhui, China
| | - Jianhong Zhang
- Department of Neonatology, Xuancheng Central Hospital, Xuancheng, Anhui, China
| | - Tongtong Dong
- Graduate School, Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Wenming Yang
- Department of Neurology, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
- *Correspondence: Wenming Yang, ; Jiuxiang Wang,
| | - Jiuxiang Wang
- Experimental Center of Clinical Research, The First Affiliated Hospital of Anhui University of Chinese Medicine, Hefei, Anhui, China
- *Correspondence: Wenming Yang, ; Jiuxiang Wang,
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13
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Zu G, Liu Y, Cao J, Zhao B, Zhang H, You L. BRPF1-KAT6A/KAT6B Complex: Molecular Structure, Biological Function and Human Disease. Cancers (Basel) 2022; 14:4068. [PMID: 36077605 PMCID: PMC9454415 DOI: 10.3390/cancers14174068] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
The bromodomain and PHD finger-containing protein1 (BRPF1) is a member of family IV of the bromodomain-containing proteins that participate in the post-translational modification of histones. It functions in the form of a tetrameric complex with a monocytic leukemia zinc finger protein (MOZ or KAT6A), MOZ-related factor (MORF or KAT6B) or HAT bound to ORC1 (HBO1 or KAT7) and two small non-catalytic proteins, the inhibitor of growth 5 (ING5) or the paralog ING4 and MYST/Esa1-associated factor 6 (MEAF6). Mounting studies have demonstrated that all the four core subunits play crucial roles in different biological processes across diverse species, such as embryonic development, forebrain development, skeletal patterning and hematopoiesis. BRPF1, KAT6A and KAT6B mutations were identified as the cause of neurodevelopmental disorders, leukemia, medulloblastoma and other types of cancer, with germline mutations associated with neurodevelopmental disorders displaying intellectual disability, and somatic variants associated with leukemia, medulloblastoma and other cancers. In this paper, we depict the molecular structures and biological functions of the BRPF1-KAT6A/KAT6B complex, summarize the variants of the complex related to neurodevelopmental disorders and cancers and discuss future research directions and therapeutic potentials.
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Affiliation(s)
- Gaoyu Zu
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Ying Liu
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Jingli Cao
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Baicheng Zhao
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Hang Zhang
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Linya You
- Department of Human Anatomy & Histoembryology, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
- Shanghai Key Laboratory of Medical Imaging Computing and Computer Assisted Intervention, Fudan University, Shanghai 200040, China
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14
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Cenik BK, Sze CC, Ryan CA, Das S, Cao K, Douillet D, Rendleman EJ, Zha D, Khan NH, Bartom E, Shilatifard A. A synthetic lethality screen reveals ING5 as a genetic dependency of catalytically dead Set1A/COMPASS in mouse embryonic stem cells. Proc Natl Acad Sci U S A 2022; 119:e2118385119. [PMID: 35500115 PMCID: PMC9171609 DOI: 10.1073/pnas.2118385119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/21/2022] [Indexed: 11/18/2022] Open
Abstract
Embryonic stem cells (ESCs) are defined by their ability to self-renew and the potential to differentiate into all tissues of the developing organism. We previously demonstrated that deleting the catalytic SET domain of the Set1A/complex of proteins associated with SET1 histone methyltransferase (Set1A/COMPASS) in mouse ESCs does not impair their viability or ability to self-renew; however, it leads to defects in differentiation. The precise mechanisms by which Set1A executes these functions remain to be elucidated. In this study, we demonstrate that mice lacking the SET domain of Set1A are embryonic lethal at a stage that is unique from null alleles. To gain insight into Set1A function in regulating pluripotency, we conducted a CRISPR/Cas9-mediated dropout screen and identified the MOZ/MORF (monocytic leukaemia zinc finger protein/monocytic leukaemia zinc finger protein-related factor) and HBO1 (HAT bound to ORC1) acetyltransferase complex member ING5 as a synthetic perturbation to Set1A. The loss of Ing5 in Set1AΔSET mouse ESCs decreases the fitness of these cells, and the simultaneous loss of ING5 and in Set1AΔSET leads to up-regulation of differentiation-associated genes. Taken together, our results point toward Set1A/COMPASS and ING5 as potential coregulators of the self-renewal and differentiation status of ESCs.
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Affiliation(s)
- Bercin K. Cenik
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Christie C. Sze
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Caila A. Ryan
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Siddhartha Das
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Kaixiang Cao
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Delphine Douillet
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Emily J. Rendleman
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Didi Zha
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Nabiha Haleema Khan
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Elizabeth Bartom
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Robert H. Lurie NCI Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
- Robert H. Lurie NCI Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL 60611
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15
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Xu Y, Shi Z, Bao L. An expanding repertoire of protein acylations. Mol Cell Proteomics 2022; 21:100193. [PMID: 34999219 PMCID: PMC8933697 DOI: 10.1016/j.mcpro.2022.100193] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 12/22/2021] [Accepted: 01/04/2022] [Indexed: 01/03/2023] Open
Abstract
Protein post-translational modifications play key roles in multiple cellular processes by allowing rapid reprogramming of individual protein functions. Acylation, one of the most important post-translational modifications, is involved in different physiological activities including cell differentiation and energy metabolism. In recent years, the progression in technologies, especially the antibodies against acylation and the highly sensitive and effective mass spectrometry–based proteomics, as well as optimized functional studies, greatly deepen our understanding of protein acylation. In this review, we give a general overview of the 12 main protein acylations (formylation, acetylation, propionylation, butyrylation, malonylation, succinylation, glutarylation, palmitoylation, myristoylation, benzoylation, crotonylation, and 2-hydroxyisobutyrylation), including their substrates (histones and nonhistone proteins), regulatory enzymes (writers, readers, and erasers), biological functions (transcriptional regulation, metabolic regulation, subcellular targeting, protein–membrane interactions, protein stability, and folding), and related diseases (cancer, diabetes, heart disease, neurodegenerative disease, and viral infection), to present a complete picture of protein acylations and highlight their functional significance in future research. Provide a general overview of the 12 main protein acylations. Acylation of viral proteins promotes viral integration and infection. Hyperacylation of histone has antitumous and neuroprotective effects. MS is widely used in the identification of acylation but has its challenges.
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Affiliation(s)
- Yuxuan Xu
- Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research center for Cancer, 300060, Tianjin, China
| | - Zhenyu Shi
- Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research center for Cancer, 300060, Tianjin, China
| | - Li Bao
- Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research center for Cancer, 300060, Tianjin, China.
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16
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Conserved Structure and Evolution of DPF Domain of PHF10-The Specific Subunit of PBAF Chromatin Remodeling Complex. Int J Mol Sci 2021; 22:ijms222011134. [PMID: 34681795 PMCID: PMC8538644 DOI: 10.3390/ijms222011134] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 11/17/2022] Open
Abstract
Transcription activation factors and multisubunit coactivator complexes get recruited at specific chromatin sites via protein domains that recognize histone modifications. Single PHDs (plant homeodomains) interact with differentially modified H3 histone tails. Double PHD finger (DPF) domains possess a unique structure different from PHD and are found in six proteins: histone acetyltransferases MOZ and MORF; chromatin remodeling complex BAF (DPF1–3); and chromatin remodeling complex PBAF (PHF10). Among them, PHF10 stands out due to the DPF sequence, structure, and functions. PHF10 is ubiquitously expressed in developing and adult organisms as four isoforms differing in structure (the presence or absence of DPF) and transcription regulation functions. Despite the importance of the DPF domain of PHF10 for transcription activation, its structure remains undetermined. We performed homology modeling of the human PHF10 DPF domain and determined common and distinct features in structure and histone modifications recognition capabilities, which can affect PBAF complex chromatin recruitment. We also traced the evolution of DPF1–3 and PHF10 genes from unicellular to vertebrate organisms. The data reviewed suggest that the DPF domain of PHF10 plays an important role in SWI/SNF-dependent chromatin remodeling during transcription activation.
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17
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The role of MOZ/KAT6A in hematological malignancies and advances in MOZ/KAT6A inhibitors. Pharmacol Res 2021; 174:105930. [PMID: 34626770 DOI: 10.1016/j.phrs.2021.105930] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/01/2021] [Accepted: 10/03/2021] [Indexed: 11/22/2022]
Abstract
Hematological malignancies, unlike solid tumors, are a group of malignancies caused by abnormal differentiation of hematopoietic stem cells. Monocytic leukemia zinc finger protein (MOZ), a member of the MYST (MOZ, Ybf2/Sas3, Sas2, Tip60) family, is a histone acetyltransferase. MOZ is involved in various cellular functions: generation and maintenance of hematopoietic stem cells, development of erythroid cells, B-lineage progenitors and myeloid cells, and regulation of cellular senescence. Studies have shown that MOZ is susceptible to translocation in chromosomal rearrangements to form fusion genes, leading to the fusion of MOZ with other cellular regulators to form MOZ fusion proteins. Different MOZ fusion proteins have different roles, such as in the development and progression of hematological malignancies and inhibition of cellular senescence. Thus, MOZ is an attractive target, and targeting MOZ to design small-molecule drugs can help to treat hematological malignancies. This review summarizes recent progress in biology and medicinal chemistry for the histone acetyltransferase MOZ. In the biology section, MOZ and cofactors, structures of MOZ and related HATs, MOZ and fusion proteins, and roles of MOZ in cancer are discussed. In medicinal chemistry, recent developments in MOZ inhibitors are summarized.
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18
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Yu B, Luo F, Sun B, Liu W, Shi Q, Cheng S, Chen C, Chen G, Li Y, Feng H. KAT6A Acetylation of SMAD3 Regulates Myeloid-Derived Suppressor Cell Recruitment, Metastasis, and Immunotherapy in Triple-Negative Breast Cancer. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100014. [PMID: 34392614 PMCID: PMC8529494 DOI: 10.1002/advs.202100014] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Aberrant SMAD3 activation has been implicated as a driving event in cancer metastasis, yet the underlying mechanisms are still elusive. Here, SMAD3 is identified as a nonhistone substrate of lysine acetyltransferase 6A (KAT6A). The acetylation of SMAD3 at K20 and K117 by KAT6A promotes SMAD3 association with oncogenic chromatin modifier tripartite motif-containing 24 (TRIM24) and disrupts SMAD3 interaction with tumor suppressor TRIM33. This event in turn promotes KAT6A-acetylated H3K23-mediated recruitment of TRIM24-SMAD3 complex to chromatin and thereby increases SMAD3 activation and immune response-related cytokine expression, leading to enhanced breast cancer stem-like cell stemness, myeloid-derived suppressor cell (MDSC) recruitment, and triple-negative breast cancer (TNBC) metastasis. Inhibiting KAT6A in combination with anti-PD-L1 therapy in treating TNBC xenograft-bearing animals markedly attenuates metastasis and provides a significant survival benefit. Thus, the work presents a KAT6A acetylation-dependent regulatory mechanism governing SMAD3 oncogenic function and provides insight into how targeting an epigenetic factor with immunotherapies enhances the antimetastasis efficacy.
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Affiliation(s)
- Bo Yu
- State Key Laboratory of Oncogenes and Related GenesRenji‐Med X Clinical Stem Cell Research CenterRen Ji HospitalShanghai Cancer InstituteSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Fei Luo
- State Key Laboratory of Oncogenes and Related GenesRenji‐Med X Clinical Stem Cell Research CenterRen Ji HospitalShanghai Cancer InstituteSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Bowen Sun
- State Key Laboratory of Oncogenes and Related GenesRenji‐Med X Clinical Stem Cell Research CenterRen Ji HospitalShanghai Cancer InstituteSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Wenxue Liu
- State Key Laboratory of Oncogenes and Related GenesRenji‐Med X Clinical Stem Cell Research CenterRen Ji HospitalShanghai Cancer InstituteSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Qiqi Shi
- State Key Laboratory of Oncogenes and Related GenesRenji‐Med X Clinical Stem Cell Research CenterRen Ji HospitalShanghai Cancer InstituteSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Shi‐Yuan Cheng
- Department of NeurologyLou and Jean Malnati Brain Tumor InstituteThe Robert H. Lurie Comprehensive Cancer CenterSimpson Querrey Institute for EpigeneticsNorthwestern University Feinberg School of MedicineChicagoIL60611USA
| | - Ceshi Chen
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan ProvinceKunming Institute of ZoologyChinese Academy of SciencesKunming650223China
| | - Guoqiang Chen
- State Key Laboratory of Oncogenes and Related GenesRenji‐Med X Clinical Stem Cell Research CenterRen Ji HospitalShanghai Cancer InstituteSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Yanxin Li
- Key Laboratory of Pediatric Hematology and Oncology Ministry of HealthDepartment of Hematology and OncologyShanghai Children's Medical CenterSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
| | - Haizhong Feng
- State Key Laboratory of Oncogenes and Related GenesRenji‐Med X Clinical Stem Cell Research CenterRen Ji HospitalShanghai Cancer InstituteSchool of MedicineShanghai Jiao Tong UniversityShanghai200127China
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19
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Cheng CLH, Tsang FHC, Wei L, Chen M, Chin DWC, Shen J, Law CT, Lee D, Wong CCL, Ng IOL, Wong CM. Bromodomain-containing protein BRPF1 is a therapeutic target for liver cancer. Commun Biol 2021; 4:888. [PMID: 34285329 PMCID: PMC8292510 DOI: 10.1038/s42003-021-02405-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 06/30/2021] [Indexed: 12/24/2022] Open
Abstract
Epigenetic deregulation plays an essential role in hepatocellular carcinoma (HCC) progression. Bromodomains are epigenetic "readers" of histone acetylation. Recently, bromodomain inhibitors have exhibited promising therapeutic potential for cancer treatment. Using transcriptome sequencing, we identified BRPF1 (bromodomain and PHD finger containing 1) as the most significantly upregulated gene among the 43 bromodomain-containing genes in human HCC. BRPF1 upregulation was significantly associated with poor patient survival. Gene ablation or pharmacological inactivation of BRPF1 significantly attenuated HCC cell growth in vitro and in vivo. BRPF1 was involved in cell cycle progression, senescence and cancer stemness. Transcriptome sequencing revealed that BRPF1 is a master regulator controlling the expression of multiple key oncogenes, including E2F2 and EZH2. We demonstrated that BRPF1 activated E2F2 and EZH2 expression by facilitating promoter H3K14 acetylation through MOZ/MORF complex. In conclusion, BRPF1 is frequently upregulated in human HCCs. Targeting BRPF1 may be an approach for HCC treatment.
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Affiliation(s)
- Carol Lai-Hung Cheng
- State Key Laboratory of Liver Research, The University of Hong Kong, Pok Fu Lam, Hong Kong.,Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Felice Hoi-Ching Tsang
- State Key Laboratory of Liver Research, The University of Hong Kong, Pok Fu Lam, Hong Kong.,Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Lai Wei
- State Key Laboratory of Liver Research, The University of Hong Kong, Pok Fu Lam, Hong Kong.,Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Mengnuo Chen
- State Key Laboratory of Liver Research, The University of Hong Kong, Pok Fu Lam, Hong Kong.,Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Don Wai-Ching Chin
- State Key Laboratory of Liver Research, The University of Hong Kong, Pok Fu Lam, Hong Kong.,Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Jialing Shen
- State Key Laboratory of Liver Research, The University of Hong Kong, Pok Fu Lam, Hong Kong.,Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Cheuk-Ting Law
- State Key Laboratory of Liver Research, The University of Hong Kong, Pok Fu Lam, Hong Kong.,Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Derek Lee
- State Key Laboratory of Liver Research, The University of Hong Kong, Pok Fu Lam, Hong Kong.,Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Carmen Chak-Lui Wong
- State Key Laboratory of Liver Research, The University of Hong Kong, Pok Fu Lam, Hong Kong.,Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Irene Oi-Lin Ng
- State Key Laboratory of Liver Research, The University of Hong Kong, Pok Fu Lam, Hong Kong.,Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong
| | - Chun-Ming Wong
- State Key Laboratory of Liver Research, The University of Hong Kong, Pok Fu Lam, Hong Kong. .,Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pok Fu Lam, Hong Kong.
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Abstract
The genetic information of human cells is stored in the context of chromatin, which is subjected to DNA methylation and various histone modifications. Such a 'language' of chromatin modification constitutes a fundamental means of gene and (epi)genome regulation, underlying a myriad of cellular and developmental processes. In recent years, mounting evidence has demonstrated that miswriting, misreading or mis-erasing of the modification language embedded in chromatin represents a common, sometimes early and pivotal, event across a wide range of human cancers, contributing to oncogenesis through the induction of epigenetic, transcriptomic and phenotypic alterations. It is increasingly clear that cancer-related metabolic perturbations and oncohistone mutations also directly impact chromatin modification, thereby promoting cancerous transformation. Phase separation-based deregulation of chromatin modulators and chromatin structure is also emerging to be an important underpinning of tumorigenesis. Understanding the various molecular pathways that underscore a misregulated chromatin language in cancer, together with discovery and development of more effective drugs to target these chromatin-related vulnerabilities, will enhance treatment of human malignancies.
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Affiliation(s)
- Shuai Zhao
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics and Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
| | - Gang Greg Wang
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics and Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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21
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Mechanistic similarities in recognition of histone tails and DNA by epigenetic readers. Curr Opin Struct Biol 2021; 71:1-6. [PMID: 33993059 DOI: 10.1016/j.sbi.2021.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/03/2021] [Accepted: 04/08/2021] [Indexed: 11/21/2022]
Abstract
The past two decades have witnessed rapid advances in the identification and characterization of epigenetic readers, capable of recognizing or reading post-translational modifications in histones. More recently, a new set of readers with the ability to interact with the nucleosome through concomitant binding to histones and DNA has emerged. In this review, we discuss mechanistic insights underlying bivalent histone and DNA recognition by newly characterized readers and highlight the importance of binding to DNA for their association with chromatin.
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22
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Ren X, Zhou Y, Xue Z, Hao N, Li Y, Guo X, Wang D, Shi X, Li H. Histone benzoylation serves as an epigenetic mark for DPF and YEATS family proteins. Nucleic Acids Res 2021; 49:114-126. [PMID: 33290558 PMCID: PMC7797077 DOI: 10.1093/nar/gkaa1130] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/24/2020] [Accepted: 11/07/2020] [Indexed: 02/01/2023] Open
Abstract
Histone modifications and their functional readout serve as an important mechanism for gene regulation. Lysine benzoylation (Kbz) on histones is a recently identified acylation mark associated with active transcription. However, it remains to be explored whether putative readers exist to recognize this epigenetic mark. Here, our systematic binding studies demonstrated that the DPF and YEATS, but not the Bromodomain family members, are readers for histone Kbz. Co-crystal structural analyses revealed a 'hydrophobic encapsulation' and a 'tip-sensor' mechanism for Kbz readout by DPF and YEATS, respectively. Moreover, the DPF and YEATS family members display subtle yet unique features to create somewhat flexible engagements of different acylation marks. For instance, YEATS2 but not the other YEATS proteins exhibits best preference for Kbz than lysine acetylation and crotonylation due to its wider 'tip-sensor' pocket. The levels of histone benzoylation in cultured cells or in mice are upregulated upon sodium benzoate treatment, highlighting its dynamic regulation. In summary, our work identifies the first readers for histone Kbz and reveals the molecular basis underlying Kbz recognition, thus paving the way for further functional dissections of histone benzoylation.
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Affiliation(s)
- Xiangle Ren
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yang Zhou
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Zhaoyu Xue
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Ning Hao
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yuanyuan Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaohuan Guo
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Daliang Wang
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xiaobing Shi
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI 49503, USA
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
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23
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Wiesel-Motiuk N, Assaraf YG. The key roles of the lysine acetyltransferases KAT6A and KAT6B in physiology and pathology. Drug Resist Updat 2020; 53:100729. [PMID: 33130515 DOI: 10.1016/j.drup.2020.100729] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/21/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022]
Abstract
Histone modifications and more specifically ε-lysine acylations are key epigenetic regulators that control chromatin structure and gene transcription, thereby impacting on various important cellular processes and phenotypes. Furthermore, lysine acetylation of many non-histone proteins is involved in key cellular processes including transcription, DNA damage repair, metabolism, cellular proliferation, mitosis, signal transduction, protein folding, and autophagy. Acetylation affects protein functions through multiple mechanisms including regulation of protein stability, enzymatic activity, subcellular localization, crosstalk with other post-translational modifications as well as regulation of protein-protein and protein-DNA interactions. The paralogous lysine acetyltransferases KAT6A and KAT6B which belong to the MYST family of acetyltransferases, were first discovered approximately 25 years ago. KAT6 acetyltransferases acylate both histone H3 and non-histone proteins. In this respect, KAT6 acetyltransferases play key roles in regulation of transcription, various developmental processes, maintenance of hematopoietic and neural stem cells, regulation of hematopoietic cell differentiation, cell cycle progression as well as mitosis. In the current review, we discuss the physiological functions of the acetyltransferases KAT6A and KAT6B as well as their functions under pathological conditions of aberrant expression, leading to several developmental syndromes and cancer. Importantly, both upregulation and downregulation of KAT6 proteins was shown to play a role in cancer formation, progression, and therapy resistance, suggesting that they can act as oncogenes or tumor suppressors. We also describe reciprocal regulation of expression between KAT6 proteins and several microRNAs as well as their involvement in cancer formation, progression and resistance to therapy.
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Affiliation(s)
- Naama Wiesel-Motiuk
- The Fred Wyszkowski Cancer Research Laboratory, Dept. of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Yehuda G Assaraf
- The Fred Wyszkowski Cancer Research Laboratory, Dept. of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel.
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24
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Soshnikova NV, Sheynov AA, Tatarskiy EV, Georgieva SG. The DPF Domain As a Unique Structural Unit Participating in Transcriptional Activation, Cell Differentiation, and Malignant Transformation. Acta Naturae 2020; 12:57-65. [PMID: 33456978 PMCID: PMC7800603 DOI: 10.32607/actanaturae.11092] [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] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 09/28/2020] [Indexed: 12/21/2022] Open
Abstract
The DPF (double PHD finger) domain consists of two PHD fingers organized in tandem. The two PHD-finger domains within a DPF form a single structure that interacts with the modification of the N-terminal histone fragment in a way different from that for single PHD fingers. Several histone modifications interacting with the DPF domain have already been identified. They include acetylation of H3K14 and H3K9, as well as crotonylation of H3K14. These modifications are found predominantly in transcriptionally active chromatin. Proteins containing DPF belong to two classes of protein complexes, which are the transcriptional coactivators involved in the regulation of the chromatin structure. These are the histone acetyltransferase complex belonging to the MYST family and the SWI/SNF chromatin-remodeling complex. The DPF domain is responsible for the specificity of the interactions between these complexes and chromatin. Proteins containing DPF play a crucial role in the activation of the transcription of a number of genes expressed during the development of an organism. These genes are important in the differentiation and malignant transformation of mammalian cells.
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Affiliation(s)
- N. V. Soshnikova
- Institute of Gene Biology Russian Academy of Sciences, Moscow, 119334 Russia
| | - A. A. Sheynov
- Institute of Gene Biology Russian Academy of Sciences, Moscow, 119334 Russia
| | - Eu. V. Tatarskiy
- Institute of Gene Biology Russian Academy of Sciences, Moscow, 119334 Russia
| | - S. G. Georgieva
- Institute of Gene Biology Russian Academy of Sciences, Moscow, 119334 Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991 Russia
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25
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Miyamoto R, Okuda H, Kanai A, Takahashi S, Kawamura T, Matsui H, Kitamura T, Kitabayashi I, Inaba T, Yokoyama A. Activation of CpG-Rich Promoters Mediated by MLL Drives MOZ-Rearranged Leukemia. Cell Rep 2020; 32:108200. [DOI: 10.1016/j.celrep.2020.108200] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 07/28/2020] [Accepted: 09/03/2020] [Indexed: 01/04/2023] Open
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26
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Koutelou E, Farria AT, Dent SYR. Complex functions of Gcn5 and Pcaf in development and disease. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194609. [PMID: 32730897 DOI: 10.1016/j.bbagrm.2020.194609] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 12/12/2022]
Abstract
A wealth of biochemical and cellular data, accumulated over several years by multiple groups, has provided a great degree of insight into the molecular mechanisms of actions of GCN5 and PCAF in gene activation. Studies of these lysine acetyltransferases (KATs) in vitro, in cultured cells, have revealed general mechanisms for their recruitment by sequence-specific binding factors and their molecular functions as transcriptional co-activators. Genetic studies indicate that GCN5 and PCAF are involved in multiple developmental processes in vertebrates, yet our understanding of their molecular functions in these contexts remains somewhat rudimentary. Understanding the functions of GCN5/PCAF in developmental processes provides clues to the roles of these KATs in disease states. Here we will review what is currently known about the developmental roles of GCN5 and PCAF, as well as emerging role of these KATs in oncogenesis.
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Affiliation(s)
- Evangelia Koutelou
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, United States of America; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States of America
| | - Aimee T Farria
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, United States of America; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States of America
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Science Park, Smithville, TX 78957, United States of America; Center for Cancer Epigenetics, University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States of America.
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27
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Small Molecules Targeting the Specific Domains of Histone-Mark Readers in Cancer Therapy. Molecules 2020; 25:molecules25030578. [PMID: 32013155 PMCID: PMC7037402 DOI: 10.3390/molecules25030578] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/11/2022] Open
Abstract
Epigenetic modifications (or epigenetic tags) on DNA and histones not only alter the chromatin structure, but also provide a recognition platform for subsequent protein recruitment and enable them to acquire executive instructions to carry out specific intracellular biological processes. In cells, different epigenetic-tags on DNA and histones are often recognized by the specific domains in proteins (readers), such as bromodomain (BRD), chromodomain (CHD), plant homeodomain (PHD), Tudor domain, Pro-Trp-Trp-Pro (PWWP) domain and malignant brain tumor (MBT) domain. Recent accumulating data reveal that abnormal intracellular histone modifications (histone marks) caused by tumors can be modulated by small molecule-mediated changes in the activity of the above domains, suggesting that small molecules targeting histone-mark reader domains may be the trend of new anticancer drug development. Here, we summarize the protein domains involved in histone-mark recognition, and introduce recent research findings about small molecules targeting histone-mark readers in cancer therapy.
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28
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Klein BJ, Jang SM, Lachance C, Mi W, Lyu J, Sakuraba S, Krajewski K, Wang WW, Sidoli S, Liu J, Zhang Y, Wang X, Warfield BM, Kueh AJ, Voss AK, Thomas T, Garcia BA, Liu WR, Strahl BD, Kono H, Li W, Shi X, Côté J, Kutateladze TG. Histone H3K23-specific acetylation by MORF is coupled to H3K14 acylation. Nat Commun 2019; 10:4724. [PMID: 31624313 PMCID: PMC6797804 DOI: 10.1038/s41467-019-12551-5] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 09/17/2019] [Indexed: 12/22/2022] Open
Abstract
Acetylation of histone H3K23 has emerged as an essential posttranslational modification associated with cancer and learning and memory impairment, yet our understanding of this epigenetic mark remains insufficient. Here, we identify the native MORF complex as a histone H3K23-specific acetyltransferase and elucidate its mechanism of action. The acetyltransferase function of the catalytic MORF subunit is positively regulated by the DPF domain of MORF (MORFDPF). The crystal structure of MORFDPF in complex with crotonylated H3K14 peptide provides mechanistic insight into selectivity of this epigenetic reader and its ability to recognize both histone and DNA. ChIP data reveal the role of MORFDPF in MORF-dependent H3K23 acetylation of target genes. Mass spectrometry, biochemical and genomic analyses show co-existence of the H3K23ac and H3K14ac modifications in vitro and co-occupancy of the MORF complex, H3K23ac, and H3K14ac at specific loci in vivo. Our findings suggest a model in which interaction of MORFDPF with acylated H3K14 promotes acetylation of H3K23 by the native MORF complex to activate transcription.
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Affiliation(s)
- Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Suk Min Jang
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC, G1R 3S3, Canada
| | - Catherine Lachance
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC, G1R 3S3, Canada
| | - Wenyi Mi
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Jie Lyu
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA.,Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shun Sakuraba
- Molecular Modeling and Simulation Group, National Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Kyoto, 619 0215, Japan
| | - Krzysztof Krajewski
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Wesley W Wang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Simone Sidoli
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, 10461, USA
| | - Jiuyang Liu
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Yi Zhang
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Xiaolu Wang
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Becka M Warfield
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Andrew J Kueh
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3050, Australia
| | - Anne K Voss
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3050, Australia
| | - Tim Thomas
- The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, 3050, Australia
| | - Benjamin A Garcia
- Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Wenshe R Liu
- Department of Chemistry, Texas A&M University, College Station, TX, 77843, USA
| | - Brian D Strahl
- Department of Biochemistry & Biophysics, The University of North Carolina School of Medicine, Chapel Hill, NC, 27599, USA
| | - Hidetoshi Kono
- Molecular Modeling and Simulation Group, National Institute for Quantum Life Science, National Institutes for Quantum and Radiological Science and Technology, Kizugawa, Kyoto, 619 0215, Japan
| | - Wei Li
- Department of Biological Chemistry, University of California, Irvine, Irvine, CA, 92697, USA.,Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Xiaobing Shi
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Jacques Côté
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC, G1R 3S3, Canada.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
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29
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TRIM66 reads unmodified H3R2K4 and H3K56ac to respond to DNA damage in embryonic stem cells. Nat Commun 2019; 10:4273. [PMID: 31537782 PMCID: PMC6753139 DOI: 10.1038/s41467-019-12126-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 08/20/2019] [Indexed: 12/19/2022] Open
Abstract
Recognition of specific chromatin modifications by distinct structural domains within “reader” proteins plays a critical role in the maintenance of genomic stability. However, the specific mechanisms involved in this process remain unclear. Here we report that the PHD-Bromo tandem domain of tripartite motif-containing 66 (TRIM66) recognizes the unmodified H3R2-H3K4 and acetylated H3K56. The aberrant deletion of Trim66 results in severe DNA damage and genomic instability in embryonic stem cells (ESCs). Moreover, we find that the recognition of histone modification by TRIM66 is critical for DNA damage repair (DDR) in ESCs. TRIM66 recruits Sirt6 to deacetylate H3K56ac, negatively regulating the level of H3K56ac and facilitating the initiation of DDR. Importantly, Trim66-deficient blastocysts also exhibit higher levels of H3K56ac and DNA damage. Collectively, the present findings indicate the vital role of TRIM66 in DDR in ESCs, establishing the relationship between histone readers and maintenance of genomic stability. TRIM66 protein has an N-terminal tripartite motif and a C-terminal PHD Bromodomain. Here the authors show the specific histone modification recognition of TRIM66-PHD-Bromodomain through crystallography and biochemistry assay, and further reveal that TRIM66 recognition of certain histone modification is important for DNA damage repair in ESCs.
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30
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Sheikh BN, Akhtar A. The many lives of KATs - detectors, integrators and modulators of the cellular environment. Nat Rev Genet 2019; 20:7-23. [PMID: 30390049 DOI: 10.1038/s41576-018-0072-4] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Research over the past three decades has firmly established lysine acetyltransferases (KATs) as central players in regulating transcription. Recent advances in genomic sequencing, metabolomics, animal models and mass spectrometry technologies have uncovered unexpected new roles for KATs at the nexus between the environment and transcriptional regulation. Thousands of reversible acetylation sites have been mapped in the proteome that respond dynamically to the cellular milieu and maintain major processes such as metabolism, autophagy and stress response. Concurrently, researchers are continuously uncovering how deregulation of KAT activity drives disease, including cancer and developmental syndromes characterized by severe intellectual disability. These novel findings are reshaping our view of KATs away from mere modulators of chromatin to detectors of the cellular environment and integrators of diverse signalling pathways with the ability to modify cellular phenotype.
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Affiliation(s)
- Bilal N Sheikh
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Asifa Akhtar
- Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
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31
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Roles and regulation of histone methylation in animal development. Nat Rev Mol Cell Biol 2019; 20:625-641. [PMID: 31267065 DOI: 10.1038/s41580-019-0151-1] [Citation(s) in RCA: 302] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2019] [Indexed: 12/26/2022]
Abstract
Histone methylation can occur at various sites in histone proteins, primarily on lysine and arginine residues, and it can be governed by multiple positive and negative regulators, even at a single site, to either activate or repress transcription. It is now apparent that histone methylation is critical for almost all stages of development, and its proper regulation is essential for ensuring the coordinated expression of gene networks that govern pluripotency, body patterning and differentiation along appropriate lineages and organogenesis. Notably, developmental histone methylation is highly dynamic. Early embryonic systems display unique histone methylation patterns, prominently including the presence of bivalent (both gene-activating and gene-repressive) marks at lineage-specific genes that resolve to monovalent marks during differentiation, which ensures that appropriate genes are expressed in each tissue type. Studies of the effects of methylation on embryonic stem cell pluripotency and differentiation have helped to elucidate the developmental roles of histone methylation. It has been revealed that methylation and demethylation of both activating and repressive marks are essential for establishing embryonic and extra-embryonic lineages, for ensuring gene dosage compensation via genomic imprinting and for establishing body patterning via HOX gene regulation. Not surprisingly, aberrant methylation during embryogenesis can lead to defects in body patterning and in the development of specific organs. Human genetic disorders arising from mutations in histone methylation regulators have revealed their important roles in the developing skeletal and nervous systems, and they highlight the overlapping and unique roles of different patterns of methylation in ensuring proper development.
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32
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Huang M, Huang J, Zheng Y, Sun Q. Histone acetyltransferase inhibitors: An overview in synthesis, structure-activity relationship and molecular mechanism. Eur J Med Chem 2019; 178:259-286. [PMID: 31195169 DOI: 10.1016/j.ejmech.2019.05.078] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 05/28/2019] [Accepted: 05/28/2019] [Indexed: 02/05/2023]
Abstract
Acetylation, a key component in post-translational modification regulated by HATs and HDACs, is relevant to many crucial cellular contexts in organisms. Based on crucial pharmacophore patterns and the structure of targeted proteins, HAT inhibitors are designed and modified for higher affinity and better bioactivity. However, there are still some challenges, such as cell permeability, selectivity, toxicity and synthetic availability, which limit the improvement of HAT inhibitors. So far, only few HAT inhibitors have been approved for commercialization, indicating the urgent need for more successful and effective structure-based drug design and synthetic strategies. Here, we summarized three classes of HAT inhibitors based on their sources and structural scaffolds, emphasizing on their synthetic methods and structure-activity relationships and molecular mechanisms, hoping to facilitate the development and further application of HAT inhibitors.
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Affiliation(s)
- Mengyuan Huang
- State Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Jiangkun Huang
- Department of Medicinal Chemistry, West China School of Pharmacy, Sichuan University, Chengdu, 610041, China
| | - Yongcheng Zheng
- State Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China
| | - Qiu Sun
- State Key Laboratory of Biotherapy, Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, 610041, China.
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33
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Acetylation & Co: an expanding repertoire of histone acylations regulates chromatin and transcription. Essays Biochem 2019; 63:97-107. [PMID: 30940741 PMCID: PMC6484784 DOI: 10.1042/ebc20180061] [Citation(s) in RCA: 135] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 12/12/2022]
Abstract
Packaging the long and fragile genomes of eukaryotic species into nucleosomes is all well and good, but how do cells gain access to the DNA again after it has been bundled away? The solution, in every species from yeast to man, is to post-translationally modify histones, altering their chemical properties to either relax the chromatin, label it for remodelling or make it more compact still. Histones are subject to a myriad of modifications: acetylation, methylation, phosphorylation, ubiquitination etc. This review focuses on histone acylations, a diverse group of modifications which occur on the ε-amino group of Lysine residues and includes the well-characterised Lysine acetylation. Over the last 50 years, histone acetylation has been extensively characterised, with the discovery of histone acetyltransferases (HATs) and histone deacetylases (HDACs), and global mapping experiments, revealing an association of hyperacetylated histones with accessible, transcriptionally active chromatin. More recently, there has been an explosion in the number of unique short chain ‘acylations’ identified by MS, including: propionylation, butyrylation, crotonylation, succinylation, malonylation and 2-hydroxyisobutyrylation. These novel modifications add a range of chemical environments to histones, and similar to acetylation, appear to accumulate at transcriptional start sites and correlate with gene activity.
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34
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Liang X, Lei M, Li F, Yang X, Zhou M, Li B, Cao Y, Gong S, Liu K, Liu J, Qi C, Liu Y. Family-Wide Characterization of Histone Binding Abilities of PHD Domains of AL Proteins in Arabidopsis thaliana. Protein J 2019; 37:531-538. [PMID: 30259302 DOI: 10.1007/s10930-018-9796-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Alfin1-like (AL) is a family of proteins homologous to the alfalfa Alfin1 in plant and bears an Alfin domain and a PHD domain at their N- and C-terminus, respectively. There are 7 AL proteins in Arabidopsis, and the PHD domains of most AL proteins are reported to bind to histone H3K4me3. Here we reported gene cloning, protein expression and purification of the PHD domains of all the AL family proteins in Arabidopsis. We then systematically characterized their histone binding abilities by quantitative isothermal titration calorimetry and fluorescence polarization binding assays. Our binding results indicate that all the PHD domains of the AL proteins bind to the histone H3K4me3 peptide with varying methylation state preference and binding affinities. Our study presented here provides the foundation for further studies of the peptide state-specific recognition by PHD domains of AL proteins.
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Affiliation(s)
- Xiao Liang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Ming Lei
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Fangzhou Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Xiajie Yang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Mengqi Zhou
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Bing Li
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Yu Cao
- Key Laboratory of Pesticide and Chemical Biology (Ministry of Education), College of Chemistry, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Siying Gong
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Ke Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Jinlin Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Chao Qi
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, People's Republic of China
| | - Yanli Liu
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan, 430079, People's Republic of China.
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35
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Akram S, Yang F, Li J, Adams G, Liu Y, Zhuang X, Chu L, Liu X, Emmett N, Thompson W, Mullen M, Muthusamy S, Wang W, Mo F, Liu X. LRIF1 interacts with HP1α to coordinate accurate chromosome segregation during mitosis. J Mol Cell Biol 2018; 10:527-538. [PMID: 30016453 PMCID: PMC6304163 DOI: 10.1093/jmcb/mjy040] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 05/05/2018] [Accepted: 07/14/2018] [Indexed: 01/26/2023] Open
Abstract
Heterochromatin protein 1α (HP1α) regulates chromatin specification and plasticity during cell fate decision. Different structural determinants account for HP1α localization and function during cell division cycle. Our earlier study showed that centromeric localization of HP1α depends on the epigenetic mark H3K9me3 in interphase, while its centromeric location in mitosis relies on uncharacterized PXVXL-containing factors. Here, we identified a PXVXL-containing protein, ligand-dependent nuclear receptor-interacting factor 1 (LRIF1), which recruits HP1α to the centromere of mitotic chromosomes and its interaction with HP1α is essential for accurate chromosome segregation during mitosis. LRIF1 interacts directly with HP1α chromoshadow domain via an evolutionarily conserved PXVXL motif within its C-terminus. Importantly, the LRIF1-HP1α interaction is critical for Aurora B activity in the inner centromere. Mutation of PXVXL motif of LRIF1 leads to defects in HP1α centromere targeting and aberrant chromosome segregation. These findings reveal a previously unrecognized direct link between LRIF1 and HP1α in centromere plasticity control and illustrate the critical role of LRIF1-HP1α interaction in orchestrating accurate cell division.
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Affiliation(s)
- Saima Akram
- Anhui Key Laboratory for Cellular Dynamics, University of Science & Technology of China School of Life Sciences, National Science Center for Physical Sciences at Nanoscale, and Chinese Academy of Science Center of Excellence on Molecular Cell Sciences, Hefei, China
| | - Fengrui Yang
- Anhui Key Laboratory for Cellular Dynamics, University of Science & Technology of China School of Life Sciences, National Science Center for Physical Sciences at Nanoscale, and Chinese Academy of Science Center of Excellence on Molecular Cell Sciences, Hefei, China
- Keck Center for Molecular Imaging, Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Junying Li
- Anhui Key Laboratory for Cellular Dynamics, University of Science & Technology of China School of Life Sciences, National Science Center for Physical Sciences at Nanoscale, and Chinese Academy of Science Center of Excellence on Molecular Cell Sciences, Hefei, China
| | - Gregory Adams
- Keck Center for Molecular Imaging, Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
- National Institutes of Health, Bethesda, MD, USA
| | - Yingying Liu
- Anhui Key Laboratory for Cellular Dynamics, University of Science & Technology of China School of Life Sciences, National Science Center for Physical Sciences at Nanoscale, and Chinese Academy of Science Center of Excellence on Molecular Cell Sciences, Hefei, China
- Keck Center for Molecular Imaging, Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Xiaoxuan Zhuang
- Anhui Key Laboratory for Cellular Dynamics, University of Science & Technology of China School of Life Sciences, National Science Center for Physical Sciences at Nanoscale, and Chinese Academy of Science Center of Excellence on Molecular Cell Sciences, Hefei, China
- National Institutes of Health, Bethesda, MD, USA
| | - Lingluo Chu
- Department of Molecular Cell Biology, Harvard University, Cambridge, MA, USA
| | - Xu Liu
- Anhui Key Laboratory for Cellular Dynamics, University of Science & Technology of China School of Life Sciences, National Science Center for Physical Sciences at Nanoscale, and Chinese Academy of Science Center of Excellence on Molecular Cell Sciences, Hefei, China
- Keck Center for Molecular Imaging, Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Nerimah Emmett
- Keck Center for Molecular Imaging, Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Winston Thompson
- Keck Center for Molecular Imaging, Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - McKay Mullen
- Keck Center for Molecular Imaging, Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Saravana Muthusamy
- Keck Center for Molecular Imaging, Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Wenwen Wang
- Anhui Key Laboratory for Cellular Dynamics, University of Science & Technology of China School of Life Sciences, National Science Center for Physical Sciences at Nanoscale, and Chinese Academy of Science Center of Excellence on Molecular Cell Sciences, Hefei, China
- Keck Center for Molecular Imaging, Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
| | - Fei Mo
- Anhui Key Laboratory for Cellular Dynamics, University of Science & Technology of China School of Life Sciences, National Science Center for Physical Sciences at Nanoscale, and Chinese Academy of Science Center of Excellence on Molecular Cell Sciences, Hefei, China
- National Institutes of Health, Bethesda, MD, USA
| | - Xing Liu
- Anhui Key Laboratory for Cellular Dynamics, University of Science & Technology of China School of Life Sciences, National Science Center for Physical Sciences at Nanoscale, and Chinese Academy of Science Center of Excellence on Molecular Cell Sciences, Hefei, China
- Keck Center for Molecular Imaging, Department of Physiology, Morehouse School of Medicine, Atlanta, GA, USA
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36
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Voss AK, Thomas T. Histone Lysine and Genomic Targets of Histone Acetyltransferases in Mammals. Bioessays 2018; 40:e1800078. [PMID: 30144132 DOI: 10.1002/bies.201800078] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/01/2018] [Indexed: 01/08/2023]
Abstract
Histone acetylation has been recognized as an important post-translational modification of core nucleosomal histones that changes access to the chromatin to allow gene transcription, DNA replication, and repair. Histone acetyltransferases were initially identified as co-activators that link DNA-binding transcription factors to the general transcriptional machinery. Over the years, more chromatin-binding modes have been discovered suggesting direct interaction of histone acetyltransferases and their protein complex partners with histone proteins. While much progress has been made in characterizing histone acetyltransferase complexes biochemically, cell-free activity assay results are often at odds with in-cell histone acetyltransferase activities. In-cell studies suggest specific histone lysine targets, but broad recruitment modes, apparently not relying on specific DNA sequences, but on chromatin of a specific functional state. Here we review the evidence for general versus specific roles of individual nuclear lysine acetyltransferases in light of in vivo and in vitro data in the mammalian system.
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Affiliation(s)
- Anne K Voss
- Walter and Eliza Hall Institute of Medical Research, 3 1G Royal Parade, Parkville, Melbourne, Victoria, 3052, Australia
| | - Tim Thomas
- Department of Medical Biology, The University of Melbourne, 1G Royal Parade, Parkville, Melbourne, Victoria, 3052, Australia
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37
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Biswas S, Rao CM. Epigenetic tools (The Writers, The Readers and The Erasers) and their implications in cancer therapy. Eur J Pharmacol 2018; 837:8-24. [PMID: 30125562 DOI: 10.1016/j.ejphar.2018.08.021] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 07/26/2018] [Accepted: 08/15/2018] [Indexed: 02/08/2023]
Abstract
Addition of chemical tags on the DNA and modification of histone proteins impart a distinct feature on chromatin architecture. With the advancement in scientific research, the key players underlying these changes have been identified as epigenetic modifiers of the chromatin. Indeed, the plethora of enzymes catalyzing these modifications, portray the diversity of epigenetic space and the intricacy in regulating gene expression. These epigenetic players are categorized as writers: that introduce various chemical modifications on DNA and histones, readers: the specialized domain containing proteins that identify and interpret those modifications and erasers: the dedicated group of enzymes proficient in removing these chemical tags. Research over the past few decades has established that these epigenetic tools are associated with numerous disease conditions especially cancer. Besides, with the involvement of epigenetics in cancer, these enzymes and protein domains provide new targets for cancer drug development. This is certain from the volume of epigenetic research conducted in universities and R&D sector of pharmaceutical industry. Here we have highlighted the different types of epigenetic enzymes and protein domains with an emphasis on methylation and acetylation. This review also deals with the recent developments in small molecule inhibitors as potential anti-cancer drugs targeting the epigenetic space.
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Affiliation(s)
- Subhankar Biswas
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - C Mallikarjuna Rao
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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38
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Ali I, Conrad RJ, Verdin E, Ott M. Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics. Chem Rev 2018; 118:1216-1252. [PMID: 29405707 PMCID: PMC6609103 DOI: 10.1021/acs.chemrev.7b00181] [Citation(s) in RCA: 232] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Post-translational acetylation of lysine residues has emerged as a key regulatory mechanism in all eukaryotic organisms. Originally discovered in 1963 as a unique modification of histones, acetylation marks are now found on thousands of nonhistone proteins located in virtually every cellular compartment. Here we summarize key findings in the field of protein acetylation over the past 20 years with a focus on recent discoveries in nuclear, cytoplasmic, and mitochondrial compartments. Collectively, these findings have elevated protein acetylation as a major post-translational modification, underscoring its physiological relevance in gene regulation, cell signaling, metabolism, and disease.
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Affiliation(s)
- Ibraheem Ali
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Ryan J. Conrad
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
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39
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Hsu CC, Shi J, Yuan C, Zhao D, Jiang S, Lyu J, Wang X, Li H, Wen H, Li W, Shi X. Recognition of histone acetylation by the GAS41 YEATS domain promotes H2A.Z deposition in non-small cell lung cancer. Genes Dev 2018; 32:58-69. [PMID: 29437725 PMCID: PMC5828395 DOI: 10.1101/gad.303784.117] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/19/2017] [Indexed: 11/24/2022]
Abstract
Histone acetylation is associated with active transcription in eukaryotic cells. It helps to open up the chromatin by neutralizing the positive charge of histone lysine residues and providing binding platforms for "reader" proteins. The bromodomain (BRD) has long been thought to be the sole protein module that recognizes acetylated histones. Recently, we identified the YEATS domain of AF9 (ALL1 fused gene from chromosome 9) as a novel acetyl-lysine-binding module and showed that the ENL (eleven-nineteen leukemia) YEATS domain is an essential acetyl-histone reader in acute myeloid leukemias. The human genome encodes four YEATS domain proteins, including GAS41, a component of chromatin remodelers responsible for H2A.Z deposition onto chromatin; however, the importance of the GAS41 YEATS domain in human cancer remains largely unknown. Here we report that GAS41 is frequently amplified in human non-small cell lung cancer (NSCLC) and is required for cancer cell proliferation, survival, and transformation. Biochemical and crystal structural studies demonstrate that GAS41 binds to histone H3 acetylated on H3K27 and H3K14, a specificity that is distinct from that of AF9 or ENL. ChIP-seq (chromatin immunoprecipitation [ChIP] followed by high-throughput sequencing) analyses in lung cancer cells reveal that GAS41 colocalizes with H3K27ac and H3K14ac on the promoters of actively transcribed genes. Depletion of GAS41 or disruption of the interaction between its YEATS domain and acetylated histones impairs the association of histone variant H2A.Z with chromatin and consequently suppresses cancer cell growth and survival both in vitro and in vivo. Overall, our study identifies GAS41 as a histone acetylation reader that promotes histone H2A.Z deposition in NSCLC.
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Affiliation(s)
- Chih-Chao Hsu
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jiejun Shi
- Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Chao Yuan
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Dan Zhao
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shiming Jiang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Jie Lyu
- Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xiaolu Wang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing 100084, China
| | - Hong Wen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA
| | - Wei Li
- Dan L. Duncan Cancer Center, Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xiaobing Shi
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas 77030, USA.,Genetics and Epigenetics Graduate Program, The University of Texas MD Anderson Cancer Center UTHealth Graduate School of Biomedical Sciences, Houston, Texas 77030, USA
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40
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Boamah D, Lin T, Poppinga FA, Basu S, Rahman S, Essel F, Chakravarty S. Characteristics of a PHD Finger Subtype. Biochemistry 2018; 57:525-539. [PMID: 29253329 DOI: 10.1021/acs.biochem.7b00705] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although the plant homeodomain (PHD) finger superfamily is known for its site-specific readouts of histone tails, the origins of the mechanistic differences in histone H3 readout by different PHD subtypes remain less clear. We show that sequences containing the xCDxCDx motif in the PHD treble clef (xCDxCDx-PHD) constitute a distinct subtype, based on the following observations: (i) the amino acid composition of the binding site is strikingly different from other subtypes due to position-specific enrichment of negatively charged and bulky nonpolar residues, (ii) the binding site positions are mutually and positively correlated, and this correlation is absent in other subtypes, and (iii) there are only small structural deviations, despite low sequence similarity. The xCDxCDx-PHD constitutes ∼20% of the PHD family, and the double PHD fingers (DPFs) are 10% of the total number of xCDxCDx-PHDs. This subtype originated early in the evolution of eukaryotes but has diversified within the metazoan lineage. Despite sequence diversification, the positions of the enriched nonpolar residues, in particular, show very small structural deviations, suggesting critical contributions of nonpolar residues in the binding mechanism of this subtype. Using mutagenesis, we probed the contributions of the binding-site positions enriched in nonpolar residues in four xCDxCDx-PHD proteins and found that they contribute to the tight packing of the H3 residues. This effect may potentially be exploited, as we observed affinity enhancement upon substituting a bulky nonpolar residue at the same binding site in another histone reader. Overall, we present a detailed characterization of PHD subtypes.
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Affiliation(s)
- Daniel Boamah
- Chemistry & Biochemistry, South Dakota State University , Brookings, South Dakota 57007, United States
| | - Tao Lin
- Chemistry & Biochemistry, South Dakota State University , Brookings, South Dakota 57007, United States
| | - Franchesca A Poppinga
- Chemistry & Biochemistry, South Dakota State University , Brookings, South Dakota 57007, United States
| | - Shraddha Basu
- Chemistry & Biochemistry, South Dakota State University , Brookings, South Dakota 57007, United States
| | - Shahariar Rahman
- Chemistry & Biochemistry, South Dakota State University , Brookings, South Dakota 57007, United States
| | - Francisca Essel
- Chemistry & Biochemistry, South Dakota State University , Brookings, South Dakota 57007, United States
| | - Suvobrata Chakravarty
- Chemistry & Biochemistry, South Dakota State University , Brookings, South Dakota 57007, United States.,BioSNTR, Brookings, South Dakota 57007, United States
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41
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Jurkowska RZ, Qin S, Kungulovski G, Tempel W, Liu Y, Bashtrykov P, Stiefelmaier J, Jurkowski TP, Kudithipudi S, Weirich S, Tamas R, Wu H, Dombrovski L, Loppnau P, Reinhardt R, Min J, Jeltsch A. H3K14ac is linked to methylation of H3K9 by the triple Tudor domain of SETDB1. Nat Commun 2017; 8:2057. [PMID: 29234025 PMCID: PMC5727127 DOI: 10.1038/s41467-017-02259-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 11/14/2017] [Indexed: 12/18/2022] Open
Abstract
SETDB1 is an essential H3K9 methyltransferase involved in silencing of retroviruses and gene regulation. We show here that its triple Tudor domain (3TD) specifically binds to doubly modified histone H3 containing K14 acetylation and K9 methylation. Crystal structures of 3TD in complex with H3K14ac/K9me peptides reveal that peptide binding and K14ac recognition occurs at the interface between Tudor domains (TD) TD2 and TD3. Structural and biochemical data demonstrate a pocket switch mechanism in histone code reading, because K9me1 or K9me2 is preferentially recognized by the aromatic cage of TD3, while K9me3 selectively binds to TD2. Mutations in the K14ac/K9me binding sites change the sub-nuclear localization of 3TD. ChIP-seq analyses show that SETDB1 is enriched at H3K9me3 regions and K9me3/K14ac is enriched at SETDB1 binding sites overlapping with LINE elements, suggesting that recruitment of the SETDB1 complex to K14ac/K9me regions has a role in silencing of active genomic regions.
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Affiliation(s)
- Renata Z Jurkowska
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Su Qin
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada.,Life Science Research Center, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Goran Kungulovski
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Wolfram Tempel
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Yanli Liu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Pavel Bashtrykov
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Judith Stiefelmaier
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Tomasz P Jurkowski
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Srikanth Kudithipudi
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Sara Weirich
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Raluca Tamas
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany
| | - Hong Wu
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Ludmila Dombrovski
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada
| | - Richard Reinhardt
- Max-Planck-Genomzentrum Köln, Carl-von-Linné-Weg 10, 50829, Köln, Germany
| | - Jinrong Min
- Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, ON, M5G 1L7, Canada. .,Department of Physiology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
| | - Albert Jeltsch
- Department of Biochemistry, Institute of Biochemistry and Technical Biochemistry, Stuttgart University, Allmandring 31, 70569, Stuttgart, Germany.
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42
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Mi W, Guan H, Lyu J, Zhao D, Xi Y, Jiang S, Andrews FH, Wang X, Gagea M, Wen H, Tora L, Dent SYR, Kutateladze TG, Li W, Li H, Shi X. YEATS2 links histone acetylation to tumorigenesis of non-small cell lung cancer. Nat Commun 2017; 8:1088. [PMID: 29057918 PMCID: PMC5651844 DOI: 10.1038/s41467-017-01173-4] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 08/24/2017] [Indexed: 12/17/2022] Open
Abstract
Recognition of modified histones by “reader” proteins constitutes a key mechanism regulating diverse chromatin-associated processes important for normal and neoplastic development. We recently identified the YEATS domain as a novel acetyllysine-binding module; however, the functional importance of YEATS domain-containing proteins in human cancer remains largely unknown. Here, we show that the YEATS2 gene is highly amplified in human non-small cell lung cancer (NSCLC) and is required for cancer cell growth and survival. YEATS2 binds to acetylated histone H3 via its YEATS domain. The YEATS2-containing ATAC complex co-localizes with H3K27 acetylation (H3K27ac) on the promoters of actively transcribed genes. Depletion of YEATS2 or disruption of the interaction between its YEATS domain and acetylated histones reduces the ATAC complex-dependent promoter H3K9ac levels and deactivates the expression of essential genes. Taken together, our study identifies YEATS2 as a histone H3K27ac reader that regulates a transcriptional program essential for NSCLC tumorigenesis. Histone modification recognition is an important mechanism for gene expression regulation in cancer. Here, the authors identify YEATS2 as a histone H3K27ac reader, regulating a transcriptional program essential for tumorigenesis in human non-small cell lung cancer.
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Affiliation(s)
- Wenyi Mi
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA.,Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Haipeng Guan
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jie Lyu
- Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Dan Zhao
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yuanxin Xi
- Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Shiming Jiang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA.,Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Forest H Andrews
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Xiaolu Wang
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA.,Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Mihai Gagea
- Department of Veterinary Medicine & Surgery, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Hong Wen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA.,Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA
| | - Laszlo Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, 67404, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, 67404, Illkirch, France.,Université de Strasbourg, 67404, Illkirch, France
| | - Sharon Y R Dent
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA.,Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA.,Genes and Development and Epigenetics & Molecular Carcinogenesis Graduate Programs, The University of Texas Graduate School of Biomedical Sciences, Houston, TX, 77030, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA
| | - Wei Li
- Department of Molecular and Cellular Biology, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, 100084, China. .,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China.
| | - Xiaobing Shi
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA. .,Center for Cancer Epigenetics, The University of Texas M.D. Anderson Cancer Center, Houston, TX, 77030, USA. .,Genes and Development and Epigenetics & Molecular Carcinogenesis Graduate Programs, The University of Texas Graduate School of Biomedical Sciences, Houston, TX, 77030, USA.
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43
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Histone-binding of DPF2 mediates its repressive role in myeloid differentiation. Proc Natl Acad Sci U S A 2017; 114:6016-6021. [PMID: 28533407 DOI: 10.1073/pnas.1700328114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Double plant homeodomain finger 2 (DPF2) is a highly evolutionarily conserved member of the d4 protein family that is ubiquitously expressed in human tissues and was recently shown to inhibit the myeloid differentiation of hematopoietic stem/progenitor and acute myelogenous leukemia cells. Here, we present the crystal structure of the tandem plant homeodomain finger domain of human DPF2 at 1.6-Å resolution. We show that DPF2 interacts with the acetylated tails of both histones 3 and 4 via bipartite binding pockets on the DPF2 surface. Blocking these interactions through targeted mutagenesis of DPF2 abolishes its recruitment to target chromatin regions as well as its ability to prevent myeloid differentiation in vivo. Our findings suggest that the histone binding of DPF2 plays an important regulatory role in the transcriptional program that drives myeloid differentiation.
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44
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Structural basis of molecular recognition of helical histone H3 tail by PHD finger domains. Biochem J 2017; 474:1633-1651. [PMID: 28341809 PMCID: PMC5415848 DOI: 10.1042/bcj20161053] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 03/22/2017] [Accepted: 03/23/2017] [Indexed: 12/20/2022]
Abstract
The plant homeodomain (PHD) fingers are among the largest family of epigenetic domains, first characterized as readers of methylated H3K4. Readout of histone post-translational modifications by PHDs has been the subject of intense investigation; however, less is known about the recognition of secondary structure features within the histone tail itself. We solved the crystal structure of the PHD finger of the bromodomain adjacent to zinc finger 2A [BAZ2A, also known as TIP5 (TTF-I/interacting protein 5)] in complex with unmodified N-terminal histone H3 tail. The peptide is bound in a helical folded-back conformation after K4, induced by an acidic patch on the protein surface that prevents peptide binding in an extended conformation. Structural bioinformatics analyses identify a conserved Asp/Glu residue that we name ‘acidic wall’, found to be mutually exclusive with the conserved Trp for K4Me recognition. Neutralization or inversion of the charges at the acidic wall patch in BAZ2A, and homologous BAZ2B, weakened H3 binding. We identify simple mutations on H3 that strikingly enhance or reduce binding, as a result of their stabilization or destabilization of H3 helicity. Our work unravels the structural basis for binding of the helical H3 tail by PHD fingers and suggests that molecular recognition of secondary structure motifs within histone tails could represent an additional layer of regulation in epigenetic processes.
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45
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Spangle JM, Roberts TM, Zhao JJ. The emerging role of PI3K/AKT-mediated epigenetic regulation in cancer. Biochim Biophys Acta Rev Cancer 2017; 1868:123-131. [PMID: 28315368 DOI: 10.1016/j.bbcan.2017.03.002] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Revised: 03/10/2017] [Accepted: 03/11/2017] [Indexed: 12/27/2022]
Abstract
The PI3-kinase/AKT pathway integrates signals from external cellular stimuli to regulate essential cellular functions, and is frequently aberrantly activated in human cancers. Recent research demonstrates that tight regulation of the epigenome is critical in preserving and restricting transcriptional activation, which can impact cellular growth and proliferation. In this review we examine mechanisms by which the PI3K/AKT pathway regulates the epigenome to promote oncogenesis, and highlight how connections between PI3K/AKT and the epigenome may impact the future therapeutic treatment of cancers featuring a hyperactivated PI3K/AKT pathway.
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Affiliation(s)
- Jennifer M Spangle
- Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 44 Binney St, Boston, MA 02115, USA.
| | - Thomas M Roberts
- Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 44 Binney St, Boston, MA 02115, USA
| | - Jean J Zhao
- Department of Cancer Biology, Dana Farber Cancer Institute, 44 Binney St, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 44 Binney St, Boston, MA 02115, USA.
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46
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Recognition of Histone H3K14 Acylation by MORF. Structure 2017; 25:650-654.e2. [PMID: 28286003 DOI: 10.1016/j.str.2017.02.003] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 02/04/2017] [Accepted: 02/10/2017] [Indexed: 12/13/2022]
Abstract
The monocytic leukemia zinc-finger protein-related factor (MORF) is a transcriptional coactivator and a catalytic subunit of the lysine acetyltransferase complex implicated in cancer and developmental diseases. We have previously shown that the double plant homeodomain finger (DPF) of MORF is capable of binding to acetylated histone H3. Here we demonstrate that the DPF of MORF recognizes many newly identified acylation marks. The mass spectrometry study provides comprehensive analysis of H3K14 acylation states in vitro and in vivo. The crystal structure of the MORF DPF-H3K14butyryl complex offers insight into the selectivity of this reader toward lipophilic acyllysine substrates. Together, our findings support the mechanism by which the acetyltransferase MORF promotes spreading of histone acylation.
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47
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Histone H3K4 and H3K36 Methylation Independently Recruit the NuA3 Histone Acetyltransferase in Saccharomyces cerevisiae. Genetics 2017; 205:1113-1123. [PMID: 28108585 DOI: 10.1534/genetics.116.199422] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2016] [Accepted: 12/23/2016] [Indexed: 11/18/2022] Open
Abstract
Histone post-translational modifications (PTMs) alter chromatin structure by promoting the interaction of chromatin-modifying complexes with nucleosomes. The majority of chromatin-modifying complexes contain multiple domains that preferentially interact with modified histones, leading to speculation that these domains function in concert to target nucleosomes with distinct combinations of histone PTMs. In Saccharomyces cerevisiae, the NuA3 histone acetyltransferase complex contains three domains, the PHD finger in Yng1, the PWWP domain in Pdp3, and the YEATS domain in Taf14; which in vitro bind to H3K4 methylation, H3K36 methylation, and acetylated and crotonylated H3K9, respectively. While the in vitro binding has been well characterized, the relative in vivo contributions of these histone PTMs in targeting NuA3 is unknown. Here, through genome-wide colocalization and by mutational interrogation, we demonstrate that the PHD finger of Yng1, and the PWWP domain of Pdp3 independently target NuA3 to H3K4 and H3K36 methylated chromatin, respectively. In contrast, we find no evidence to support the YEATS domain of Taf14 functioning in NuA3 recruitment. Collectively our results suggest that the presence of multiple histone PTM binding domains within NuA3, rather than restricting it to nucleosomes containing distinct combinations of histone PTMs, can serve to increase the range of nucleosomes bound by the complex. Interestingly, however, the simple presence of NuA3 is insufficient to ensure acetylation of the associated nucleosomes, suggesting a secondary level of acetylation regulation that does not involve control of HAT-nucleosome interactions.
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48
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Soffers JHM, Li X, Abmayr SM, Workman JL. Reading and Interpreting the Histone Acylation Code. GENOMICS PROTEOMICS & BIOINFORMATICS 2016; 14:329-332. [PMID: 28007607 PMCID: PMC5200937 DOI: 10.1016/j.gpb.2016.12.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2016] [Revised: 12/01/2016] [Accepted: 12/01/2016] [Indexed: 11/30/2022]
Affiliation(s)
| | - Xuanying Li
- Stowers Institute for Medical Research, Kansas City, MO 64111, USA; Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Susan M Abmayr
- Stowers Institute for Medical Research, Kansas City, MO 64111, USA; Department of Anatomy and Cell Biology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Jerry L Workman
- Stowers Institute for Medical Research, Kansas City, MO 64111, USA.
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49
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Metabolic regulation of gene expression through histone acylations. Nat Rev Mol Cell Biol 2016; 18:90-101. [PMID: 27924077 DOI: 10.1038/nrm.2016.140] [Citation(s) in RCA: 647] [Impact Index Per Article: 80.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Eight types of short-chain Lys acylations have recently been identified on histones: propionylation, butyrylation, 2-hydroxyisobutyrylation, succinylation, malonylation, glutarylation, crotonylation and β-hydroxybutyrylation. Emerging evidence suggests that these histone modifications affect gene expression and are structurally and functionally different from the widely studied histone Lys acetylation. In this Review, we discuss the regulation of non-acetyl histone acylation by enzymatic and metabolic mechanisms, the acylation 'reader' proteins that mediate the effects of different acylations and their physiological functions, which include signal-dependent gene activation, spermatogenesis, tissue injury and metabolic stress. We propose a model to explain our present understanding of how differential histone acylation is regulated by the metabolism of the different acyl-CoA forms, which in turn modulates the regulation of gene expression.
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50
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Xiong X, Panchenko T, Yang S, Zhao S, Yan P, Zhang W, Xie W, Li Y, Zhao Y, Allis CD, Li H. Selective recognition of histone crotonylation by double PHD fingers of MOZ and DPF2. Nat Chem Biol 2016; 12:1111-1118. [PMID: 27775714 DOI: 10.1038/nchembio.2218] [Citation(s) in RCA: 134] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2016] [Accepted: 09/14/2016] [Indexed: 02/05/2023]
Abstract
Recognition of histone covalent modifications by 'reader' modules constitutes a major mechanism for epigenetic regulation. A recent upsurge of newly discovered histone lysine acylations, such as crotonylation (Kcr), butyrylation (Kbu), and propionylation (Kpr), greatly expands the coding potential of histone lysine modifications. Here we demonstrate that the histone acetylation-binding double PHD finger (DPF) domains of human MOZ (also known as KAT6A) and DPF2 (also known as BAF45d) accommodate a wide range of histone lysine acylations with the strongest preference for Kcr. Crystal structures of the DPF domain of MOZ in complex with H3K14cr, H3K14bu, and H3K14pr peptides reveal that these non-acetyl acylations are anchored in a hydrophobic 'dead-end' pocket with selectivity for crotonylation arising from intimate encapsulation and an amide-sensing hydrogen bonding network. Immunofluorescence and chromatin immunoprecipitation (ChIP)-quantitative PCR (qPCR) showed that MOZ and H3K14cr colocalize in a DPF-dependent manner. Our studies call attention to a new regulatory mechanism centered on histone crotonylation readout by DPF family members.
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Affiliation(s)
- Xiaozhe Xiong
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Tatyana Panchenko
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York, USA
| | - Shuang Yang
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Shuai Zhao
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Peiqiang Yan
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China
| | - Wenhao Zhang
- School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Wei Xie
- School of Life Sciences, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Yuanyuan Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, Illinois, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, New York, USA
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, China.,Collaborative Innovation Center for Biotherapy, West China Hospital, Sichuan University, Chengdu, China
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