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Guo K, Cao Y, Zhao Z, Zhao J, Liu L, Wang H. GGNBP2 regulates histone ubiquitination and methylation in spermatogenesis. Epigenetics 2024; 19:2381849. [PMID: 39109527 DOI: 10.1080/15592294.2024.2381849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 06/19/2024] [Accepted: 07/14/2024] [Indexed: 09/17/2024] Open
Abstract
Gametogenetin binding protein 2 (GGNBP2) was indispensable in normal spermatids for transformation into mature spermatozoa in mice, and when Gametogenetin binding protein 2 is bound to BRCC36 and RAD51, the complex participates in repairing DNA double-strand breaks (DSB) during the meiotic progression of spermatocytes. Ggnbp2 knockout resulted in the up-regulation of H2AK119ubi and down-regulation of H2BK120ubi in GC-2 cells (mouse spermatogonia-derived cell line) and postnatal day 18 testis lysate. Our results also demonstrated that Gametogenetin binding protein 2 inducedASXL1 to activate the deubiquitinating enzyme BAP1 in deubiquitinating H2A, while Gametogenetin binding protein 2 knockout disrupted the interaction between ASXL1 and BAP1, resulting in BAP1 localization change. Furthermore, the Gametogenetin binding protein 2 deletion reduced H2B ubiquitination by affecting E2 enzymes and E3 ligase binding. Gametogenetin binding protein 2 regulated H2A and H2B ubiquitination levels and controlled H3K27 and H3K79 methylation by PRC2 subunits and histone H3K79 methyltransferase. Altogether, our results suggest that Ggnbp2 knockout increased DNA damage response by promoting H2A ubiquitination and H3K27trimethylation (H3K27me3) and reduced nucleosome stability by decreasing H2B ubiquitination and H3K79 dimethylation (H3K79me2), revealing new mechanisms of epigenetic phenomenon during spermatogenesis. Gametogenetin binding protein 2 seems critical in regulating histone modification and chromatin structure in spermatogenesis.
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Affiliation(s)
- Kaimin Guo
- Department of Andrology, First hospital of Jilin University, Changchun, China
| | - Yin Cao
- Department of Andrology, First hospital of Jilin University, Changchun, China
| | - Zhiyi Zhao
- Department of Andrology, First hospital of Jilin University, Changchun, China
| | - Jiantao Zhao
- Department of Andrology, First hospital of Jilin University, Changchun, China
| | - Lingyun Liu
- Department of Andrology, First hospital of Jilin University, Changchun, China
| | - Hongliang Wang
- Department of Andrology, First hospital of Jilin University, Changchun, China
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2
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Branch MC, Weber M, Li MY, Flora P, Ezhkova E. Overview of chromatin regulatory processes during surface ectodermal development and homeostasis. Dev Biol 2024; 515:30-45. [PMID: 38971398 PMCID: PMC11317222 DOI: 10.1016/j.ydbio.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 05/02/2024] [Accepted: 07/02/2024] [Indexed: 07/08/2024]
Abstract
The ectoderm is the outermost of the three germ layers of the early embryo that arise during gastrulation. Once the germ layers are established, the complex interplay of cellular proliferation, differentiation, and migration results in organogenesis. The ectoderm is the progenitor of both the surface ectoderm and the neural ectoderm. Notably, the surface ectoderm develops into the epidermis and its associated appendages, nails, external exocrine glands, olfactory epithelium, and the anterior pituitary. Specification, development, and homeostasis of these organs demand a tightly orchestrated gene expression program that is often dictated by epigenetic regulation. In this review, we discuss the recent discoveries that have highlighted the importance of chromatin regulatory mechanisms mediated by transcription factors, histone and DNA modifications that aid in the development of surface ectodermal organs and maintain their homeostasis post-development.
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Affiliation(s)
- Meagan C Branch
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Madison Weber
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Meng-Yen Li
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Pooja Flora
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| | - Elena Ezhkova
- Black Family Stem Cell Institute, Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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3
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Ghate NB, Nadkarni KS, Barik GK, Tat SS, Sahay O, Santra MK. Histone ubiquitination: Role in genome integrity and chromatin organization. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195044. [PMID: 38763317 DOI: 10.1016/j.bbagrm.2024.195044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 05/21/2024]
Abstract
Maintenance of genome integrity is a precise but tedious and complex job for the cell. Several post-translational modifications (PTMs) play vital roles in maintaining the genome integrity. Although ubiquitination is one of the most crucial PTMs, which regulates the localization and stability of the nonhistone proteins in various cellular and developmental processes, ubiquitination of the histones is a pivotal epigenetic event critically regulating chromatin architecture. In addition to genome integrity, importance of ubiquitination of core histones (H2A, H2A, H3, and H4) and linker histone (H1) have been reported in several cellular processes. However, the complex interplay of histone ubiquitination and other PTMs, as well as the intricate chromatin architecture and dynamics, pose a significant challenge to unravel how histone ubiquitination safeguards genome stability. Therefore, further studies are needed to elucidate the interactions between histone ubiquitination and other PTMs, and their role in preserving genome integrity. Here, we review all types of histone ubiquitinations known till date in maintaining genomic integrity during transcription, replication, cell cycle, and DNA damage response processes. In addition, we have also discussed the role of histone ubiquitination in regulating other histone PTMs emphasizing methylation and acetylation as well as their potential implications in chromatin architecture. Further, we have also discussed the involvement of deubiquitination enzymes (DUBs) in controlling histone ubiquitination in modulating cellular processes.
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Affiliation(s)
- Nikhil Baban Ghate
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India.
| | - Kaustubh Sanjay Nadkarni
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Ganesh Kumar Barik
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Sharad Shriram Tat
- Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Osheen Sahay
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Manas Kumar Santra
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India.
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4
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Dasgupta A, Nandi S, Gupta S, Roy S, Das C. To Ub or not to Ub: The epic dilemma of histones that regulate gene expression and epigenetic cross-talk. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195033. [PMID: 38750882 DOI: 10.1016/j.bbagrm.2024.195033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Revised: 01/04/2024] [Accepted: 05/06/2024] [Indexed: 05/23/2024]
Abstract
A dynamic array of histone post-translational modifications (PTMs) regulate diverse cellular processes in the eukaryotic chromatin. Among them, histone ubiquitination is particularly complex as it alters nucleosome surface area fostering intricate cross-talk with other chromatin modifications. Ubiquitin signaling profoundly impacts DNA replication, repair, and transcription. Histones can undergo varied extent of ubiquitination such as mono, multi-mono, and polyubiquitination, which brings about distinct cellular fates. Mechanistic studies of the ubiquitin landscape in chromatin have unveiled a fascinating tapestry of events that orchestrate gene regulation. In this review, we summarize the key contributors involved in mediating different histone ubiquitination and deubiquitination events, and discuss their mechanism which impacts cell transcriptional identity and DNA damage response. We also focus on the proteins bearing epigenetic reader modules critical in discerning site-specific histone ubiquitination, pivotal for establishing complex epigenetic crosstalk. Moreover, we highlight the role of histone ubiquitination in different human diseases including neurodevelopmental disorders and cancer. Overall the review elucidates the intricate orchestration of histone ubiquitination impacting diverse cellular functions and disease pathogenesis, and provides insights into the current challenges of targeting them for therapeutic interventions.
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Affiliation(s)
- Anirban Dasgupta
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India; Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390-9148, USA
| | - Sandhik Nandi
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India
| | - Sayan Gupta
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India
| | - Siddhartha Roy
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, India; Homi Bhabha National Institute, Training School Complex, Anushaktinagar, Mumbai 400094, India.
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5
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Lv Y, Li J, Wang Z, Liu Y, Jiang Y, Li Y, Lv Z, Huang X, Peng X, Cao Y, Yang H. Polycomb proteins RING1A/B promote H2A monoubiquitination to regulate female gametophyte development in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:4822-4836. [PMID: 38717070 DOI: 10.1093/jxb/erae208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Accepted: 05/07/2024] [Indexed: 08/29/2024]
Abstract
A functional female gametophyte is the basis of successful sexual reproduction in flowering plants. During female gametophyte development, the megaspore mother cell (MMC), which differentiates from a single subepidermal somatic cell in the nucellus, undergoes meiosis to produce four megaspores; only the one at the chalazal end, referred to as the functional megaspore (FM), then undergoes three rounds of mitosis and develops into a mature embryo sac. Here, we report that RING1A and RING1B (RING1A/B), two functionally redundant Polycomb proteins in Arabidopsis, are critical for female gametophyte development. Mutations of RING1A/B resulted in defects in the specification of the MMC and the FM, and in the subsequent mitosis of the FM, thereby leading to aborted ovules. Detailed analysis revealed that several genes essential for female gametophyte development were ectopically expressed in the ring1a ring1b mutant, including Argonaute (AGO) family genes and critical transcription factors. Furthermore, RING1A/B bound to some of these genes to promote H2A monoubiquitination (H2Aub). Taken together, our study shows that RING1A/B promote H2Aub modification at key genes for female gametophyte development, suppressing their expression to ensure that the development progresses correctly.
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Affiliation(s)
- Yanfang Lv
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jian Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China
| | - Zheng Wang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China
| | - Yue Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yili Jiang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yanzhuo Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhaopeng Lv
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiaoyi Huang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiongbo Peng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Ying Cao
- College of Life Sciences, RNA Center, Capital Normal University, Beijing 100048, China
| | - Hongchun Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan 430072, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- RNA Institute, Wuhan University, Wuhan 430072, China
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6
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Wang D, Zhao J, Yang X, Ji Y, Yu J, Li Z, Shi Y, Guo J, Zhou J, Hou L, Liu J. E3 ligase RNF2 inhibits porcine circovirus type 3 replication by targeting its capsid protein for ubiquitination-dependent degradation. J Virol 2024; 98:e0022324. [PMID: 39046246 PMCID: PMC11334428 DOI: 10.1128/jvi.00223-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 06/21/2024] [Indexed: 07/25/2024] Open
Abstract
Porcine circovirus type 3 (PCV3) is closely associated with various diseases, such as the porcine dermatitis, nephropathy syndrome, and multisystemic clinicopathological diseases. PCV3-associated diseases are increasingly recognized as severe diseases in the global swine industry. Ring finger protein 2 (RNF2), an E3 ubiquitin ligase exclusively located in the nucleus, contributes to various biological processes. This ligase interacts with the PCV3 Cap. However, its role in PCV3 replication remains unclear. This study confirmed that the nuclear localization signal domain of the Cap and the RNF2 N-terminal RING domain facilitate the interaction between the Cap and RNF2. Furthermore, RNF2 promoted the binding of K48-linked polyubiquitination chains to lysine at positions 139 and 140 (K139 and K140) of the PCV3 Cap, thereby degrading the Cap. RNF2 knockdown and overexpression increased or decreased PCV3 replication, respectively. Moreover, the RING domain-deleted RNF2 mutant eliminated the RNF2-induced degradation of the PCV3 Cap and RNF2-mediated inhibition of viral replication. This indicates that both processes were associated with its E3 ligase activity. Our findings demonstrate that RNF2 can interact with and degrade the PCV3 Cap via its N-terminal RING domain in a ubiquitination-dependent manner, thereby inhibiting PCV3 replication.IMPORTANCEPorcine circovirus type 3 is a recently described pathogen that is prevalent worldwide, causing substantial economic losses to the swine industry. However, the mechanisms through which host proteins regulate its replication remain unclear. Here, we demonstrate that ring finger protein 2 inhibits porcine circovirus type 3 replication by interacting with and degrading the Cap of this pathogen in a ubiquitination-dependent manner, requiring its N-terminal RING domain. Ring finger protein 2-mediated degradation of the Cap relies on its E3 ligase activity and the simultaneous existence of K139 and K140 within the Cap. These findings reveal the mechanism by which this protein interacts with and degrades the Cap to inhibit porcine circovirus type 3 replication. This consequently provides novel insights into porcine circovirus type 3 pathogenesis and facilitates the development of preventative measures against this pathogen.
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Affiliation(s)
- Dedong Wang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jie Zhao
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Xiaoyu Yang
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Ying Ji
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Ju Yu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Zhaoyang Li
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Yongyan Shi
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jinshuo Guo
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jianwei Zhou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Lei Hou
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Jue Liu
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
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7
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Tamburri S, Rustichelli S, Amato S, Pasini D. Navigating the complexity of Polycomb repression: Enzymatic cores and regulatory modules. Mol Cell 2024:S1097-2765(24)00628-2. [PMID: 39178860 DOI: 10.1016/j.molcel.2024.07.030] [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: 05/18/2024] [Revised: 07/12/2024] [Accepted: 07/30/2024] [Indexed: 08/26/2024]
Abstract
Polycomb proteins are a fundamental repressive system that plays crucial developmental roles by orchestrating cell-type-specific transcription programs that govern cell identity. Direct alterations of Polycomb activity are indeed implicated in human pathologies, including developmental disorders and cancer. General Polycomb repression is coordinated by three distinct activities that regulate the deposition of two histone post-translational modifications: tri-methylation of histone H3 lysine 27 (H3K27me3) and histone H2A at lysine 119 (H2AK119ub1). These activities exist in large and heterogeneous multiprotein ensembles consisting of common enzymatic cores regulated by heterogeneous non-catalytic modules composed of a large number of accessory proteins with diverse biochemical properties. Here, we have analyzed the current molecular knowledge, focusing on the functional interaction between the core enzymatic activities and their regulation mediated by distinct accessory modules. This provides a comprehensive analysis of the molecular details that control the establishment and maintenance of Polycomb repression, examining their underlying coordination and highlighting missing information and emerging new features of Polycomb-mediated transcriptional control.
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Affiliation(s)
- Simone Tamburri
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via A. di Rudinì 8, 20142 Milan, Italy.
| | - Samantha Rustichelli
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Simona Amato
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy
| | - Diego Pasini
- IEO, European Institute of Oncology IRCCS, Department of Experimental Oncology, Via Adamello 16, 20139 Milan, Italy; University of Milan, Department of Health Sciences, Via A. di Rudinì 8, 20142 Milan, Italy.
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8
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Zhang Z, Liang C, Ren Y, Lv Z, Huang J. Interaction of ubiquitin-like protein SILENCING DEFECTIVE 2 with LIKE HETEROCHROMATIN PROTEIN 1 is required for regulation of anthocyanin biosynthesis in Arabidopsis thaliana in response to sucrose. THE NEW PHYTOLOGIST 2024; 243:1374-1386. [PMID: 38558017 DOI: 10.1111/nph.19725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 03/13/2024] [Indexed: 04/04/2024]
Abstract
The regulatory mechanisms of anthocyanin biosynthesis have been well documented at the transcriptional and translational levels. By contrast, how anthocyanin biosynthesis is epigenetically regulated remains largely unknown. In this study, we employed genetic, molecular biology, and chromatin immunoprecipitation-quantitative polymerase chain reaction assays to identify a regulatory module essential for repressing the expression of genes involved in anthocyanin biosynthesis through chromatin remodeling. We found that SILENCING DEFECTIVE 2 (SDE2), which was previously identified as a negative regulator for sucrose-induced anthocyanin accumulation in Arabidopsis, is cleaved into N-terminal SDE2-UBL and C-terminal SDE2-C fragments at the first diglycine motif, and the cleaved SDE2-C, which can fully complement the sde2 mutant, is localized in the nucleus and physically interacts with LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) in vitro and in vivo. Genetic analyses showed that both SDE2 and LHP1 act as negative factors for anthocyanin biosynthesis. Consistently, immunoblot analysis revealed that the level of LHP1-bound histone H3 lysine 27 trimethylation (H3K27me3) significantly decreases in sde2 and lhp1 mutants, compared to wild-type (WT). In addition, we found that sugar can induce expression of SDE2 and LHP1, and enhance the level of the nucleus-localized SDE2-C. Taken together, our data suggest that the SDE2-C-LHP1 module is required for repression of gene expression through H3K27me3 modification during sugar-induced anthocyanin biosynthesis in Arabidopsis thaliana.
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Affiliation(s)
- Zhiyi Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Chengcheng Liang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yulong Ren
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Zhaojun Lv
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Jirong Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
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9
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Tan M, Park L, Chou E, Hoesel M, Toh L, Suzuki Y. Polycomb group proteins confer robustness to aposematic coloration in the milkweed bug, Oncopeltus fasciatus. Proc Biol Sci 2024; 291:20240713. [PMID: 39106954 PMCID: PMC11303025 DOI: 10.1098/rspb.2024.0713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 06/03/2024] [Accepted: 07/10/2024] [Indexed: 08/09/2024] Open
Abstract
Aposematic coloration offers an opportunity to explore the molecular mechanisms underlying canalization. In this study, the role of epigenetic regulation underlying robustness was explored in the aposematic coloration of the milkweed bug, Oncopeltus fasciatus. Polycomb (Pc) and Enhancer of zeste (E(z)), which encode components of the Polycomb repressive complex 1 (PRC1) and PRC2, respectively, and jing, which encodes a component of the PRC2.2 subcomplex, were knocked down in the fourth instar of O. fasciatus. Knockdown of these genes led to alterations in scutellar morphology and melanization. In particular, when Pc was knocked down, the adults developed a highly melanized abdomen, head and forewings at all temperatures examined. In contrast, the E(z) and jing knockdown led to increased plasticity of the dorsal forewing melanization across different temperatures. Moreover, jing knockdown adults exhibited increased plasticity in the dorsal melanization of the head and the thorax. These observations demonstrate that histone modifiers may play a key role during the process of canalization to confer robustness in the aposematic coloration.
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Affiliation(s)
- Marie Tan
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA02481, USA
| | - Laura Park
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA02481, USA
| | - Elizabeth Chou
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA02481, USA
| | - Madeline Hoesel
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA02481, USA
| | - Lyanna Toh
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA02481, USA
| | - Yuichiro Suzuki
- Department of Biological Sciences, Wellesley College, 106 Central St., Wellesley, MA02481, USA
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10
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Luo Y, Lu J, Lei Z, Zhu H, Rao D, Wang T, Fu C, Zhang Z, Xia L, Huang W. Lysine methylation modifications in tumor immunomodulation and immunotherapy: regulatory mechanisms and perspectives. Biomark Res 2024; 12:74. [PMID: 39080807 PMCID: PMC11289998 DOI: 10.1186/s40364-024-00621-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2024] [Accepted: 07/17/2024] [Indexed: 08/02/2024] Open
Abstract
Lysine methylation is a crucial post-translational modification (PTM) that significantly impacts gene expression regulation. This modification not only influences cancer development directly but also has significant implications for the immune system. Lysine methylation modulates immune cell functions and shapes the anti-tumor immune response, highlighting its dual role in both tumor progression and immune regulation. In this review, we provide a comprehensive overview of the intrinsic role of lysine methylation in the activation and function of immune cells, detailing how these modifications affect cellular processes and signaling pathways. We delve into the mechanisms by which lysine methylation contributes to tumor immune evasion, allowing cancer cells to escape immune surveillance and thrive. Furthermore, we discuss the therapeutic potential of targeting lysine methylation in cancer immunotherapy. Emerging strategies, such as immune checkpoint inhibitors (ICIs) and chimeric antigen receptor T-cell (CAR-T) therapy, are being explored for their efficacy in modulating lysine methylation to enhance anti-tumor immune responses. By targeting these modifications, we can potentially improve the effectiveness of existing treatments and develop novel therapeutic approaches to combat cancer more effectively.
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Affiliation(s)
- Yiming Luo
- Hepatic Surgery Centre, Tongji Hospital, Tongji Medical College, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Junli Lu
- Hepatic Surgery Centre, Tongji Hospital, Tongji Medical College, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Zhen Lei
- Hepatic Surgery Centre, Tongji Hospital, Tongji Medical College, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - He Zhu
- Hepatic Surgery Centre, Tongji Hospital, Tongji Medical College, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Dean Rao
- Hepatic Surgery Centre, Tongji Hospital, Tongji Medical College, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Tiantian Wang
- Hepatic Surgery Centre, Tongji Hospital, Tongji Medical College, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Chenan Fu
- Hepatic Surgery Centre, Tongji Hospital, Tongji Medical College, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
| | - Zhiwei Zhang
- Hepatic Surgery Centre, Tongji Hospital, Tongji Medical College, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China
- Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, 430030, Hubei, China
| | - Limin Xia
- Department of Gastroenterology, Institute of Liver and Gastrointestinal Diseases, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
| | - Wenjie Huang
- Hepatic Surgery Centre, Tongji Hospital, Tongji Medical College, Hubei Key Laboratory of Hepato-Pancreato-Biliary Diseases, Huazhong University of Science and Technology, Wuhan, 430030, Hubei, China.
- Clinical Medicine Research Center for Hepatic Surgery of Hubei Province, Key Laboratory of Organ Transplantation, Ministry of Education and Ministry of Public Health, Wuhan, 430030, Hubei, China.
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11
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Chen X, Guo Y, Zhao T, Lu J, Fang J, Wang Y, Wang GG, Song J. Structural basis for the H2AK119ub1-specific DNMT3A-nucleosome interaction. Nat Commun 2024; 15:6217. [PMID: 39043678 PMCID: PMC11266573 DOI: 10.1038/s41467-024-50526-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 07/12/2024] [Indexed: 07/25/2024] Open
Abstract
Isoform 1 of DNA methyltransferase DNMT3A (DNMT3A1) specifically recognizes nucleosome monoubiquitylated at histone H2A lysine-119 (H2AK119ub1) for establishment of DNA methylation. Mis-regulation of this process may cause aberrant DNA methylation and pathogenesis. However, the molecular basis underlying DNMT3A1-nucleosome interaction remains elusive. Here we report the cryo-EM structure of DNMT3A1's ubiquitin-dependent recruitment (UDR) fragment complexed with H2AK119ub1-modified nucleosome. DNMT3A1 UDR occupies an extensive nucleosome surface, involving the H2A-H2B acidic patch, a surface groove formed by H2A and H3, nucleosomal DNA, and H2AK119ub1. The DNMT3A1 UDR's interaction with H2AK119ub1 affects the functionality of DNMT3A1 in cells in a context-dependent manner. Our structural and biochemical analysis also reveals competition between DNMT3A1 and JARID2, a cofactor of polycomb repression complex 2 (PRC2), for nucleosome binding, suggesting the interplay between different epigenetic pathways. Together, this study reports a molecular basis for H2AK119ub1-dependent DNMT3A1-nucleosome association, with important implications in DNMT3A1-mediated DNA methylation in development.
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Affiliation(s)
- Xinyi Chen
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Yiran Guo
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA
| | - Ting Zhao
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, 92521, USA
| | - Jiuwei Lu
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Jian Fang
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, CA, 92521, USA
- Department of Chemistry, University of California, Riverside, CA, 92521, USA
| | - Gang Greg Wang
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, 27710, USA.
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC, 27710, USA.
- Department of Pathology, Duke University School of Medicine, Durham, NC, 27710, USA.
| | - Jikui Song
- Department of Biochemistry, University of California, Riverside, CA, 92521, USA.
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12
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Cannea FB, Diana D, Rossino R, Padiglia A. ECPUB5 Polyubiquitin Gene in Euphorbia characias: Molecular Characterization and Seasonal Expression Analysis. Genes (Basel) 2024; 15:957. [PMID: 39062736 PMCID: PMC11275293 DOI: 10.3390/genes15070957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Revised: 07/17/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
The spurge Euphorbia characias is known for its latex, which is rich in antioxidant enzymes and anti-phytopathogen molecules. In this study, we identified a novel polyubiquitin protein in the latex and leaves, leading to the first molecular characterization of its coding gene and expressed protein in E. characias. Using consensus-degenerate hybrid oligonucleotide primers (CODEHOP) and rapid amplification of cDNA ends (5'/3'-RACE), we reconstructed the entire open reading frame (ORF) and noncoding regions. Our analysis revealed that the polyubiquitin gene encodes five tandemly repeated sequences, each coding for a ubiquitin monomer with amino acid variations in four of the five repeats. In silico studies have suggested functional differences among monomers. Gene expression peaked during the summer, correlating with high temperatures and suggesting a role in heat stress response. Western blotting confirmed the presence of polyubiquitin in the latex and leaf tissues, indicating active ubiquitination processes. These findings enhance our understanding of polyubiquitin's regulatory mechanisms and functions in E. characias, highlighting its unique structural and functional features.
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Affiliation(s)
- Faustina Barbara Cannea
- Biomedical Section, Department of Life and Environmental Sciences (DiSVA), Cittadella Universitaria di Monserrato, University of Cagliari, 09042 Cagliari, Italy;
| | - Daniela Diana
- Department of Medical Sciences and Public Health (DSMSP), AOU Presidio Microcitemico, University of Cagliari, 09121 Cagliari, Italy; (D.D.); (R.R.)
| | - Rossano Rossino
- Department of Medical Sciences and Public Health (DSMSP), AOU Presidio Microcitemico, University of Cagliari, 09121 Cagliari, Italy; (D.D.); (R.R.)
| | - Alessandra Padiglia
- Biomedical Section, Department of Life and Environmental Sciences (DiSVA), Cittadella Universitaria di Monserrato, University of Cagliari, 09042 Cagliari, Italy;
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13
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Ciapponi M, Karlukova E, Schkölziger S, Benda C, Müller J. Structural basis of the histone ubiquitination read-write mechanism of RYBP-PRC1. Nat Struct Mol Biol 2024; 31:1023-1027. [PMID: 38528151 PMCID: PMC11257959 DOI: 10.1038/s41594-024-01258-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 02/26/2024] [Indexed: 03/27/2024]
Abstract
Histone H2A monoubiquitination (H2Aub1) by the PRC1 subunit RING1B entails a positive feedback loop, mediated by the RING1B-interacting protein RYBP. We uncover that human RYBP-PRC1 binds unmodified nucleosomes via RING1B but H2Aub1-modified nucleosomes via RYBP. RYBP interactions with both ubiquitin and the nucleosome acidic patch create the high binding affinity that favors RYBP- over RING1B-directed PRC1 binding to H2Aub1-modified nucleosomes; this enables RING1B to monoubiquitinate H2A in neighboring unmodified nucleosomes.
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Affiliation(s)
- Maria Ciapponi
- Laboratory of Chromatin Biology, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Elena Karlukova
- Laboratory of Chromatin Biology, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Sven Schkölziger
- Laboratory of Chromatin Biology, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Christian Benda
- Department of Structural Cell Biology, Max-Planck Institute of Biochemistry, Martinsried, Germany.
| | - Jürg Müller
- Laboratory of Chromatin Biology, Max-Planck Institute of Biochemistry, Martinsried, Germany.
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14
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Ai H, He Z, Deng Z, Chu GC, Shi Q, Tong Z, Li JB, Pan M, Liu L. Structural and mechanistic basis for nucleosomal H2AK119 deubiquitination by single-subunit deubiquitinase USP16. Nat Struct Mol Biol 2024:10.1038/s41594-024-01342-2. [PMID: 38918638 DOI: 10.1038/s41594-024-01342-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 05/29/2024] [Indexed: 06/27/2024]
Abstract
Epigenetic regulators have a crucial effect on gene expression based on their manipulation of histone modifications. Histone H2AK119 monoubiquitination (H2AK119Ub), a well-established hallmark in transcription repression, is dynamically regulated by the opposing activities of Polycomb repressive complex 1 (PRC1) and nucleosome deubiquitinases including the primary human USP16 and Polycomb repressive deubiquitinase (PR-DUB) complex. Recently, the catalytic mechanism for the multi-subunit PR-DUB complex has been described, but how the single-subunit USP16 recognizes the H2AK119Ub nucleosome and cleaves the ubiquitin (Ub) remains unknown. Here we report the cryo-EM structure of USP16-H2AK119Ub nucleosome complex, which unveils a fundamentally distinct mode of H2AK119Ub deubiquitination compared to PR-DUB, encompassing the nucleosome recognition pattern independent of the H2A-H2B acidic patch and the conformational heterogeneity in the Ub motif and the histone H2A C-terminal tail. Our work highlights the mechanism diversity of H2AK119Ub deubiquitination and provides a structural framework for understanding the disease-causing mutations of USP16.
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Affiliation(s)
- Huasong Ai
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
- Institute of Translational Medicine, School of Pharmacy, School of Chemistry and Chemical Engineering, National Center for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai, China
| | - Zaozhen He
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Zhiheng Deng
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Guo-Chao Chu
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, China
| | - Qiang Shi
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Zebin Tong
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Jia-Bin Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Man Pan
- Institute of Translational Medicine, School of Pharmacy, School of Chemistry and Chemical Engineering, National Center for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai, China.
| | - Lei Liu
- New Cornerstone Science Laboratory, Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China.
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15
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Lopes M, Lund PJ, Garcia BA. An optimized and robust workflow for quantifying the canonical histone ubiquitination marks H2AK119ub and H2BK120ub by LC-MS/MS. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.11.596744. [PMID: 38915586 PMCID: PMC11195131 DOI: 10.1101/2024.06.11.596744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
The eukaryotic genome is packaged around histone proteins, which are subject to a myriad of post-translational modifications. By controlling DNA accessibility and the recruitment of protein complexes that mediate chromatin-related processes, these modifications constitute a key mechanism of epigenetic regulation. Since mass spectrometry can easily distinguish between these different modifications, it has become an essential technique in deciphering the histone code. Although robust LC-MS/MS methods are available to analyze modifications on the histone N-terminal tails, routine methods for characterizing ubiquitin marks on histone C-terminal regions, especially H2AK119ub, are less robust. Here we report the development of a simple workflow for the detection and improved quantification of the canonical histone ubiquitination marks H2AK119ub and H2BK120ub. The method entails a fully tryptic digestion of acid-extracted histones followed by derivatization with heavy or light propionic anhydride. A pooled sample is then spiked into oppositely labeled single samples as a reference channel for relative quantification, and data is acquired using PRM-based nanoLC-MS/MS. We validated our approach with synthetic peptides as well as treatments known to modulate the levels of H2AK119ub and H2BK120ub. This new method complements existing histone workflows, largely focused on the lysine-rich N-terminal regions, by extending modification analysis to other sequence contexts.
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Affiliation(s)
- Mariana Lopes
- Penn Epigenetics Institute, Dept. of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Peder J. Lund
- Penn Epigenetics Institute, Dept. of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
| | - Benjamin A. Garcia
- Penn Epigenetics Institute, Dept. of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
- Dept. of Biochemistry and Molecular Biophysics, School of Medicine, Washington University in St. Louis, St. Louis, MO 63110
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16
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Ni S, Takada Y, Ando T, Yu S, Yamashita Y, Takahashi Y, Sawada M, Oba M, Itoh Y, Suzuki T. Identification of a novel histone H2A mono-ubiquitination-inhibiting cell-active small molecule. Bioorg Med Chem Lett 2024; 105:129759. [PMID: 38636717 DOI: 10.1016/j.bmcl.2024.129759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
Histone H2A mono-ubiquitination plays important roles in epigenetic gene expression and is also involved in tumorigenesis. Small molecules controlling H2A ubiquitination are of interest as potential chemical tools and anticancer drugs. To identify novel small molecule inhibitors of H2A ubiquitination, we synthesized and evaluated several compounds designed based on PRT4165 (1), which is a reported histone ubiquitin ligase RING1A inhibitor. We found that compound 11b strongly inhibited the viability and reduced histone H2A mono-ubiquitination in human osteosarcoma U2OS cells. Therefore, compound 11b is a promising lead compound for the development of H2A histone ubiquitination-inhibiting small molecules.
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Affiliation(s)
- Siyao Ni
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Yuri Takada
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Takaaki Ando
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Shengwang Yu
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | | | - Yukari Takahashi
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Miho Sawada
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Makoto Oba
- Department of Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
| | - Yukihiro Itoh
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
| | - Takayoshi Suzuki
- SANKEN, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan.
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17
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Chen YZ, Zhu XM, Lv P, Hou XK, Pan Y, Li A, Du Z, Xuan JF, Guo X, Xing JX, Liu K, Yao J. Association of histone modification with the development of schizophrenia. Biomed Pharmacother 2024; 175:116747. [PMID: 38744217 DOI: 10.1016/j.biopha.2024.116747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 05/06/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024] Open
Abstract
Schizophrenia, influenced by genetic and environmental factors, may involve epigenetic alterations, notably histone modifications, in its pathogenesis. This review summarizes various histone modifications including acetylation, methylation, phosphorylation, ubiquitination, serotonylation, lactylation, palmitoylation, and dopaminylation, and their implications in schizophrenia. Current research predominantly focuses on histone acetylation and methylation, though other modifications also play significant roles. These modifications are crucial in regulating transcription through chromatin remodeling, which is vital for understanding schizophrenia's development. For instance, histone acetylation enhances transcriptional efficiency by loosening chromatin, while increased histone methyltransferase activity on H3K9 and altered histone phosphorylation, which reduces DNA affinity and destabilizes chromatin structure, are significant markers of schizophrenia.
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Affiliation(s)
- Yun-Zhou Chen
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Xiu-Mei Zhu
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Peng Lv
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Xi-Kai Hou
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Ying Pan
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Ang Li
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Zhe Du
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Jin-Feng Xuan
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China
| | - Xiaochong Guo
- Laboratory Animal Center, China Medical University, PR China
| | - Jia-Xin Xing
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China.
| | - Kun Liu
- Key Laboratory of Health Ministry in Congenital Malformation, Shengjing Hospital of China Medical University, PR China.
| | - Jun Yao
- School of Forensic Medicine, China Medical University, PR China; Key Laboratory of Forensic Bio-evidence Sciences, Liaoning Province, PR China; China Medical University Center of Forensic Investigation, PR China.
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18
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Rivard RS, Chang YC, Ragland RL, Thu YM, Kassab M, Mandal RS, Van Riper SK, Kulej K, Higgins L, Markowski TM, Shang D, Hedberg J, Erber L, Garcia B, Chen Y, Bielinsky AK, Brown EJ. Improved detection of DNA replication fork-associated proteins. Cell Rep 2024; 43:114178. [PMID: 38703364 DOI: 10.1016/j.celrep.2024.114178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 03/06/2024] [Accepted: 04/16/2024] [Indexed: 05/06/2024] Open
Abstract
Innovative methods to retrieve proteins associated with actively replicating DNA have provided a glimpse into the molecular dynamics of replication fork stalling. We report that a combination of density-based replisome enrichment by isolating proteins on nascent DNA (iPOND2) and label-free quantitative mass spectrometry (iPOND2-DRIPPER) substantially increases both replication factor yields and the dynamic range of protein quantification. Replication protein abundance in retrieved nascent DNA is elevated up to 300-fold over post-replicative controls, and recruitment of replication stress factors upon fork stalling is observed at similar levels. The increased sensitivity of iPOND2-DRIPPER permits direct measurement of ubiquitination events without intervening retrieval of diglycine tryptic fragments of ubiquitin. Using this approach, we find that stalled replisomes stimulate the recruitment of a diverse cohort of DNA repair factors, including those associated with poly-K63-ubiquitination. Finally, we uncover the temporally controlled association of stalled replisomes with nuclear pore complex components and nuclear cytoskeleton networks.
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Affiliation(s)
- Rebecca S Rivard
- Department of Cancer Biology and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ya-Chu Chang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Ryan L Ragland
- Department of Cancer Biology and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yee-Mon Thu
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Muzaffer Kassab
- Department of Cancer Biology and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul Shubhra Mandal
- Department of Cancer Biology and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Susan K Van Riper
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, MN, USA
| | - Katarzyna Kulej
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - LeeAnn Higgins
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Todd M Markowski
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - David Shang
- Department of Cancer Biology and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jack Hedberg
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Luke Erber
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Benjamin Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yue Chen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
| | - Eric J Brown
- Department of Cancer Biology and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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19
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Shafiq TA, Yu J, Feng W, Zhang Y, Zhou H, Paulo JA, Gygi SP, Moazed D. Genomic context- and H2AK119 ubiquitination-dependent inheritance of human Polycomb silencing. SCIENCE ADVANCES 2024; 10:eadl4529. [PMID: 38718120 PMCID: PMC11078181 DOI: 10.1126/sciadv.adl4529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 04/04/2024] [Indexed: 05/12/2024]
Abstract
Polycomb repressive complexes 1 and 2 (PRC1 and 2) are required for heritable repression of developmental genes. The cis- and trans-acting factors that contribute to epigenetic inheritance of mammalian Polycomb repression are not fully understood. Here, we show that, in human cells, ectopically induced Polycomb silencing at initially active developmental genes, but not near ubiquitously expressed housekeeping genes, is inherited for many cell divisions. Unexpectedly, silencing is heritable in cells with mutations in the H3K27me3 binding pocket of the Embryonic Ectoderm Development (EED) subunit of PRC2, which are known to disrupt H3K27me3 recognition and lead to loss of H3K27me3. This mode of inheritance is less stable and requires intact PRC2 and recognition of H2AK119ub1 by PRC1. Our findings suggest that maintenance of Polycomb silencing is sensitive to local genomic context and can be mediated by PRC1-dependent H2AK119ub1 and PRC2 independently of H3K27me3 recognition.
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Affiliation(s)
- Tiasha A. Shafiq
- Department of Cell Biology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Juntao Yu
- Department of Cell Biology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Wenzhi Feng
- Department of Cell Biology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Yizhe Zhang
- Department of Cell Biology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Haining Zhou
- Department of Cell Biology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Joao A. Paulo
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Steven P. Gygi
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Danesh Moazed
- Department of Cell Biology, Howard Hughes Medical Institute, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
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20
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Shi TH, Sugishita H, Gotoh Y. Crosstalk within and beyond the Polycomb repressive system. J Cell Biol 2024; 223:e202311021. [PMID: 38506728 PMCID: PMC10955045 DOI: 10.1083/jcb.202311021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/01/2024] [Accepted: 03/04/2024] [Indexed: 03/21/2024] Open
Abstract
The development of multicellular organisms depends on spatiotemporally controlled differentiation of numerous cell types and their maintenance. To generate such diversity based on the invariant genetic information stored in DNA, epigenetic mechanisms, which are heritable changes in gene function that do not involve alterations to the underlying DNA sequence, are required to establish and maintain unique gene expression programs. Polycomb repressive complexes represent a paradigm of epigenetic regulation of developmentally regulated genes, and the roles of these complexes as well as the epigenetic marks they deposit, namely H3K27me3 and H2AK119ub, have been extensively studied. However, an emerging theme from recent studies is that not only the autonomous functions of the Polycomb repressive system, but also crosstalks of Polycomb with other epigenetic modifications, are important for gene regulation. In this review, we summarize how these crosstalk mechanisms have improved our understanding of Polycomb biology and how such knowledge could help with the design of cancer treatments that target the dysregulated epigenome.
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Affiliation(s)
- Tianyi Hideyuki Shi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroki Sugishita
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- International Research Center for Neurointelligence, The University of Tokyo, Tokyo, Japan
| | - Yukiko Gotoh
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, Japan
- International Research Center for Neurointelligence, The University of Tokyo, Tokyo, Japan
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Xu BY, Yu XL, Gao WX, Gao TT, Hu HY, Wu TT, Shen C, Huang XY, Zheng B, Wu YB. RNF187 governs the maintenance of mouse GC-2 cell development by facilitating histone H3 ubiquitination at K57/80. Asian J Androl 2024; 26:272-281. [PMID: 38156805 PMCID: PMC11156453 DOI: 10.4103/aja202368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 10/19/2023] [Indexed: 01/03/2024] Open
Abstract
RING finger 187 (RNF187), a ubiquitin-ligating (E3) enzyme, plays a crucial role in the proliferation of cancer cells. However, it remains unclear whether RNF187 exhibits comparable functionality in the development of germline cells. To investigate the potential involvement of RNF187 in germ cell development, we conducted interference and overexpression assays using GC-2 cells, a mouse spermatocyte-derived cell line. Our findings reveal that the interaction between RNF187 and histone H3 increases the viability, proliferation, and migratory capacity of GC-2 cells. Moreover, we provide evidence demonstrating that RNF187 interacts with H3 and mediates the ubiquitination of H3 at lysine 57 (K57) or lysine 80 (K80), directly or indirectly resulting in increased cellular transcription. This is a study to report the role of RNF187 in maintaining the development of GC-2 cells by mediating histone H3 ubiquitination, thus highlighting the involvement of the K57 and K80 residues of H3 in the epistatic regulation of gene transcription. These discoveries provide a new theoretical foundation for further comprehensive investigations into the function of RNF187 in the reproductive system.
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Affiliation(s)
- Bing-Ya Xu
- Human Reproductive and Genetic Center, Affiliated Hospital of Jiangnan University, Wuxi 214122, China
| | - Xiang-Ling Yu
- Human Reproductive and Genetic Center, Affiliated Hospital of Jiangnan University, Wuxi 214122, China
| | - Wen-Xin Gao
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, China
| | - Ting-Ting Gao
- Changzhou Maternal and Child Health Care Hospital, Changzhou Medical Center, Nanjing Medical University, Changzhou 213000, China
| | - Hao-Yue Hu
- Human Reproductive and Genetic Center, Affiliated Hospital of Jiangnan University, Wuxi 214122, China
| | - Tian-Tian Wu
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, China
| | - Cong Shen
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou 215002, China
| | - Xiao-Yan Huang
- State Key Laboratory of Reproductive Medicine, Department of Histology and Embryology, School of Basic Medical Sciences, Nanjing Medical University, Nanjing 211166, China
| | - Bo Zheng
- State Key Laboratory of Reproductive Medicine, Center for Reproduction and Genetics, Suzhou Municipal Hospital, The Affiliated Suzhou Hospital of Nanjing Medical University, Gusu School, Nanjing Medical University, Suzhou 215002, China
| | - Yi-Bo Wu
- Human Reproductive and Genetic Center, Affiliated Hospital of Jiangnan University, Wuxi 214122, China
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22
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Mousa M, Liang Y, Tung LT, Wang H, Krawczyk C, Langlais D, Nijnik A. Chromatin-binding deubiquitinase MYSM1 acts in haematopoietic progenitors to control dendritic cell development and to program dendritic cell responses to microbial stimulation. Immunology 2024; 172:109-126. [PMID: 38316548 DOI: 10.1111/imm.13758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 01/08/2024] [Indexed: 02/07/2024] Open
Abstract
Dendritic cells (DCs) are the most significant antigen presenting cells of the immune system, critical for the activation of naïve T cells. The pathways controlling DC development, maturation, and effector function therefore require precise regulation to allow for an effective induction of adaptive immune response. MYSM1 is a chromatin binding deubiquitinase (DUB) and an activator of gene expression via its catalytic activity for monoubiquitinated histone H2A (H2A-K119ub), which is a highly abundant repressive epigenetic mark. MYSM1 is an important regulator of haematopoiesis in mouse and human, and a systemic constitutive loss of Mysm1 in mice results in a depletion of many haematopoietic progenitors, including DC precursors, with the downstream loss of most DC lineage cells. However, the roles of MYSM1 at the later checkpoints in DC development, maturation, activation, and effector function at present remain unknown. In the current work, using a range of novel mouse models (Mysm1flCreERT2, Mysm1flCD11c-cre, Mysm1DN), we further the understanding of MYSM1 functions in the DC lineage: assessing the requirement for MYSM1 in DC development independently of other complex developmental phenotypes, exploring its role at the later checkpoints in DC maintenance and activation in response to microbial stimulation, and testing the requirement for the DUB catalytic activity of MYSM1 in these processes. Surprisingly, we demonstrate that MYSM1 expression and catalytic activity in DCs are dispensable for the maintenance of DC numbers in vivo or for DC activation in response to microbial stimulation. In contrast, MYSM1 acts via its DUB catalytic activity specifically in haematopoietic progenitors to allow normal DC lineage development, and its loss results not only in a severe DC depletion but also in the production of functionally altered DCs, with a dysregulation of many housekeeping transcriptional programs and significantly altered responses to microbial stimulation.
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Affiliation(s)
- Marwah Mousa
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec, Canada
| | - Yue Liang
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec, Canada
| | - Lin Tze Tung
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec, Canada
| | - HanChen Wang
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec, Canada
| | - Connie Krawczyk
- Department of Metabolism and Nutritional Programming, Van Andel Institute, Grand Rapids, Michigan, United States
| | - David Langlais
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University Genome Centre, McGill University, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, Quebec, Canada
| | - Anastasia Nijnik
- Department of Physiology, McGill University, Montreal, Quebec, Canada
- McGill University Research Centre on Complex Traits, McGill University, Montreal, Quebec, Canada
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23
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Mandal K, Tomar SK, Kumar Santra M. Decoding the ubiquitin language: Orchestrating transcription initiation and gene expression through chromatin remodelers and histones. Gene 2024; 904:148218. [PMID: 38307220 DOI: 10.1016/j.gene.2024.148218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 01/22/2024] [Accepted: 01/25/2024] [Indexed: 02/04/2024]
Abstract
Eukaryotic transcription is a finely orchestrated process and it is controlled by transcription factors as well as epigenetic regulators. Transcription factors and epigenetic regulators undergo different types of posttranslational modifications including ubiquitination to control transcription process. Ubiquitination, traditionally associated with protein degradation, has emerged as a crucial contributor to the regulation of chromatin structure through ubiquitination of histone and chromatin remodelers. Ubiquitination introduces new layers of intricacy to the regulation of transcription initiation through controlling the equilibrium between euchromatin and heterochromatin states. Nucleosome, the fundamental units of chromatin, spacing in euchromatin and heterochromatin states are regulated by histone modification and chromatin remodeling complexes. Chromatin remodeling complexes actively sculpt the chromatin architecture and thereby influence the transcriptional states of genes. Therefore, understanding the dynamic behavior of nucleosome spacing is critical as it impacts various cellular functions through controlling gene expression profiles. In this comprehensive review, we discussed the intricate interplay between ubiquitination and transcription initiation, and illuminated the underlying molecular mechanisms that occur in a variety of biological contexts. This exploration sheds light on the complex regulatory networks that govern eukaryotic transcription, providing important insights into the fine orchestration of gene expression and chromatin dynamics.
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Affiliation(s)
- Kartik Mandal
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Shiva Kumar Tomar
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India; Department of Biotechnology, Savitribai Phule Pune University, Ganeshkhind Road, Pune, Maharashtra 411007, India
| | - Manas Kumar Santra
- Cancer Biology Division, National Centre for Cell Science, Ganeshkhind Road, Pune, Maharashtra 411007, India.
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24
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Veronezi GMB, Ramachandran S. Nucleation and spreading maintain Polycomb domains every cell cycle. Cell Rep 2024; 43:114090. [PMID: 38607915 PMCID: PMC11179494 DOI: 10.1016/j.celrep.2024.114090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/07/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Gene repression by the Polycomb pathway is essential for metazoan development. Polycomb domains, characterized by trimethylation of histone H3 lysine 27 (H3K27me3), carry the memory of repression and hence need to be maintained to counter the dilution of parental H3K27me3 with unmodified H3 during replication. Yet, how locus-specific H3K27me3 is maintained through replication is unclear. To understand H3K27me3 recovery post-replication, we first define nucleation sites within each Polycomb domain in mouse embryonic stem cells. To map dynamics of H3K27me3 domains across the cell cycle, we develop CUT&Flow (coupling cleavage under target and tagmentation with flow cytometry). We show that post-replication recovery of Polycomb domains occurs by nucleation and spreading, using the same nucleation sites used during de novo domain formation. By using Polycomb repressive complex 2 (PRC2) subunit-specific inhibitors, we find that PRC2 targets nucleation sites post-replication independent of pre-existing H3K27me3. Thus, competition between H3K27me3 deposition and nucleosome turnover drives both de novo domain formation and maintenance during every cell cycle.
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Affiliation(s)
- Giovana M B Veronezi
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Srinivas Ramachandran
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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25
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Din MAU, Lin Y, Wang N, Wang B, Mao F. Ferroptosis and the ubiquitin-proteasome system: exploring treatment targets in cancer. Front Pharmacol 2024; 15:1383203. [PMID: 38666028 PMCID: PMC11043542 DOI: 10.3389/fphar.2024.1383203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/02/2024] [Indexed: 04/28/2024] Open
Abstract
Ferroptosis is an emerging mode of programmed cell death fueled by iron buildup and lipid peroxidation. Recent evidence points to the function of ferroptosis in the aetiology and development of cancer and other disorders. Consequently, harnessing iron death for disease treatment has diverted the interest of the researchers in the field of basic and clinical research. The ubiquitin-proteasome system (UPS) represents a primary protein degradation pathway in eukaryotes. It involves labelling proteins to be degraded by ubiquitin (Ub), followed by recognition and degradation by the proteasome. Dysfunction of the UPS can contribute to diverse pathological processes, emphasizing the importance of maintaining organismal homeostasis. The regulation of protein stability is a critical component of the intricate molecular mechanism underlying iron death. Moreover, the intricate involvement of the UPS in regulating iron death-related molecules and signaling pathways, providing valuable insights for targeted treatment strategies. Besides, it highlights the potential of ferroptosis as a promising target for cancer therapy, emphasizing the combination between ferroptosis and the UPS. The molecular mechanisms underlying ferroptosis, including key regulators such as glutathione peroxidase 4 (GPX4), cysteine/glutamate transporter (system XC-), and iron metabolism, are thoroughly examined, alongside the role of the UPS in modulating the abundance and activity of crucial proteins for ferroptotic cell death, such as GPX4, and nuclear factor erythroid 2-related factor 2 (NRF2). As a pivotal regulatory system for macromolecular homeostasis, the UPS substantially impacts ferroptosis by directly or indirectly modulating iron death-related molecules or associated signaling pathways. This review explores the involvement of the UPS in regulating iron death-related molecules and signaling pathways, providing valuable insights for the targeted treatment of diseases associated with ferroptosis.
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Affiliation(s)
- Muhammad Azhar Ud Din
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine Jiangsu University, Zhenjiang, Jiangsu, China
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu, China
| | - Yan Lin
- The People’s Hospital of Danyang, Affiliated Danyang Hospital of Nantong University, Zhenjiang, Jiangsu, China
| | - Naijian Wang
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine Jiangsu University, Zhenjiang, Jiangsu, China
| | - Bo Wang
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine Jiangsu University, Zhenjiang, Jiangsu, China
| | - Fei Mao
- Key Laboratory of Medical Science and Laboratory Medicine of Jiangsu Province, School of Medicine Jiangsu University, Zhenjiang, Jiangsu, China
- Department of Laboratory Medicine, Lianyungang Clinical College, Jiangsu University, Lianyungang, Jiangsu, China
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26
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Nie H, Kong X, Song X, Guo X, Li Z, Fan C, Zhai B, Yang X, Wang Y. Roles of histone post-translational modifications in meiosis†. Biol Reprod 2024; 110:648-659. [PMID: 38224305 DOI: 10.1093/biolre/ioae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/16/2024] Open
Abstract
Histone post-translational modifications, such as phosphorylation, methylation, acetylation, and ubiquitination, play vital roles in various chromatin-based cellular processes. Meiosis is crucial for organisms that depend on sexual reproduction to produce haploid gametes, during which chromatin undergoes intricate conformational changes. An increasing body of evidence is clarifying the essential roles of histone post-translational modifications during meiotic divisions. In this review, we concentrate on the post-translational modifications of H2A, H2B, H3, and H4, as well as the linker histone H1, that are required for meiosis, and summarize recent progress in understanding how these modifications influence diverse meiotic events. Finally, challenges and exciting open questions for future research in this field are discussed. Summary Sentence Diverse histone post-translational modifications exert important effects on the meiotic cell cycle and these "histone codes" in meiosis might lead to the development of novel therapeutic strategies against reproductive diseases.
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Affiliation(s)
- Hui Nie
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Xueyu Kong
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Xiaoyu Song
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Xiaoyu Guo
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Zhanyu Li
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Cunxian Fan
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Binyuan Zhai
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Xiao Yang
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
| | - Ying Wang
- Center for Cell Structure and Function, Shandong Provincial Key Laboratory of Animal Resistance Biology, College of Life Sciences, Shandong Normal University, Jinan, Shandong, China
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27
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Park J, Kim JJ, Ryu JK. Mechanism of phase condensation for chromosome architecture and function. Exp Mol Med 2024; 56:809-819. [PMID: 38658703 PMCID: PMC11059216 DOI: 10.1038/s12276-024-01226-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/23/2024] [Accepted: 02/28/2024] [Indexed: 04/26/2024] Open
Abstract
Chromosomal phase separation is involved in a broad spectrum of chromosome organization and functional processes. Nonetheless, the intricacy of this process has left its molecular mechanism unclear. Here, we introduce the principles governing phase separation and its connections to physiological roles in this context. Our primary focus is contrasting two phase separation mechanisms: self-association-induced phase separation (SIPS) and bridging-induced phase separation (BIPS). We provide a comprehensive discussion of the distinct features characterizing these mechanisms and offer illustrative examples that suggest their broad applicability. With a detailed understanding of these mechanisms, we explore their associations with nucleosomes and chromosomal biological functions. This comprehensive review contributes to the exploration of uncharted territory in the intricate interplay between chromosome architecture and function.
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Affiliation(s)
- Jeongveen Park
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, South Korea
| | - Jeong-Jun Kim
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, South Korea
| | - Je-Kyung Ryu
- Department of Physics and Astronomy, Seoul National University, Seoul, 08826, South Korea.
- Institute of Applied Physics of Seoul National University, Seoul, 08826, South Korea.
- Institute of Molecular Biology and Genetics, Seoul National University, Seoul, 08826, South Korea.
- Department of Biological Sciences, Seoul National University, Seoul, 08826, South Korea.
- Interdisciplinary Program in Neuroscience, Seoul National University, Seoul, 08826, South Korea.
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28
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Konuma T, Zhou MM. Distinct Histone H3 Lysine 27 Modifications Dictate Different Outcomes of Gene Transcription. J Mol Biol 2024; 436:168376. [PMID: 38056822 DOI: 10.1016/j.jmb.2023.168376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/08/2023]
Abstract
Site-specific histone modifications have long been recognized to play an important role in directing gene transcription in chromatin in biology of health and disease. However, concrete illustration of how different histone modifications in a site-specific manner dictate gene transcription outcomes, as postulated in the influential "Histone code hypothesis", introduced by Allis and colleagues in 2000, has been lacking. In this review, we summarize our latest understanding of the dynamic regulation of gene transcriptional activation, silence, and repression in chromatin that is directed distinctively by histone H3 lysine 27 acetylation, methylation, and crotonylation, respectively. This represents a special example of a long-anticipated verification of the "Histone code hypothesis."
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Affiliation(s)
- Tsuyoshi Konuma
- Graduate School of Medical Life Science, Yokohama 230-0045, Japan; School of Science, Yokohama City University, Yokohama 230-0045, Japan
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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29
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Mathias B, O'Leary D, Saucier N, Ahmad F, White LS, Russell L, Shinawi M, Smith MJ, Abraham RS, Cooper MA, Kitcharoensakkul M, Green AM, Bednarski JJ. MYSM1 attenuates DNA damage signals triggered by physiologic and genotoxic DNA breaks. J Allergy Clin Immunol 2024; 153:1113-1124.e7. [PMID: 38065233 DOI: 10.1016/j.jaci.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 11/27/2023] [Accepted: 12/01/2023] [Indexed: 12/31/2023]
Abstract
BACKGROUND Patients with deleterious variants in MYSM1 have an immune deficiency characterized by B-cell lymphopenia, hypogammaglobulinemia, and increased radiosensitivity. MYSM1 is a histone deubiquitinase with established activity in regulating gene expression. MYSM1 also localizes to sites of DNA injury but its function in cellular responses to DNA breaks has not been elucidated. OBJECTIVES This study sought to determine the activity of MYSM1 in regulating DNA damage responses (DDRs) to DNA double-stranded breaks (DSBs) generated during immunoglobulin receptor gene (Ig) recombination and by ionizing radiation. METHODS MYSM1-deficient pre- and non-B cells were used to determine the role of MYSM1 in DSB generation, DSB repair, and termination of DDRs. RESULTS Genetic testing in a newborn with abnormal screen for severe combined immune deficiency, T-cell lymphopenia, and near absence of B cells identified a novel splice variant in MYSM1 that results in nearly absent protein expression. Radiosensitivity testing in patient's peripheral blood lymphocytes showed constitutive γH2AX, a marker of DNA damage, in B cells in the absence of irradiation, suggesting a role for MYSM1 in response to DSBs generated during Ig recombination. Suppression of MYSM1 in pre-B cells did not alter generation or repair of Ig DSBs. Rather, loss of MYSM1 resulted in persistent DNA damage foci and prolonged DDR signaling. Loss of MYSM1 also led to protracted DDRs in U2OS cells with irradiation induced DSBs. CONCLUSIONS MYSM1 regulates termination of DNA damage responses but does not function in DNA break generation and repair.
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Affiliation(s)
- Brendan Mathias
- Department of Pediatrics, Washington University School of Medicine, St Louis, Mo
| | - David O'Leary
- Department of Pediatrics, Washington University School of Medicine, St Louis, Mo
| | - Nermina Saucier
- Department of Pediatrics, Washington University School of Medicine, St Louis, Mo
| | - Faiz Ahmad
- Department of Medicine, Washington University School of Medicine, St Louis, Mo
| | - Lynn S White
- Department of Pediatrics, Washington University School of Medicine, St Louis, Mo
| | - Le'Mark Russell
- Department of Pediatrics, Washington University School of Medicine, St Louis, Mo
| | - Marwan Shinawi
- Department of Pediatrics, Washington University School of Medicine, St Louis, Mo
| | - Matthew J Smith
- Division of Hematology Research, Mayo Clinic, Rochester, Minn
| | - Roshini S Abraham
- Department of Pathology and Laboratory Medicine, Nationwide Children's Hospital, Columbus, Ohio
| | - Megan A Cooper
- Department of Pediatrics, Washington University School of Medicine, St Louis, Mo
| | | | - Abby M Green
- Department of Pediatrics, Washington University School of Medicine, St Louis, Mo
| | - Jeffrey J Bednarski
- Department of Pediatrics, Washington University School of Medicine, St Louis, Mo.
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30
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Franz P, Fierz B. Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective. J Mol Biol 2024; 436:168442. [PMID: 38211893 DOI: 10.1016/j.jmb.2024.168442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/05/2024] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
Since Strahl and Allis proposed the "language of covalent histone modifications", a host of experimental studies have shed light on the different facets of chromatin regulation by epigenetic mechanisms. Initially proposed as a concept for controlling gene transcription, the regulation of deposition and removal of histone post-translational modifications (PTMs), such as acetylation, methylation, and phosphorylation, have been implicated in many chromatin regulation pathways. However, large PTMs such as ubiquitylation challenge research on many levels due to their chemical complexity. In recent years, chemical tools have been developed to generate chromatin in defined ubiquitylation states in vitro. Chemical biology approaches are now used to link specific histone ubiquitylation marks with downstream chromatin regulation events on the molecular level. Here, we want to highlight how chemical biology approaches have empowered the mechanistic study of chromatin ubiquitylation in the context of gene regulation and DNA repair with attention to future challenges.
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Affiliation(s)
- Pauline Franz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Beat Fierz
- Laboratory of Biophysical Chemistry of Macromolecules, Institute of Chemical Sciences and Engineering (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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31
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Wilson B, Esmaeili F, Parsons M, Salah W, Su Z, Dutta A. sRNA-Effector: A tool to expedite discovery of small RNA regulators. iScience 2024; 27:109300. [PMID: 38469560 PMCID: PMC10926228 DOI: 10.1016/j.isci.2024.109300] [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: 08/03/2023] [Revised: 11/08/2023] [Accepted: 02/16/2024] [Indexed: 03/13/2024] Open
Abstract
microRNAs (miRNAs) are small regulatory RNAs that repress target mRNA transcripts through base pairing. Although the mechanisms of miRNA production and function are clearly established, new insights into miRNA regulation or miRNA-mediated gene silencing are still emerging. In order to facilitate the discovery of miRNA regulators or effectors, we have developed sRNA-Effector, a machine learning algorithm trained on enhanced crosslinking and immunoprecipitation sequencing and RNA sequencing data following knockdown of specific genes. sRNA-Effector can accurately identify known miRNA biogenesis and effector proteins and identifies 9 putative regulators of miRNA function, including serine/threonine kinase STK33, splicing factor SFPQ, and proto-oncogene BMI1. We validated the role of STK33, SFPQ, and BMI1 in miRNA regulation, showing that sRNA-Effector is useful for identifying new players in small RNA biology. sRNA-Effector will be a web tool available for all researchers to identify potential miRNA regulators in any cell line of interest.
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Affiliation(s)
- Briana Wilson
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA
| | - Fatemeh Esmaeili
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Matthew Parsons
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA
| | - Wafa Salah
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22901, USA
| | - Zhangli Su
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Anindya Dutta
- Department of Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
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Liang Y, Wang H, Seija N, Lin YH, Tung LT, Di Noia JM, Langlais D, Nijnik A. B-cell intrinsic regulation of antibody mediated immunity by histone H2A deubiquitinase BAP1. Front Immunol 2024; 15:1353138. [PMID: 38529289 PMCID: PMC10961346 DOI: 10.3389/fimmu.2024.1353138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 02/15/2024] [Indexed: 03/27/2024] Open
Abstract
Introduction BAP1 is a deubiquitinase (DUB) of the Ubiquitin C-terminal Hydrolase (UCH) family that regulates gene expression and other cellular processes, through its direct catalytic activity on the repressive epigenetic mark histone H2AK119ub, as well as on several other substrates. BAP1 is also a highly important tumor suppressor, expressed and functional across many cell types and tissues. In recent work, we demonstrated a cell intrinsic role of BAP1 in the B cell lineage development in murine bone marrow, however the role of BAP1 in the regulation of B cell mediated humoral immune response has not been previously explored. Methods and results In the current study, we demonstrate that a B-cell intrinsic loss of BAP1 in activated B cells in the Bap1 fl/fl Cγ1-cre murine model results in a severe defect in antibody production, with altered dynamics of germinal centre B cell, memory B cell, and plasma cell numbers. At the cellular and molecular level, BAP1 was dispensable for B cell immunoglobulin class switching but resulted in an impaired proliferation of activated B cells, with genome-wide dysregulation in histone H2AK119ub levels and gene expression. Conclusion and discussion In summary, our study establishes the B-cell intrinsic role of BAP1 in antibody mediated immune response and indicates its central role in the regulation of the genome-wide landscapes of histone H2AK119ub and downstream transcriptional programs of B cell activation and humoral immunity.
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Affiliation(s)
- Yue Liang
- Department of Physiology, McGill University, Montreal, QC, Canada
- McGill University Research Centre on Complex Traits, McGill University, Montreal, QC, Canada
| | - HanChen Wang
- Department of Physiology, McGill University, Montreal, QC, Canada
- McGill University Research Centre on Complex Traits, McGill University, Montreal, QC, Canada
- McGill Genome Centre, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Noé Seija
- Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
- Molecular Biology Programs, Université de Montréal, Montreal, QC, Canada
| | - Yun Hsiao Lin
- Department of Physiology, McGill University, Montreal, QC, Canada
- McGill University Research Centre on Complex Traits, McGill University, Montreal, QC, Canada
| | - Lin Tze Tung
- Department of Physiology, McGill University, Montreal, QC, Canada
- McGill University Research Centre on Complex Traits, McGill University, Montreal, QC, Canada
- McGill Genome Centre, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Javier M. Di Noia
- Institut de Recherches Cliniques de Montréal, Montreal, QC, Canada
- Molecular Biology Programs, Université de Montréal, Montreal, QC, Canada
- Department of Medicine, Université de Montréal, Montreal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - David Langlais
- McGill University Research Centre on Complex Traits, McGill University, Montreal, QC, Canada
- McGill Genome Centre, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Anastasia Nijnik
- Department of Physiology, McGill University, Montreal, QC, Canada
- McGill University Research Centre on Complex Traits, McGill University, Montreal, QC, Canada
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de Groot AP, de Haan G. How CBX proteins regulate normal and leukemic blood cells. FEBS Lett 2024. [PMID: 38426219 DOI: 10.1002/1873-3468.14839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/26/2024] [Accepted: 02/09/2024] [Indexed: 03/02/2024]
Abstract
Hematopoietic stem cell (HSC) fate decisions are dictated by epigenetic landscapes. The Polycomb Repressive Complex 1 (PRC1) represses genes that induce differentiation, thereby maintaining HSC self-renewal. Depending on which chromobox (CBX) protein (CBX2, CBX4, CBX6, CBX7, or CBX8) is part of the PRC1 complex, HSC fate decisions differ. Here, we review how this occurs. We describe how CBX proteins dictate age-related changes in HSCs and stimulate oncogenic HSC fate decisions, either as canonical PRC1 members or by alternative interactions, including non-epigenetic regulation. CBX2, CBX7, and CBX8 enhance leukemia progression. To target, reprogram, and kill leukemic cells, we suggest and describe multiple therapeutic strategies to interfere with the epigenetic functions of oncogenic CBX proteins. Future studies should clarify to what extent the non-epigenetic function of cytoplasmic CBX proteins is important for normal, aged, and leukemic blood cells.
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Affiliation(s)
- Anne P de Groot
- European Research Institute for Biology of Ageing (ERIBA), University Medical Center Groningen (UMCG), The Netherlands
- Sanquin Research, Landsteiner Laboratory, Sanquin Blood Supply, Amsterdam, The Netherlands
| | - Gerald de Haan
- European Research Institute for Biology of Ageing (ERIBA), University Medical Center Groningen (UMCG), The Netherlands
- Sanquin Research, Landsteiner Laboratory, Sanquin Blood Supply, Amsterdam, The Netherlands
- Department of Hematology, Amsterdam UMC, University of Amsterdam, The Netherlands
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34
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Ito S, Umehara T, Koseki H. Polycomb-mediated histone modifications and gene regulation. Biochem Soc Trans 2024; 52:151-161. [PMID: 38288743 DOI: 10.1042/bst20230336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/03/2024] [Accepted: 01/05/2024] [Indexed: 02/29/2024]
Abstract
Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) are transcriptional repressor complexes that play a fundamental role in epigenomic regulation and the cell-fate decision; these complexes are widely conserved in multicellular organisms. PRC1 is an E3 ubiquitin (ub) ligase that generates histone H2A ubiquitinated at lysine (K) 119 (H2AK119ub1), whereas PRC2 is a histone methyltransferase that specifically catalyzes tri-methylation of histone H3K27 (H3K27me3). Genome-wide analyses have confirmed that these two key epigenetic marks highly overlap across the genome and contribute to gene repression. We are now beginning to understand the molecular mechanisms that enable PRC1 and PRC2 to identify their target sites in the genome and communicate through feedback mechanisms to create Polycomb chromatin domains. Recently, it has become apparent that PRC1-induced H2AK119ub1 not only serves as a docking site for PRC2 but also affects the dynamics of the H3 tail, both of which enhance PRC2 activity, suggesting that trans-tail communication between H2A and H3 facilitates the formation of the Polycomb chromatin domain. In this review, we discuss the emerging principles that define how PRC1 and PRC2 establish the Polycomb chromatin domain and regulate gene expression in mammals.
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Affiliation(s)
- Shinsuke Ito
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Takashi Umehara
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Laboratory for Epigenetics Drug Discovery, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
| | - Haruhiko Koseki
- Laboratory of Developmental Genetics, RIKEN Center for Integrative Medical Sciences, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Department of Cellular and Molecular Medicine, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8670, Japan
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35
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Santarelli P, Rosti V, Vivo M, Lanzuolo C. Chromatin organization of muscle stem cell. Curr Top Dev Biol 2024; 158:375-406. [PMID: 38670713 DOI: 10.1016/bs.ctdb.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
The proper functioning of skeletal muscles is essential throughout life. A crucial crosstalk between the environment and several cellular mechanisms allows striated muscles to perform successfully. Notably, the skeletal muscle tissue reacts to an injury producing a completely functioning tissue. The muscle's robust regenerative capacity relies on the fine coordination between muscle stem cells (MuSCs or "satellite cells") and their specific microenvironment that dictates stem cells' activation, differentiation, and self-renewal. Critical for the muscle stem cell pool is a fine regulation of chromatin organization and gene expression. Acquiring a lineage-specific 3D genome architecture constitutes a crucial modulator of muscle stem cell function during development, in the adult stage, in physiological and pathological conditions. The context-dependent relationship between genome structure, such as accessibility and chromatin compartmentalization, and their functional effects will be analysed considering the improved 3D epigenome knowledge, underlining the intimate liaison between environmental encounters and epigenetics.
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Affiliation(s)
- Philina Santarelli
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy
| | - Valentina Rosti
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy; CNR Institute of Biomedical Technologies, Milan, Italy
| | - Maria Vivo
- Università degli studi di Salerno, Fisciano, Italy.
| | - Chiara Lanzuolo
- INGM Istituto Nazionale Genetica Molecolare Romeo ed Enrica Invernizzi, Milan, Italy; CNR Institute of Biomedical Technologies, Milan, Italy.
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Raghubeer S. The influence of epigenetics and inflammation on cardiometabolic risks. Semin Cell Dev Biol 2024; 154:175-184. [PMID: 36804178 DOI: 10.1016/j.semcdb.2023.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023]
Abstract
Cardiometabolic diseases include metabolic syndrome, obesity, type 2 diabetes mellitus, and hypertension. Epigenetic modifications participate in cardiometabolic diseases through several pathways, including inflammation, vascular dysfunction, and insulin resistance. Epigenetic modifications, which encompass alterations to gene expression without mutating the DNA sequence, have gained much attention in recent years, since they have been correlated with cardiometabolic diseases and may be targeted for therapeutic interventions. Epigenetic modifications are greatly influenced by environmental factors, such as diet, physical activity, cigarette smoking, and pollution. Some modifications are heritable, indicating that the biological expression of epigenetic alterations may be observed across generations. Moreover, many patients with cardiometabolic diseases present with chronic inflammation, which can be influenced by environmental and genetic factors. The inflammatory environment worsens the prognosis of cardiometabolic diseases and further induces epigenetic modifications, predisposing patients to the development of other metabolism-associated diseases and complications. A deeper understanding of inflammatory processes and epigenetic modifications in cardiometabolic diseases is necessary to improve our diagnostic capabilities, personalized medicine approaches, and the development of targeted therapeutic interventions. Further understanding may also assist in predicting disease outcomes, especially in children and young adults. This review describes epigenetic modifications and inflammatory processes underlying cardiometabolic diseases, and further discusses advances in the research field with a focus on specific points for interventional therapy.
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Affiliation(s)
- Shanel Raghubeer
- SAMRC/CPUT/Cardiometabolic Health Research Unit, Department of Biomedical Sciences, Faculty of Health & Wellness Sciences, Cape Peninsula University of Technology, South Africa.
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Malcore RM, Kalantry S. A Comparative Analysis of Mouse Imprinted and Random X-Chromosome Inactivation. EPIGENOMES 2024; 8:8. [PMID: 38390899 PMCID: PMC10885068 DOI: 10.3390/epigenomes8010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/01/2024] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
The mammalian sexes are distinguished by the X and Y chromosomes. Whereas males harbor one X and one Y chromosome, females harbor two X chromosomes. To equalize X-linked gene expression between the sexes, therian mammals have evolved X-chromosome inactivation as a dosage compensation mechanism. During X-inactivation, most genes on one of the two X chromosomes in females are transcriptionally silenced, thus equalizing X-linked gene expression between the sexes. Two forms of X-inactivation characterize eutherian mammals, imprinted and random. Imprinted X-inactivation is defined by the exclusive inactivation of the paternal X chromosome in all cells, whereas random X-inactivation results in the silencing of genes on either the paternal or maternal X chromosome in individual cells. Both forms of X-inactivation have been studied intensively in the mouse model system, which undergoes both imprinted and random X-inactivation early in embryonic development. Stable imprinted and random X-inactivation requires the induction of the Xist long non-coding RNA. Following its induction, Xist RNA recruits proteins and complexes that silence genes on the inactive-X. In this review, we present a current understanding of the mechanisms of Xist RNA induction, and, separately, the establishment and maintenance of gene silencing on the inactive-X by Xist RNA during imprinted and random X-inactivation.
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Affiliation(s)
| | - Sundeep Kalantry
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48105, USA
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38
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McGrath KE, Koniski AD, Murphy K, Getman M, An HH, Schulz VP, Kim AR, Zhang B, Schofield TL, Papoin J, Blanc L, Kingsley PD, Westhoff CM, Gallagher PG, Chou ST, Steiner LA, Palis J. BMI1 regulates human erythroid self-renewal through both gene repression and gene activation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.02.578704. [PMID: 38370741 PMCID: PMC10871261 DOI: 10.1101/2024.02.02.578704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
The limited proliferative capacity of erythroid precursors is a major obstacle to generate sufficient numbers of in vitro-derived red blood cells (RBC) for clinical purposes. We and others have determined that BMI1, a member of the polycomb repressive complex 1 (PRC1), is both necessary and sufficient to drive extensive proliferation of self-renewing erythroblasts (SREs). However, the mechanisms of BMI1 action remain poorly understood. BMI1 overexpression led to 10 billion-fold increase BMI1-induced (i)SRE self-renewal. Despite prolonged culture and BMI1 overexpression, human iSREs can terminally mature and agglutinate with typing reagent monoclonal antibodies against conventional RBC antigens. BMI1 and RING1B occupancy, along with repressive histone marks, were identified at known BMI1 target genes, including the INK-ARF locus, consistent with an altered cell cycle following BMI1 inhibition. We also identified upregulated BMI1 target genes with low repressive histone modifications, including key regulator of cholesterol homeostasis. Functional studies suggest that both cholesterol import and synthesis are essential for BMI1-associated self-renewal. These findings support the hypothesis that BMI1 regulates erythroid self-renewal not only through gene repression but also through gene activation and offer a strategy to expand the pool of immature erythroid precursors for eventual clinical uses.
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Affiliation(s)
- Kathleen E. McGrath
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY USA
| | - Anne D. Koniski
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY USA
| | - Kristin Murphy
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY USA
| | - Michael Getman
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY USA
| | - Hyun Hyung An
- Dept. of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | | | - Ah Ram Kim
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY USA
| | - Bin Zhang
- Department of Pathology and Laboratory Medicine, University of Rochester Medical Center, Rochester, NY, USA
| | - Taylor L. Schofield
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY USA
| | - Julien Papoin
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Lionel Blanc
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Paul D. Kingsley
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY USA
| | | | - Patrick G. Gallagher
- Dept. of Pediatrics, Yale School of Medicine, New Haven, CT, USA
- Nationwide Children’s Hospital, Ohio State University, Columbus, OH, USA
| | - Stella T. Chou
- Dept. of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA, USA
| | - Laurie A. Steiner
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY USA
| | - James Palis
- Department of Pediatrics, University of Rochester Medical Center, Rochester, NY USA
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39
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Shao R, Suzuki T, Suyama M, Tsukada Y. The impact of selective HDAC inhibitors on the transcriptome of early mouse embryos. BMC Genomics 2024; 25:143. [PMID: 38317092 PMCID: PMC10840191 DOI: 10.1186/s12864-024-10029-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 01/18/2024] [Indexed: 02/07/2024] Open
Abstract
BACKGROUND Histone acetylation, which is regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), plays a crucial role in the control of gene expression. HDAC inhibitors (HDACi) have shown potential in cancer therapy; however, the specific roles of HDACs in early embryos remain unclear. Moreover, although some pan-HDACi have been used to maintain cellular undifferentiated states in early embryos, the specific mechanisms underlying their effects remain unknown. Thus, there remains a significant knowledge gap regarding the application of selective HDACi in early embryos. RESULTS To address this gap, we treated early embryos with two selective HDACi (MGCD0103 and T247). Subsequently, we collected and analyzed their transcriptome data at different developmental stages. Our findings unveiled a significant effect of HDACi treatment during the crucial 2-cell stage of zygotes, leading to a delay in embryonic development after T247 and an arrest at 2-cell stage after MGCD0103 administration. Furthermore, we elucidated the regulatory targets underlying this arrested embryonic development, which pinpointed the G2/M phase as the potential period of embryonic development arrest caused by MGCD0103. Moreover, our investigation provided a comprehensive profile of the biological processes that are affected by HDACi, with their main effects being predominantly localized in four aspects of zygotic gene activation (ZGA): RNA splicing, cell cycle regulation, autophagy, and transcription factor regulation. By exploring the transcriptional regulation and epigenetic features of the genes affected by HDACi, we made inferences regarding the potential main pathways via which HDACs affect gene expression in early embryos. Notably, Hdac7 exhibited a distinct response, highlighting its potential as a key player in early embryonic development. CONCLUSIONS Our study conducted a comprehensive analysis of the effects of HDACi on early embryonic development at the transcriptional level. The results demonstrated that HDACi significantly affected ZGA in embryos, elucidated the distinct actions of various selective HDACi, and identified specific biological pathways and mechanisms via which these inhibitors modulated early embryonic development.
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Affiliation(s)
- Ruiqi Shao
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, 812-8582, Fukuoka, Japan
| | - Takayoshi Suzuki
- SANKEN, Osaka University, 8-1 Mihogaoka, 567-0047, Ibaraki, Osaka, Japan
| | - Mikita Suyama
- Division of Bioinformatics, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, 812-8582, Fukuoka, Japan.
| | - Yuichi Tsukada
- Advanced Biological Information Research Division, INAMORI Frontier Research Center, Kyushu University, 744 Motooka, Nishi-ku, 819-0395, Fukuoka, Japan.
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40
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Tong Z, Ai H, Xu Z, He K, Chu GC, Shi Q, Deng Z, Xue Q, Sun M, Du Y, Liang L, Li JB, Pan M, Liu L. Synovial sarcoma X breakpoint 1 protein uses a cryptic groove to selectively recognize H2AK119Ub nucleosomes. Nat Struct Mol Biol 2024; 31:300-310. [PMID: 38177667 DOI: 10.1038/s41594-023-01141-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 09/27/2023] [Indexed: 01/06/2024]
Abstract
The cancer-specific fusion oncoprotein SS18-SSX1 disturbs chromatin accessibility by hijacking the BAF complex from the promoters and enhancers to the Polycomb-repressed chromatin regions. This process relies on the selective recognition of H2AK119Ub nucleosomes by synovial sarcoma X breakpoint 1 (SSX1). However, the mechanism underlying the selective recognition of H2AK119Ub nucleosomes by SSX1 in the absence of ubiquitin (Ub)-binding capacity remains unknown. Here we report the cryo-EM structure of SSX1 bound to H2AK119Ub nucleosomes at 3.1-Å resolution. Combined in vitro biochemical and cellular assays revealed that the Ub recognition by SSX1 is unique and depends on a cryptic basic groove formed by H3 and the Ub motif on the H2AK119 site. Moreover, this unorthodox binding mode of SSX1 induces DNA unwrapping at the entry/exit sites. Together, our results describe a unique mode of site-specific ubiquitinated nucleosome recognition that underlies the specific hijacking of the BAF complex to Polycomb regions by SS18-SSX1 in synovial sarcoma.
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Affiliation(s)
- Zebin Tong
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Huasong Ai
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China.
- Institute of Translational Medicine, School of Pharmacy, School of Chemistry and Chemical Engineering, National Center for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai, China.
| | - Ziyu Xu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Kezhang He
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Guo-Chao Chu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Qiang Shi
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Zhiheng Deng
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Qiaomei Xue
- School of Pharmaceutical Sciences, Tsinghua University, Beijing, China
| | - Maoshen Sun
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Yunxiang Du
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Lujun Liang
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China
- Institute of Translational Medicine, School of Pharmacy, School of Chemistry and Chemical Engineering, National Center for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai, China
| | - Jia-Bin Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Man Pan
- Institute of Translational Medicine, School of Pharmacy, School of Chemistry and Chemical Engineering, National Center for Translational Medicine (Shanghai), Shanghai Jiao Tong University, Shanghai, China.
| | - Lei Liu
- Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing, China.
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41
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Wu KJ, Chen Q, Leung CH, Sun N, Gao F, Chen Z. Recent discoveries of the role of histone modifications and related inhibitors in pathological cardiac hypertrophy. Drug Discov Today 2024; 29:103878. [PMID: 38211819 DOI: 10.1016/j.drudis.2024.103878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/19/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
Pathological cardiac hypertrophy is a common response of the heart to various pathological stimuli. In recent years, various histone modifications, including acetylation, methylation, phosphorylation and ubiquitination, have been identified to have crucial roles in regulating chromatin remodeling and cardiac hypertrophy. Novel drugs targeting these epigenetic changes have emerged as potential treatments for pathological cardiac hypertrophy. In this review, we provide a comprehensive summary of the roles of histone modifications in regulating the development of pathological cardiac hypertrophy, and discuss potential therapeutic targets that could be utilized for its treatment.
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Affiliation(s)
- Ke-Jia Wu
- Wuxi School of Medicine, Jiangnan University, Jiangsu 214082, PR China
| | - Qi Chen
- Wuxi School of Medicine, Jiangnan University, Jiangsu 214082, PR China
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa 999078, Macau; Department of Biomedical Sciences, Faculty of Health Sciences, University of Macau, Taipa 999078, Macau; Macao Centre for Research and Development in Chinese Medicine, University of Macau, Taipa 999078, Macau; MoE Frontiers Science Centre for Precision Oncology, University of Macau, Taipa 999078, Macau.
| | - Ning Sun
- Wuxi School of Medicine, Jiangnan University, Jiangsu 214082, PR China.
| | - Fei Gao
- Department of Cardiology, Beijing An Zhen Hospital, Capital Medical University, Chaoyang District, Beijing 100029, PR China.
| | - Zhaoyang Chen
- Department of Cardiology, Heart Center of Fujian Province, Fujian Medical University Union Hospital, 29 Xin-Quan Road, Fuzhou, Fujian 350001, PR China.
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42
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Rahman S, Wolberger C. Breaking the K48-chain: linking ubiquitin beyond protein degradation. Nat Struct Mol Biol 2024; 31:216-218. [PMID: 38366227 DOI: 10.1038/s41594-024-01221-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 02/18/2024]
Abstract
The discovery of ubiquitin conjugation to lysines and the role of K48-linked polyubiquitin in targeting substrates for proteasomal degradation was followed by revelation of non-degradative roles of ubiquitination and, more recently, of non-canonical covalent ubiquitin linkages. Here we summarize findings of the ever-expanding array of ubiquitin signals and their biological roles.
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Affiliation(s)
- Sanim Rahman
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Shen X, Chen C, Wang Y, Zheng W, Zheng J, Jones AE, Zhu B, Zhang H, Lyons C, Rijal A, Moley JA, Cao G, Liu K, Winn R, Dickinson A, Zhang K, Wang H. Role of histone variants H2BC1 and H2AZ.2 in H2AK119ub nucleosome organization and Polycomb gene silencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575234. [PMID: 38293106 PMCID: PMC10827191 DOI: 10.1101/2024.01.16.575234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Ubiquitination of histone H2A at lysine 119 residue (H2AK119ub) plays critical roles in a wide range of physiological processes, including Polycomb gene silencing 1,2 , replication 3-5 , DNA damage repair 6-10 , X inactivation 11,12 , and heterochromatin organization 13,14 . However, the underlying mechanism and structural basis of H2AK119ub remains largely elusive. In this study, we report that H2AK119ub nucleosomes have a unique composition, containing histone variants H2BC1 and H2AZ.2, and importantly, this composition is required for H2AK119ub and Polycomb gene silencing. Using the UAB domain of RSF1, we purified H2AK119ub nucleosomes to a sufficient amount and purity. Mass spectrometry analyses revealed that H2AK119ub nucleosomes contain the histone variants H2BC1 and H2AZ.2. A cryo-EM study resolved the structure of native H2AK119ub nucleosomes to a 2.6A resolution, confirming H2BC1 in one subgroup of H2AK119ub nucleosomes. Tandem GST-UAB pulldown, Flag-H2AZ.2, and HA-H2BC1 immunoprecipitation revealed that H2AK119ub nucleosomes could be separated into distinct subgroups, suggesting their composition heterogeneity and potential dynamic organization. Knockout or knockdown of H2BC1 or H2AZ.2 reduced cellular H2AK119ub levels, establishing H2BC1 and H2AZ.2 as critical determinants of H2AK119ub. Furthermore, genomic binding profiles of H2BC1 and H2AZ.2 overlapped significantly with H2AK119ub binding, with the most significant overlapping in the gene body and intergenic regions. Finally, assays in developing embryos reveal an interaction of H2AZ.2, H2BC1, and RING1A in vivo . Thus, this study revealed, for the first time, that the H2AK119ub nucleosome has a unique composition, and this composition is required for H2AK119ub and Polycomb gene silencing.
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Seif E, Francis NJ. A Two-Step Mechanism for Creating Stable, Condensed Chromatin with the Polycomb Complex PRC1. Molecules 2024; 29:323. [PMID: 38257239 PMCID: PMC10821450 DOI: 10.3390/molecules29020323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 12/26/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
The Drosophila PRC1 complex regulates gene expression by modifying histone proteins and chromatin architecture. Two PRC1 subunits, PSC and Ph, are most implicated in chromatin architecture. In vitro, PRC1 compacts chromatin and inhibits transcription and nucleosome remodeling. The long disordered C-terminal region of PSC (PSC-CTR) is important for these activities, while Ph has little effect. In cells, Ph is important for condensate formation, long-range chromatin interactions, and gene regulation, and its polymerizing sterile alpha motif (SAM) is implicated in these activities. In vitro, truncated Ph containing the SAM and two other conserved domains (mini-Ph) undergoes phase separation with chromatin, suggesting a mechanism for SAM-dependent condensate formation in vivo. How the distinct activities of PSC and Ph on chromatin function together in PRC1 is not known. To address this question, we analyzed structures formed with large chromatin templates and PRC1 in vitro. PRC1 bridges chromatin into extensive fibrillar networks. Ph, its SAM, and SAM polymerization activity have little effect on these structures. Instead, the PSC-CTR controls their growth, and is sufficient for their formation. To understand how phase separation driven by Ph SAM intersects with the chromatin bridging activity of the PSC-CTR, we used mini-Ph to form condensates with chromatin and then challenged them with PRC1 lacking Ph (PRC1ΔPh). PRC1ΔPh converts mini-Ph chromatin condensates into clusters of small non-fusing condensates and bridged fibers. These condensates retain a high level of chromatin compaction and do not intermix. Thus, phase separation of chromatin by mini-Ph, followed by the action of the PSC-CTR, creates a unique chromatin organization with regions of high nucleosome density and extraordinary stability. We discuss how this coordinated sequential activity of two proteins found in the same complex may occur and the possible implications of stable chromatin architectures in maintaining transcription states.
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Affiliation(s)
- Elias Seif
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada;
| | - Nicole J. Francis
- Institut de Recherches Cliniques de Montréal, 110 Avenue des Pins Ouest, Montréal, QC H2W 1R7, Canada;
- Division of Experimental Medicine, McGill University, 1001 Decarie Boulevard, Montréal, QC H4A 3J1, Canada
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC H3T 1J4, Canada
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Worthmann A, Ridder J, Piel SYL, Evangelakos I, Musfeldt M, Voß H, O'Farrell M, Fischer AW, Adak S, Sundd M, Siffeti H, Haumann F, Kloth K, Bierhals T, Heine M, Pertzborn P, Pauly M, Scholz JJ, Kundu S, Fuh MM, Neu A, Tödter K, Hempel M, Knippschild U, Semenkovich CF, Schlüter H, Heeren J, Scheja L, Kubisch C, Schlein C. Fatty acid synthesis suppresses dietary polyunsaturated fatty acid use. Nat Commun 2024; 15:45. [PMID: 38167725 PMCID: PMC10762034 DOI: 10.1038/s41467-023-44364-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/11/2023] [Indexed: 01/05/2024] Open
Abstract
Dietary polyunsaturated fatty acids (PUFA) are increasingly recognized for their health benefits, whereas a high production of endogenous fatty acids - a process called de novo lipogenesis (DNL) - is closely linked to metabolic diseases. Determinants of PUFA incorporation into complex lipids are insufficiently understood and may influence the onset and progression of metabolic diseases. Here we show that fatty acid synthase (FASN), the key enzyme of DNL, critically determines the use of dietary PUFA in mice and humans. Moreover, the combination of FASN inhibition and PUFA-supplementation decreases liver triacylglycerols (TAG) in mice fed with high-fat diet. Mechanistically, FASN inhibition causes higher PUFA uptake via the lysophosphatidylcholine transporter MFSD2A, and a diacylglycerol O-acyltransferase 2 (DGAT2)-dependent incorporation of PUFA into TAG. Overall, the outcome of PUFA supplementation may depend on the degree of endogenous DNL and combining PUFA supplementation and FASN inhibition might be a promising approach to target metabolic disease.
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Affiliation(s)
- Anna Worthmann
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julius Ridder
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sharlaine Y L Piel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ioannis Evangelakos
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Melina Musfeldt
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hannah Voß
- Section / Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Marie O'Farrell
- Sagimet Biosciences Inc., 155 Bovet Rd., San Mateo, CA, 94402, USA
| | - Alexander W Fischer
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Sangeeta Adak
- Division of Endocrinology, Metabolism & Lipid Research, Department of Medicine, Washington University, St. Louis, MO, USA
| | - Monica Sundd
- National Institute of Immunology, New Delhi, India
| | - Hasibullah Siffeti
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Friederike Haumann
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katja Kloth
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tatjana Bierhals
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Markus Heine
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Paul Pertzborn
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Mira Pauly
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia-Josefine Scholz
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Suman Kundu
- Department of Biochemistry, University of Delhi South Campus, New Delhi 110021 and Department of Biological Sciences, Birla Institute of Technology and Science Pilani, K K Birla Goa Campus, Goa, 403726, India
| | - Marceline M Fuh
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Axel Neu
- Department of Pediatrics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Klaus Tödter
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maja Hempel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Institute of Human Genetics, University Hospital Heidelberg, Im Neuenheimer Feld 440, 69120, Heidelberg, Germany
| | - Uwe Knippschild
- Department of General and Visceral Surgery, University Hospital Ulm, Ulm, Germany
| | - Clay F Semenkovich
- Division of Endocrinology, Metabolism & Lipid Research, Department of Medicine, Washington University, St. Louis, MO, USA
| | - Hartmut Schlüter
- Section / Core Facility Mass Spectrometry and Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Joerg Heeren
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ludger Scheja
- Department of Biochemistry and Molecular Cell Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Kubisch
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Christian Schlein
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
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Miller A, Dasen JS. Establishing and maintaining Hox profiles during spinal cord development. Semin Cell Dev Biol 2024; 152-153:44-57. [PMID: 37029058 PMCID: PMC10524138 DOI: 10.1016/j.semcdb.2023.03.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/18/2023] [Accepted: 03/30/2023] [Indexed: 04/09/2023]
Abstract
The chromosomally-arrayed Hox gene family plays central roles in embryonic patterning and the specification of cell identities throughout the animal kingdom. In vertebrates, the relatively large number of Hox genes and pervasive expression throughout the body has hindered understanding of their biological roles during differentiation. Studies on the subtype diversification of spinal motor neurons (MNs) have provided a tractable system to explore the function of Hox genes during differentiation, and have provided an entry point to explore how neuronal fate determinants contribute to motor circuit assembly. Recent work, using both in vitro and in vivo models of MN subtype differentiation, have revealed how patterning morphogens and regulation of chromatin structure determine cell-type specific programs of gene expression. These studies have not only shed light on basic mechanisms of rostrocaudal patterning in vertebrates, but also have illuminated mechanistic principles of gene regulation that likely operate in the development and maintenance of terminal fates in other systems.
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Affiliation(s)
- Alexander Miller
- NYU Neuroscience Institute and Developmental Genetics Programs, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA.
| | - Jeremy S Dasen
- NYU Neuroscience Institute and Developmental Genetics Programs, Department of Neuroscience and Physiology, NYU School of Medicine, New York, NY 10016, USA.
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47
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Liu J, Fan H, Liang X, Chen Y. Polycomb repressor complex: Its function in human cancer and therapeutic target strategy. Biomed Pharmacother 2023; 169:115897. [PMID: 37981459 DOI: 10.1016/j.biopha.2023.115897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 11/07/2023] [Accepted: 11/13/2023] [Indexed: 11/21/2023] Open
Abstract
The Polycomb Repressor Complex (PRC) plays a pivotal role in gene regulation during development and disease, with dysregulation contributing significantly to various human cancers. The intricate interplay between PRC and cellular signaling pathways sheds light on cancer complexity. PRC presents promising therapeutic opportunities, with inhibitors undergoing rigorous evaluation in preclinical and clinical studies. In this review, we emphasize the critical role of PRC complex in gene regulation, particularly PcG proteins mediated chromatin compaction through phase separation. We also highlight the pathological implications of PRC complex dysregulation in various tumors, elucidating underlying mechanisms driving cancer progression. The burgeoning field of therapeutic strategies targeting PRC complexes, notably EZH2 inhibitors, has advanced significantly. However, we explore the need for combination therapies to enhance PRC targeted treatments efficacy, providing a glimpse into the future of cancer therapeutics.
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Affiliation(s)
- Jingrong Liu
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
| | - Hongjie Fan
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China
| | - Xinmiao Liang
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
| | - Yang Chen
- Ganjiang Chinese Medicine Innovation Center, Nanchang 330000, China; CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
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48
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Shi P, Wu J, Li M, Cao Y, Wu J, Ren P, Liu K, Zhou J, Sha Y, Zhang Q, Sun H. Upregulation of Hsp27 via further inhibition of histone H2A ubiquitination confers protection against myocardial ischemia/reperfusion injury by promoting glycolysis and enhancing mitochondrial function. Cell Death Discov 2023; 9:466. [PMID: 38114486 PMCID: PMC10730859 DOI: 10.1038/s41420-023-01762-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 11/28/2023] [Accepted: 12/06/2023] [Indexed: 12/21/2023] Open
Abstract
Research suggests that ischemic glycolysis improves myocardial tolerance to anoxia and low-flow ischemia. The rate of glycolysis during ischemia reflects the severity of the injury caused by ischemia and subsequent functional recovery following reperfusion. Histone H2AK119 ubiquitination (H2Aub) is a common modification that is primarily associated with gene silencing. Recent studies have demonstrated that H2Aub contributes to the development of cardiovascular diseases. However, the underlying mechanism remains unclear. This study identified Hsp27 (heat shock protein 27) as a H2Aub binding protein and explored its involvement in mediating glycolysis and mitochondrial function. Functional studies revealed that inhibition of PRC1 (polycomb repressive complex 1) decreased H2Aub occupancy and promoted Hsp27 expression through inhibiting ubiquitination. Additionally, it increased glycolysis by activating the NF-κB/PFKFB3 signaling pathway during myocardial ischemia. Furthermore, Hsp27 reduced mitochondrial ROS production by chaperoning COQ9, and suppressed ferroptosis during reperfusion. A delivery system was developed based on PCL-PEG-MAL (PPM)-PCM-SH (CWLSEAGPVVTVRALRGTGSW) to deliver PRT4165 (PRT), a potent inhibitor of PRC1, to damaged myocardium, resulting in decreased H2Aub. These findings revealed a novel epigenetic mechanism connecting glycolysis and ferroptosis in protecting the myocardium against ischemia/reperfusion injury.
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Affiliation(s)
- Pilong Shi
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, Heilongjiang, 163319, China
| | - Jiawei Wu
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, Heilongjiang, 163319, China
| | - Minghui Li
- Department of Pharmaceutics, Harbin Medical University-Daqing, Daqing, Heilongjiang, 163319, China
| | - Yonggang Cao
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, Heilongjiang, 163319, China
| | - Jiabi Wu
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, Heilongjiang, 163319, China
| | - Ping Ren
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, Heilongjiang, 163319, China
| | - Kai Liu
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, Heilongjiang, 163319, China
| | - Jiajun Zhou
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, Heilongjiang, 163319, China
| | - Yuetong Sha
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, Heilongjiang, 163319, China
| | - Qianhui Zhang
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, Heilongjiang, 163319, China
| | - Hongli Sun
- Department of Pharmacology, Harbin Medical University-Daqing, Daqing, Heilongjiang, 163319, China.
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49
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Kim SJ, Kiser PK, Asfaha S, DeKoter RP, Dick FA. EZH2 inhibition stimulates repetitive element expression and viral mimicry in resting splenic B cells. EMBO J 2023; 42:e114462. [PMID: 37934086 PMCID: PMC10711652 DOI: 10.15252/embj.2023114462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 11/08/2023] Open
Abstract
Mammalian cells repress expression of repetitive genomic sequences by forming heterochromatin. However, the consequences of ectopic repeat expression remain unclear. Here we demonstrate that inhibitors of EZH2, the catalytic subunit of the Polycomb repressive complex 2 (PRC2), stimulate repeat misexpression and cell death in resting splenic B cells. B cells are uniquely sensitive to these agents because they exhibit high levels of histone H3 lysine 27 trimethylation (H3K27me3) and correspondingly low DNA methylation at repeat elements. We generated a pattern recognition receptor loss-of-function mouse model, called RIC, with mutations in Rigi (encoding for RIG-I), Ifih1 (MDA5), and Cgas. In both wildtype and RIC mutant B cells, EZH2 inhibition caused loss of H3K27me3 at repetitive elements and upregulated their expression. However, NF-κB-dependent expression of inflammatory chemokines and subsequent cell death was suppressed by the RIC mutations. We further show that inhibition of EZH2 in cancer cells requires the same pattern recognition receptors to activate an interferon response. Together, the results reveal chemokine expression induced by EZH2 inhibitors in B cells as a novel inflammatory response to genomic repeat expression. Given the overlap of genes induced by EZH2 inhibitors and Epstein-Barr virus infection, this response can be described as a form of viral mimicry.
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Affiliation(s)
- Seung J Kim
- London Regional Cancer ProgramChildren's Health Research InstituteLondonONCanada
- London Health Sciences Research InstituteLondonONCanada
- Department of BiochemistryWestern UniversityLondonONCanada
| | - Patti K Kiser
- Department of Pathology and Laboratory MedicineWestern UniversityLondonONCanada
| | - Samuel Asfaha
- London Regional Cancer ProgramChildren's Health Research InstituteLondonONCanada
- London Health Sciences Research InstituteLondonONCanada
- Department of Pathology and Laboratory MedicineWestern UniversityLondonONCanada
- Department of MedicineWestern UniversityLondonONCanada
| | - Rodney P DeKoter
- Department of Microbiology & ImmunologyWestern UniversityLondonONCanada
| | - Frederick A Dick
- London Regional Cancer ProgramChildren's Health Research InstituteLondonONCanada
- London Health Sciences Research InstituteLondonONCanada
- Department of Pathology and Laboratory MedicineWestern UniversityLondonONCanada
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50
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Bsteh D, Moussa HF, Michlits G, Yelagandula R, Wang J, Elling U, Bell O. Loss of cohesin regulator PDS5A reveals repressive role of Polycomb loops. Nat Commun 2023; 14:8160. [PMID: 38071364 PMCID: PMC10710464 DOI: 10.1038/s41467-023-43869-w] [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: 06/27/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023] Open
Abstract
Polycomb Repressive Complexes 1 and 2 (PRC1, PRC2) are conserved epigenetic regulators that promote transcriptional gene silencing. PRC1 and PRC2 converge on shared targets, catalyzing repressive histone modifications. Additionally, a subset of PRC1/PRC2 targets engage in long-range interactions whose functions in gene silencing are poorly understood. Using a CRISPR screen in mouse embryonic stem cells, we found that the cohesin regulator PDS5A links transcriptional silencing by Polycomb and 3D genome organization. PDS5A deletion impairs cohesin unloading and results in derepression of a subset of endogenous PRC1/PRC2 target genes. Importantly, derepression is not linked to loss of Polycomb chromatin domains. Instead, PDS5A removal causes aberrant cohesin activity leading to ectopic insulation sites, which disrupt the formation of ultra-long Polycomb loops. We show that these loops are important for robust silencing at a subset of PRC1/PRC2 target genes and that maintenance of cohesin-dependent genome architecture is critical for Polycomb regulation.
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Affiliation(s)
- Daniel Bsteh
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
- Departments of Biochemistry and Molecular Medicine, and Stem Cell and Regenerative Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Division of Medical Oncology, Department of Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Hagar F Moussa
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
- Department of Biomedical Engineering and Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Georg Michlits
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, Vienna, Austria
- JLP Health GmbH, Himmelhofgasse 62, 1130, Vienna, Austria
| | - Ramesh Yelagandula
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Laboratory of Epigenetics, Cell Fate & Disease, Centre for DNA Fingerprinting and Diagnostics (CDFD), Uppal, Hyderabad, 500039, India
| | - Jingkui Wang
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
- Research Institute of Molecular Pathology (IMP), Vienna BioCenter (VBC), Vienna, Austria
| | - Ulrich Elling
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria
| | - Oliver Bell
- Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Vienna, Austria.
- Departments of Biochemistry and Molecular Medicine, and Stem Cell and Regenerative Medicine, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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