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Woo H, Oh J, Cho YJ, Oh GT, Kim SY, Dan K, Han D, Lee JS, Kim T. N-terminal acetylation of Set1-COMPASS fine-tunes H3K4 methylation patterns. SCIENCE ADVANCES 2024; 10:eadl6280. [PMID: 38996018 PMCID: PMC11244526 DOI: 10.1126/sciadv.adl6280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 06/07/2024] [Indexed: 07/14/2024]
Abstract
H3K4 methylation by Set1-COMPASS (complex of proteins associated with Set1) is a conserved histone modification. Although it is critical for gene regulation, the posttranslational modifications of this complex that affect its function are largely unexplored. This study showed that N-terminal acetylation of Set1-COMPASS proteins by N-terminal acetyltransferases (NATs) can modulate H3K4 methylation patterns. Specifically, deleting NatA substantially decreased global H3K4me3 levels and caused the H3K4me2 peak in the 5' transcribed regions to shift to the promoters. NatA was required for N-terminal acetylation of three subunits of Set1-COMPASS: Shg1, Spp1, and Swd2. Moreover, deleting Shg1 or blocking its N-terminal acetylation via proline mutation of the target residue drastically reduced H3K4 methylation. Thus, NatA-mediated N-terminal acetylation of Shg1 shapes H3K4 methylation patterns. NatB also regulates H3K4 methylation, likely via N-terminal acetylation of the Set1-COMPASS protein Swd1. Thus, N-terminal acetylation of Set1-COMPASS proteins can directly fine-tune the functions of this complex, thereby substantially shaping H3K4 methylation patterns.
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Affiliation(s)
- Hyeonju Woo
- Department of Life Science and Multitasking Macrophage Research Center, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Junsoo Oh
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Yong-Joon Cho
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
- Multidimensional Genomics Research Center, Kangwon National University, Chuncheon, Republic of Korea
| | - Goo Taeg Oh
- Department of Life Science and Multitasking Macrophage Research Center, Ewha Womans University, Seoul 03760, Republic of Korea
| | - Seon-Young Kim
- Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Kisoon Dan
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul 03082, Republic of Korea
| | - Dohyun Han
- Proteomics Core Facility, Biomedical Research Institute, Seoul National University Hospital, Seoul 03082, Republic of Korea
- Department of Transdisciplinary Medicine, Seoul National University Hospital, Seoul 03082, Republic of Korea
- Department of Medicine, Seoul National University College of Medicine, Seoul 03082, Republic of Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - TaeSoo Kim
- Department of Life Science and Multitasking Macrophage Research Center, Ewha Womans University, Seoul 03760, Republic of Korea
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Wang H, Helin K. Roles of H3K4 methylation in biology and disease. Trends Cell Biol 2024:S0962-8924(24)00115-6. [PMID: 38909006 DOI: 10.1016/j.tcb.2024.06.001] [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: 03/01/2024] [Revised: 05/13/2024] [Accepted: 06/03/2024] [Indexed: 06/24/2024]
Abstract
Epigenetic modifications, including posttranslational modifications of histones, are closely linked to transcriptional regulation. Trimethylated H3 lysine 4 (H3K4me3) is one of the most studied histone modifications owing to its enrichment at the start sites of transcription and its association with gene expression and processes determining cell fate, development, and disease. In this review, we focus on recent studies that have yielded insights into how levels and patterns of H3K4me3 are regulated, how H3K4me3 contributes to the regulation of specific phases of transcription such as RNA polymerase II initiation, pause-release, heterogeneity, and consistency. The conclusion from these studies is that H3K4me3 by itself regulates gene expression and its precise regulation is essential for normal development and preventing disease.
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Affiliation(s)
- Hua Wang
- Peking University International Cancer Institute, Peking University Cancer Hospital and Institute, State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China; Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
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Fetian T, Grover A, Arndt KM. Histone H2B ubiquitylation: Connections to transcription and effects on chromatin structure. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195018. [PMID: 38331024 PMCID: PMC11098702 DOI: 10.1016/j.bbagrm.2024.195018] [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: 10/06/2023] [Revised: 01/30/2024] [Accepted: 02/05/2024] [Indexed: 02/10/2024]
Abstract
Nucleosomes are major determinants of eukaryotic genome organization and regulation. Many studies, incorporating a diversity of experimental approaches, have been focused on identifying and discerning the contributions of histone post-translational modifications to DNA-centered processes. Among these, monoubiquitylation of H2B (H2Bub) on K120 in humans or K123 in budding yeast is a critical histone modification that has been implicated in a wide array of DNA transactions. H2B is co-transcriptionally ubiquitylated and deubiquitylated via the concerted action of an extensive network of proteins. In addition to altering the chemical and physical properties of the nucleosome, H2Bub is important for the proper control of gene expression and for the deposition of other histone modifications. In this review, we discuss the molecular mechanisms underlying the ubiquitylation cycle of H2B and how it connects to the regulation of transcription and chromatin structure.
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Affiliation(s)
- Tasniem Fetian
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Aakash Grover
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States of America
| | - Karen M Arndt
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260, United States of America.
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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] [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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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] [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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Oh J, Park S, Kim J, Yeom S, Lee JM, Lee EJ, Cho YJ, Lee JS. Swd2/Cps35 determines H3K4 tri-methylation via interactions with Set1 and Rad6. BMC Biol 2024; 22:105. [PMID: 38702628 PMCID: PMC11069235 DOI: 10.1186/s12915-024-01903-3] [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: 09/19/2023] [Accepted: 04/24/2024] [Indexed: 05/06/2024] Open
Abstract
BACKGROUND Histone H3K4 tri-methylation (H3K4me3) catalyzed by Set1/COMPASS, is a prominent epigenetic mark found in promoter-proximal regions of actively transcribed genes. H3K4me3 relies on prior monoubiquitination at the histone H2B (H2Bub) by Rad6 and Bre1. Swd2/Cps35, a Set1/COMPASS component, has been proposed as a key player in facilitating H2Bub-dependent H3K4me3. However, a more comprehensive investigation regarding the relationship among Rad6, Swd2, and Set1 is required to further understand the mechanisms and functions of the H3K4 methylation. RESULTS We investigated the genome-wide occupancy patterns of Rad6, Swd2, and Set1 under various genetic conditions, aiming to clarify the roles of Set1 and Rad6 for occupancy of Swd2. Swd2 peaks appear on both the 5' region and 3' region of genes, which are overlapped with its tightly bound two complexes, Set1 and cleavage and polyadenylation factor (CPF), respectively. In the absence of Rad6/H2Bub, Set1 predominantly localized to the 5' region of genes, while Swd2 lost all the chromatin binding. However, in the absence of Set1, Swd2 occupancy near the 5' region was impaired and rather increased in the 3' region. CONCLUSIONS This study highlights that the catalytic activity of Rad6 is essential for all the ways of Swd2's binding to the transcribed genes and Set1 redistributes the Swd2 to the 5' region for accomplishments of H3K4me3 in the genome-wide level.
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Affiliation(s)
- Junsoo Oh
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
- Institue of Life Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Shinae Park
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
- Institue of Life Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Jueun Kim
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
- Kangwon Institute of Inclusive Technology, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Soojin Yeom
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
- Institue of Life Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Ji Min Lee
- Graduate School of Medical Science & Engineering, Korea Advanced Institute of Science and Technology, 291 Daehak-Ro, Yuseong-Gu, Daejeon, 34141, Republic of Korea
| | - Eun-Jin Lee
- Department of Life Sciences, Korea University, Seoul, 02841, Republic of Korea.
| | - Yong-Joon Cho
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
- Multidimensional Genomics Research Center, Kangwon National University, Chuncheon, 24341, Republic of Korea.
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.
- Institue of Life Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea.
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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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Lyu Y, Yang Y, Talwar V, Lu H, Chen C, Salman S, Wicks EE, Huang TYT, Drehmer D, Wang Y, Zuo Q, Datan E, Jackson W, Dordai D, Wang R, Semenza GL. Hypoxia-inducible factor 1 recruits FACT and RNF20/40 to mediate histone ubiquitination and transcriptional activation of target genes. Cell Rep 2024; 43:113972. [PMID: 38517892 DOI: 10.1016/j.celrep.2024.113972] [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: 09/18/2023] [Revised: 02/01/2024] [Accepted: 03/01/2024] [Indexed: 03/24/2024] Open
Abstract
Hypoxia-inducible factor 1 (HIF-1) is a transcriptional activator that mediates cellular adaptation to decreased oxygen availability. HIF-1 recruits chromatin-modifying enzymes leading to changes in histone acetylation, citrullination, and methylation at target genes. Here, we demonstrate that hypoxia-inducible gene expression in estrogen receptor (ER)-positive MCF7 and ER-negative SUM159 human breast cancer cells requires the histone H2A/H2B chaperone facilitates chromatin transcription (FACT) and the H2B ubiquitin ligase RING finger protein 20/40 (RNF20/40). Knockdown of FACT or RNF20/40 expression leads to decreased transcription initiation and elongation at HIF-1 target genes. Mechanistically, FACT and RNF20/40 are recruited to hypoxia response elements (HREs) by HIF-1 and stabilize binding of HIF-1 (and each other) at HREs. Hypoxia induces the monoubiquitination of histone H2B at lysine 120 at HIF-1 target genes in an HIF-1-dependent manner. Together, these findings delineate a cooperative molecular mechanism by which FACT and RNF20/40 stabilize multiprotein complex formation at HREs and mediate histone ubiquitination to facilitate HIF-1 transcriptional activity.
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Affiliation(s)
- Yajing Lyu
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yongkang Yang
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21205, USA
| | - Varen Talwar
- Johns Hopkins University, Baltimore, MD 21218, USA
| | - Haiquan Lu
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21205, USA
| | - Chelsey Chen
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Shaima Salman
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Elizabeth E Wicks
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tina Yi-Ting Huang
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daiana Drehmer
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Yufeng Wang
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Qiaozhu Zuo
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Emmanuel Datan
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Walter Jackson
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Dominic Dordai
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Ru Wang
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Gregg L Semenza
- Armstrong Oxygen Biology Research Center and Vascular Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins, Baltimore, MD 21205, USA.
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Mbonye U, Karn J. The cell biology of HIV-1 latency and rebound. Retrovirology 2024; 21:6. [PMID: 38580979 PMCID: PMC10996279 DOI: 10.1186/s12977-024-00639-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2024] Open
Abstract
Transcriptionally latent forms of replication-competent proviruses, present primarily in a small subset of memory CD4+ T cells, pose the primary barrier to a cure for HIV-1 infection because they are the source of the viral rebound that almost inevitably follows the interruption of antiretroviral therapy. Over the last 30 years, many of the factors essential for initiating HIV-1 transcription have been identified in studies performed using transformed cell lines, such as the Jurkat T-cell model. However, as highlighted in this review, several poorly understood mechanisms still need to be elucidated, including the molecular basis for promoter-proximal pausing of the transcribing complex and the detailed mechanism of the delivery of P-TEFb from 7SK snRNP. Furthermore, the central paradox of HIV-1 transcription remains unsolved: how are the initial rounds of transcription achieved in the absence of Tat? A critical limitation of the transformed cell models is that they do not recapitulate the transitions between active effector cells and quiescent memory T cells. Therefore, investigation of the molecular mechanisms of HIV-1 latency reversal and LRA efficacy in a proper physiological context requires the utilization of primary cell models. Recent mechanistic studies of HIV-1 transcription using latently infected cells recovered from donors and ex vivo cellular models of viral latency have demonstrated that the primary blocks to HIV-1 transcription in memory CD4+ T cells are restrictive epigenetic features at the proviral promoter, the cytoplasmic sequestration of key transcription initiation factors such as NFAT and NF-κB, and the vanishingly low expression of the cellular transcription elongation factor P-TEFb. One of the foremost schemes to eliminate the residual reservoir is to deliberately reactivate latent HIV-1 proviruses to enable clearance of persisting latently infected cells-the "Shock and Kill" strategy. For "Shock and Kill" to become efficient, effective, non-toxic latency-reversing agents (LRAs) must be discovered. Since multiple restrictions limit viral reactivation in primary cells, understanding the T-cell signaling mechanisms that are essential for stimulating P-TEFb biogenesis, initiation factor activation, and reversing the proviral epigenetic restrictions have become a prerequisite for the development of more effective LRAs.
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Affiliation(s)
- Uri Mbonye
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
| | - Jonathan Karn
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA.
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Burenkova OV, Grigorenko EL. The role of epigenetic mechanisms in the long-term effects of early-life adversity and mother-infant relationship on physiology and behavior of offspring in laboratory rats and mice. Dev Psychobiol 2024; 66:e22479. [PMID: 38470450 PMCID: PMC10959231 DOI: 10.1002/dev.22479] [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] [Revised: 01/23/2024] [Accepted: 02/16/2024] [Indexed: 03/13/2024]
Abstract
Maternal care during the early postnatal period of altricial mammals is a key factor in the survival and adaptation of offspring to environmental conditions. Natural variations in maternal care and experimental manipulations with maternal-child relationships modeling early-life adversity (ELA) in laboratory rats and mice have a strong long-term influence on the physiology and behavior of offspring in rats and mice. This literature review is devoted to the latest research on the role of epigenetic mechanisms in these effects of ELA and mother-infant relationship, with a focus on the regulation of hypothalamic-pituitary-adrenal axis and brain-derived neurotrophic factor. An important part of this review is dedicated to pharmacological interventions and epigenetic editing as tools for studying the causal role of epigenetic mechanisms in the development of physiological and behavioral profiles. A special section of the manuscript will discuss the translational potential of the discussed research.
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Affiliation(s)
- Olga V. Burenkova
- Department of Psychology, University of Houston, Houston, Texas, USA
- Texas Institute for Measurement, Evaluation, and Statistics, University of Houston, Houston, Texas, USA
- Department of Integrative Biology, University of Guelph, Guelph, Ontario, Canada
| | - Elena L. Grigorenko
- Department of Psychology, University of Houston, Houston, Texas, USA
- Texas Institute for Measurement, Evaluation, and Statistics, University of Houston, Houston, Texas, USA
- Center for Cognitive Sciences, Sirius University of Science and Technology, Sochi, Russia
- Departments of Molecular and Human Genetics and Pediatrics, Baylor College of Medicine, Houston, Texas, USA
- Child Study Center, Yale University, New Haven, Connecticut, USA
- Research Administration, Moscow State University for Psychology and Education, Moscow, Russia
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11
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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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12
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Luo XC, Yu L, Xu SY, Ying SH, Feng MG. Rad6, a ubiquitin conjugator required for insect-pathogenic lifestyle, UV damage repair, and genomic expression of Beauveria bassiana. Microbiol Res 2024; 281:127622. [PMID: 38246123 DOI: 10.1016/j.micres.2024.127622] [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: 10/30/2023] [Revised: 11/09/2023] [Accepted: 01/13/2024] [Indexed: 01/23/2024]
Abstract
The E2 ubiquitin conjugator Rad6 is required for DNA damage bypass in budding yeast but remain functionally unknown in filamentous fungi. Here, we report pleiotropic effect of Rad6 ortholog in Beauveria bassiana, a wide-spectrum fungal insecticide. Global ubiquitination signal was greatly attenuated in the absence of rad6. The blocked ubiquitination led to severe growth defect, blocked asexual development, and abolished infectivity/insect pathogenicity, which correlated with compromised conidial quality (including viability, hydrophobicity, adherence to insect cuticle, and thermotolerance) and blocked secretion of cuticle-degrading enzymes including Pr1 family proteases. Importantly, Rad6 played much greater role in photoreactivation of UVB-impaired conidia by a 3- or 5-h light plus 9- or 7-h dark incubation than in dark reactivation of those impaired conidia by a 12-h dark incubation. The high activity of Rad6 in photoreactivation in vivo was derived from its link to a protein complex cored by the photolyase regulators WC1 and WC2 via the strong interactions of Rad6 with the E3 partner Rad18 and Rad18 with WC2 revealed in yeast two-hybrid assays. Transcriptomic analysis resulted in identification of 2700 differentially regulated genes involved in various function categories and metabolism pathways, indicating a regulatory role of Rad6-mediated ubiquitination in gene expression networks and genomic stability. Conclusively, Rad6 is required for asexual and insect-pathogenic lifecycles, solar UV damage repair, and genomic expression of B. bassiana. The primary dependence of its strong anti-UV role on photoreactivation in vivo unveils a scenario distinct from the core role of its yeast ortholog in DNA damage bypass.
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Affiliation(s)
- Xin-Cheng Luo
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lei Yu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Si-Yuan Xu
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Sheng-Hua Ying
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ming-Guang Feng
- Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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13
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Onishi S, Uchiyama K, Sato K, Okada C, Kobayashi S, Hamada K, Nishizawa T, Nureki O, Ogata K, Sengoku T. Structure of the human Bre1 complex bound to the nucleosome. Nat Commun 2024; 15:2580. [PMID: 38519511 PMCID: PMC10959955 DOI: 10.1038/s41467-024-46910-8] [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: 06/07/2023] [Accepted: 03/10/2024] [Indexed: 03/25/2024] Open
Abstract
Histone H2B monoubiquitination (at Lys120 in humans) regulates transcription elongation and DNA repair. In humans, H2B monoubiquitination is catalyzed by the heterodimeric Bre1 complex composed of Bre1A/RNF20 and Bre1B/RNF40. The Bre1 proteins generally function as tumor suppressors, while in certain cancers, they facilitate cancer cell proliferation. To obtain structural insights of H2BK120 ubiquitination and its regulation, we report the cryo-electron microscopy structure of the human Bre1 complex bound to the nucleosome. The two RING domains of Bre1A and Bre1B recognize the acidic patch and the nucleosomal DNA phosphates around SHL 6.0-6.5, which are ideally located to recruit the E2 enzyme and ubiquitin for H2BK120-specific ubiquitination. Mutational experiments suggest that the two RING domains bind in two orientations and that ubiquitination occurs when Bre1A binds to the acidic patch. Our results provide insights into the H2BK120-specific ubiquitination by the Bre1 proteins and suggest that H2B monoubiquitination can be regulated by nuclesomal DNA flexibility.
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Affiliation(s)
- Shuhei Onishi
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Kotone Uchiyama
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Ko Sato
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Chikako Okada
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Shunsuke Kobayashi
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Keisuke Hamada
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan
| | - Tomohiro Nishizawa
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Kazuhiro Ogata
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
| | - Toru Sengoku
- Department of Biochemistry, Yokohama City University Graduate School of Medicine, Yokohama, Japan.
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14
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Das A, Giri AK, Bhattacharjee P. Targeting 'histone mark': Advanced approaches in epigenetic regulation of telomere dynamics in cancer. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195007. [PMID: 38237857 DOI: 10.1016/j.bbagrm.2024.195007] [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: 08/01/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 01/23/2024]
Abstract
Telomere integrity is required for the maintenance of genome stability and prevention of oncogenic transformation of cells. Recent evidence suggests the presence of epigenetic modifications as an important regulator of mammalian telomeres. Telomeric and subtelomeric regions are rich in epigenetic marks that regulate telomere length majorly through DNA methylation and post-translational histone modifications. Specific histone modifying enzymes play an integral role in establishing telomeric histone codes necessary for the maintenance of structural integrity. Alterations of crucial histone moieties and histone modifiers cause deregulations in the telomeric chromatin leading to carcinogenic manifestations. This review delves into the significance of histone modifications and their influence on telomere dynamics concerning cancer. Additionally, it highlights the existing research gaps that hold the potential to drive the development of therapeutic interventions targeting the telomere epigenome.
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Affiliation(s)
- Ankita Das
- Department of Environmental Science, University of Calcutta, Kolkata 700019, India; Department of Zoology, University of Calcutta, Kolkata 700019, India
| | - Ashok K Giri
- Molecular Genetics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700032, India
| | - Pritha Bhattacharjee
- Department of Environmental Science, University of Calcutta, Kolkata 700019, India.
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15
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Navabpour S, Farrell K, Kincaid SE, Omar N, Musaus M, Lin Y, Xie H, Jarome TJ. Monoubiquitination of histone H2B is a crucial regulator of the transcriptome during memory formation. Learn Mem 2024; 31:a053912. [PMID: 38580378 PMCID: PMC11000578 DOI: 10.1101/lm.053912.123] [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: 12/20/2023] [Accepted: 03/07/2024] [Indexed: 04/07/2024]
Abstract
Posttranslational modification of histone proteins is critical for memory formation. Recently, we showed that monoubiquitination of histone H2B at lysine 120 (H2Bub) is critical for memory formation in the hippocampus. However, the transcriptome controlled by H2Bub remains unknown. Here, we found that fear conditioning in male rats increased or decreased the expression of 86 genes in the hippocampus but, surprisingly, siRNA-mediated knockdown of the H2Bub ligase, Rnf20, abolished changes in all but one of these genes. These findings suggest that monoubiquitination of histone H2B is a crucial regulator of the transcriptome during memory formation.
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Affiliation(s)
- Shaghayegh Navabpour
- Translational Biology, Medicine and Health Graduate Program, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Kayla Farrell
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Shannon E Kincaid
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Nour Omar
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Madeline Musaus
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
| | - Yu Lin
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia 24061, USA
| | - Hehuang Xie
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, Virginia 24061, USA
- Fralin Life Science Institute at Virginia Tech, Blacksburg, Virginia 24061, USA
| | - Timothy J Jarome
- Translational Biology, Medicine and Health Graduate Program, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
- School of Animal Sciences, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
- School of Neuroscience, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA
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16
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Yang Z, Zheng Y, Gao Q. Lysine lactylation in the regulation of tumor biology. Trends Endocrinol Metab 2024:S1043-2760(24)00025-0. [PMID: 38395657 DOI: 10.1016/j.tem.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/25/2024]
Abstract
Lysine lactylation (Kla), a newly discovered post-translational modification (PTM) of lysine residues, is progressively revealing its crucial role in tumor biology. A growing body of evidence supports its capacity of transcriptional regulation through histone modification and modulation of non-histone protein function. It intricately participates in a myriad of events in the tumor microenvironment (TME) by orchestrating the transitions of immune states and augmenting tumor malignancy. Its preferential modification of metabolic proteins underscores its specific regulatory influence on metabolism. This review focuses on the effect and the probable mechanisms of Kla-mediated regulation of tumor metabolism, the upstream factors that determine Kla intensity, and its potential implications for the clinical diagnosis and treatment of tumors.
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Affiliation(s)
- Zijian Yang
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yingqi Zheng
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Qiang Gao
- Department of Liver Surgery and Transplantation, and Key Laboratory of Carcinogenesis and Cancer Invasion (Ministry of Education), Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China; Key Laboratory of Medical Epigenetics and Metabolism, Institutes of Biomedical Sciences, Fudan University, Shanghai, China; State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, China.
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17
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Weinzapfel EN, Fedder-Semmes KN, Sun ZW, Keogh MC. Beyond the tail: the consequence of context in histone post-translational modification and chromatin research. Biochem J 2024; 481:219-244. [PMID: 38353483 PMCID: PMC10903488 DOI: 10.1042/bcj20230342] [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: 12/30/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
The role of histone post-translational modifications (PTMs) in chromatin structure and genome function has been the subject of intense debate for more than 60 years. Though complex, the discourse can be summarized in two distinct - and deceptively simple - questions: What is the function of histone PTMs? And how should they be studied? Decades of research show these queries are intricately linked and far from straightforward. Here we provide a historical perspective, highlighting how the arrival of new technologies shaped discovery and insight. Despite their limitations, the tools available at each period had a profound impact on chromatin research, and provided essential clues that advanced our understanding of histone PTM function. Finally, we discuss recent advances in the application of defined nucleosome substrates, the study of multivalent chromatin interactions, and new technologies driving the next era of histone PTM research.
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18
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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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19
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Yagci ZB, Kelkar GR, Johnson TJ, Sen D, Keung AJ. Designing Epigenome Editors: Considerations of Biochemical and Locus Specificities. Methods Mol Biol 2024; 2842:23-55. [PMID: 39012589 DOI: 10.1007/978-1-0716-4051-7_2] [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] [Indexed: 07/17/2024]
Abstract
The advent of locus-specific protein recruitment technologies has enabled a new class of studies in chromatin biology. Epigenome editors (EEs) enable biochemical modifications of chromatin at almost any specific endogenous locus. Their locus-specificity unlocks unique information including the functional roles of distinct modifications at specific genomic loci. Given the growing interest in using these tools for biological and translational studies, there are many specific design considerations depending on the scientific question or clinical need. Here, we present and discuss important design considerations and challenges regarding the biochemical and locus specificities of epigenome editors. These include how to: account for the complex biochemical diversity of chromatin; control for potential interdependency of epigenome editors and their resultant modifications; avoid sequestration effects; quantify the locus specificity of epigenome editors; and improve locus-specificity by considering concentration, affinity, avidity, and sequestration effects.
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Affiliation(s)
- Z Begum Yagci
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Gautami R Kelkar
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Tyler J Johnson
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Dilara Sen
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - Albert J Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
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20
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Yadav P, Gupta M, Wazahat R, Islam Z, Tsutakawa SE, Kamthan M, Kumar P. Structural basis for the role of C-terminus acidic tail of Saccharomyces cerevisiae ubiquitin-conjugating enzyme (Rad6) in E3 ligase (Bre1) mediated recognition of histones. Int J Biol Macromol 2024; 254:127717. [PMID: 37923031 DOI: 10.1016/j.ijbiomac.2023.127717] [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: 08/15/2023] [Revised: 10/07/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023]
Abstract
Ubiquitination of histone H2B on chromatin is key to gene regulation. E3 ligase Bre1 and E2 Rad6 in Saccharomyces cerevisiae associate together to catalyze mono-ubiquitination at histone H2BK123. Prior studies identified the role of a highly dynamic C-terminal acidic tail of Rad6 indispensable for H2BK123 mono-ubiquitination. However, the mechanistic basis for the Rad6-acidic tail role remained elusive. Using different structural and biophysical approaches, this study for the first time uncovers the direct role of Rad6-acidic tail in interaction with the Bre1 Rad6-Binding Domain (RBD) and recognition of histones surface to facilitate histone H2B mono-ubiquitination. A combination of NMR, SAXS, ITC, site-directed mutagenesis and molecular dynamics studies reveal that RBD domain of Bre1 interacts with Rad6 to stabilize the dynamics of acidic tail. This Bre1-RBD mediated stability in acidic tail of Rad6 could be one of the key factors for facilitating correct recognition of histone surface and ubiquitin-transfer at H2BK123. We provide biophysical evidence that Rad6-acidic tail and a positivity charged surface on histone H2B are involved in recognition of E2:Histones. Taken together, this study uncovers the mechanistic basis for the role of Rad6-acidic in Bre1-RBD mediated recognition of histone surface that ensure the histone H2B mono-ubiquitination.
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Affiliation(s)
- Pawan Yadav
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard University, New Delhi 110062, India
| | - Manish Gupta
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Rushna Wazahat
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard University, New Delhi 110062, India
| | - Zeyaul Islam
- Qatar Biomedical Research Institute (QBRI), Hamad Bin Khalifa University (HBKU), Qatar Foundation, Doha, Qatar
| | - Susan E Tsutakawa
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Mohan Kamthan
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard University, New Delhi 110062, India
| | - Pankaj Kumar
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard University, New Delhi 110062, India.
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21
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Liu H, Marayati BF, de la Cerda D, Lemezis BM, Gao J, Song Q, Chen M, Reid KZ. The Cross-Regulation Between Set1, Clr4, and Lsd1/2 in Schizosaccharomyces pombe. PLoS Genet 2024; 20:e1011107. [PMID: 38181050 PMCID: PMC10795994 DOI: 10.1371/journal.pgen.1011107] [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: 08/10/2023] [Revised: 01/18/2024] [Accepted: 12/12/2023] [Indexed: 01/07/2024] Open
Abstract
Eukaryotic chromatin is organized into either silenced heterochromatin or relaxed euchromatin regions, which controls the accessibility of transcriptional machinery and thus regulates gene expression. In fission yeast, Schizosaccharomyces pombe, Set1 is the sole H3K4 methyltransferase and is mainly enriched at the promoters of actively transcribed genes. In contrast, Clr4 methyltransferase initiates H3K9 methylation, which has long been regarded as a hallmark of heterochromatic silencing. Lsd1 and Lsd2 are two highly conserved H3K4 and H3K9 demethylases. As these histone-modifying enzymes perform critical roles in maintaining histone methylation patterns and, consequently, gene expression profiles, cross-regulations among these enzymes are part of the complex regulatory networks. Thus, elucidating the mechanisms that govern their signaling and mutual regulations remains crucial. Here, we demonstrated that C-terminal truncation mutants, lsd1-ΔHMG and lsd2-ΔC, do not compromise the integrity of the Lsd1/2 complex but impair their chromatin-binding capacity at the promoter region of target genomic loci. We identified protein-protein interactions between Lsd1/2 and Raf2 or Swd2, which are the subunits of the Clr4 complex (CLRC) and Set1-associated complex (COMPASS), respectively. We showed that Clr4 and Set1 modulate the protein levels of Lsd1 and Lsd2 in opposite ways through the ubiquitin-proteasome-dependent pathway. During heat stress, the protein levels of Lsd1 and Lsd2 are upregulated in a Set1-dependent manner. The increase in protein levels is crucial for differential gene expression under stress conditions. Together, our results support a cross-regulatory model by which Set1 and Clr4 methyltransferases control the protein levels of Lsd1/2 demethylases to shape the dynamic chromatin landscape.
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Affiliation(s)
- Haoran Liu
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Bahjat Fadi Marayati
- Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - David de la Cerda
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Brendan Matthew Lemezis
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Jieyu Gao
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Qianqian Song
- Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, Florida, United States of America
| | - Minghan Chen
- Department of Computer Science, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | - Ke Zhang Reid
- Department of Biology, Wake Forest University, Winston-Salem, North Carolina, United States of America
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22
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Cho US. The Core Complex of Yeast COMPASS and Human Mixed-Lineage Leukemia (MLL), Structure, Function, and Recognition of the Nucleosome. Subcell Biochem 2024; 104:101-117. [PMID: 38963485 DOI: 10.1007/978-3-031-58843-3_6] [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] [Indexed: 07/05/2024]
Abstract
Yeast COMPASS (complex of proteins associated with Set1) and human MLL (mixed-lineage leukemia) complexes are histone H3 lysine 4 methyltransferases with critical roles in gene regulation and embryonic development. Both complexes share a conserved C-terminal SET domain, responsible for catalyzing histone H3 K4 methylation on nucleosomes. Notably, their catalytic activity toward nucleosomes is enhanced and optimized with assembly of auxiliary subunits. In this review, we aim to illustrate the recent X-ray and cryo-EM structures of yeast COMPASS and human MLL1 core complexes bound to either unmodified nucleosome core particle (NCP) or H2B mono-ubiquitinated NCP (H2Bub.NCP). We further delineate how each auxiliary component of the complex contributes to the NCP and ubiquitin recognition to maximize the methyltransferase activity.
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Affiliation(s)
- Uhn-Soo Cho
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.
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23
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Aoi Y, Shilatifard A. Transcriptional elongation control in developmental gene expression, aging, and disease. Mol Cell 2023; 83:3972-3999. [PMID: 37922911 DOI: 10.1016/j.molcel.2023.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/23/2023] [Accepted: 10/11/2023] [Indexed: 11/07/2023]
Abstract
The elongation stage of transcription by RNA polymerase II (RNA Pol II) is central to the regulation of gene expression in response to developmental and environmental cues in metazoan. Dysregulated transcriptional elongation has been associated with developmental defects as well as disease and aging processes. Decades of genetic and biochemical studies have painstakingly identified and characterized an ensemble of factors that regulate RNA Pol II elongation. This review summarizes recent findings taking advantage of genetic engineering techniques that probe functions of elongation factors in vivo. We propose a revised model of elongation control in this accelerating field by reconciling contradictory results from the earlier biochemical evidence and the recent in vivo studies. We discuss how elongation factors regulate promoter-proximal RNA Pol II pause release, transcriptional elongation rate and processivity, RNA Pol II stability and RNA processing, and how perturbation of these processes is associated with developmental disorders, neurodegenerative disease, cancer, and aging.
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Affiliation(s)
- Yuki Aoi
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Ali Shilatifard
- Simpson Querrey Institute for Epigenetics, Department of Biochemistry and Molecular Genetics Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA.
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24
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Dhahri H, Fondufe-Mittendorf YN. Exploring the interplay between PARP1 and circRNA biogenesis and function. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 15:e1823. [PMID: 37957925 PMCID: PMC11089078 DOI: 10.1002/wrna.1823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 11/15/2023]
Abstract
PARP1 (poly-ADP-ribose polymerase 1) is a multidomain protein with a flexible and self-folding structure that allows it to interact with a wide range of biomolecules, including nucleic acids and target proteins. PARP1 interacts with its target molecules either covalently via PARylation or non-covalently through its PAR moieties induced by auto-PARylation. These diverse interactions allow PARP1 to participate in complex regulatory circuits and cellular functions. Although the most studied PARP1-mediated functions are associated with DNA repair and cellular stress response, subsequent discoveries have revealed additional biological functions. Based on these findings, PARP1 is now recognized as a major modulator of gene expression. Several discoveries show that this multifunctional protein has been intimately connected to several steps of mRNA biogenesis, from transcription initiation to mRNA splicing, polyadenylation, export, and translation of mRNA to proteins. Nevertheless, our understanding of PARP1's involvement in the biogenesis of both coding and noncoding RNA, notably circular RNA (circRNA), remains restricted. In this review, we outline the possible roles of PARP1 in circRNA biogenesis. A full examination of the regulatory roles of PARP1 in nuclear processes with an emphasis on circRNA may reveal new avenues to control dysregulation implicated in the pathogenesis of several diseases such as neurodegenerative disorders and cancers. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Hejer Dhahri
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky, USA
- Department of Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan, USA
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25
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Radmall KS, Shukla PK, Leng AM, Chandrasekharan MB. Structure-function analysis of histone H2B and PCNA ubiquitination dynamics using deubiquitinase-deficient strains. Sci Rep 2023; 13:16731. [PMID: 37794081 PMCID: PMC10550974 DOI: 10.1038/s41598-023-43969-z] [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: 05/21/2023] [Accepted: 09/30/2023] [Indexed: 10/06/2023] Open
Abstract
Post-translational covalent conjugation of ubiquitin onto proteins or ubiquitination is important in nearly all cellular processes. Steady-state ubiquitination of individual proteins in vivo is maintained by two countering enzymatic activities: conjugation of ubiquitin by E1, E2 and E3 enzymes and removal by deubiquitinases. Here, we deleted one or more genes encoding deubiquitinases in yeast and evaluated the requirements for ubiquitin conjugation onto a target protein. Our proof-of-principle studies demonstrate that absence of relevant deubiquitinase(s) provides a facile and versatile method that can be used to study the nuances of ubiquitin conjugation and deubiquitination of target proteins in vivo. We verified our method using mutants lacking the deubiquitinases Ubp8 and/or Ubp10 that remove ubiquitin from histone H2B or PCNA. Our studies reveal that the C-terminal coiled-domain of the adapter protein Lge1 and the C-terminal acidic tail of Rad6 E2 contribute to monoubiquitination of histone H2BK123, whereas the distal acidic residues of helix-4 of Rad6, but not the acidic tail, is required for monoubiquitination of PCNA. Further, charged substitution at alanine-120 in the H2B C-terminal helix adversely affected histone H2BK123 monoubiquitination by inhibiting Rad6-Bre1-mediated ubiquitin conjugation and by promoting Ubp8/Ubp10-mediated deubiquitination. In summary, absence of yeast deubiquitinases UBP8 and/or UBP10 allows uncovering the regulation of and requirements for ubiquitin addition and removal from their physiological substrates such as histone H2B or PCNA in vivo.
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Affiliation(s)
- Kaitlin S Radmall
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Prakash K Shukla
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Andrew M Leng
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Mahesh B Chandrasekharan
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.
- Huntsman Cancer Institute, University of Utah School of Medicine, 2000, Circle of Hope, Room 3715, Salt Lake City, UT, 84112, USA.
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26
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Radmall KS, Shukla PK, Leng AM, Chandrasekharan MB. Structure-function analysis of histone H2B and PCNA ubiquitination dynamics using deubiquitinase-deficient strains. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.18.545485. [PMID: 37873190 PMCID: PMC10592830 DOI: 10.1101/2023.06.18.545485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Post-translational covalent conjugation of ubiquitin onto proteins or ubiquitination is important in nearly all cellular processes. Steady-state ubiquitination of individual proteins in vivo is maintained by two countering enzymatic activities: conjugation of ubiquitin by E1, E2 and E3 enzymes and removal by deubiquitinases. Here, we deleted one or more genes encoding deubiquitinases in yeast and evaluated the requirements for ubiquitin conjugation onto a target protein. Our proof-of-principle studies demonstrate that absence of relevant deubiquitinase(s) provides a facile and versatile method that can be used to study the nuances of ubiquitin conjugation and deubiquitination of target proteins in vivo . We verified our method using mutants lacking the deubiquitinases Ubp8 and/or Ubp10 that remove ubiquitin from histone H2B or PCNA. Our studies reveal that the C-terminal coiled-domain of the adapter protein Lge1 and the C-terminal acidic tail of Rad6 E2 contribute to monoubiquitination of histone H2BK123, whereas the distal acidic residues of helix-4 of Rad6, but not the acidic tail, is required for monoubiquitination of PCNA. Further, charged substitution at alanine-120 in the H2B C-terminal helix adversely affected histone H2BK123 monoubiquitination by inhibiting Rad6-Bre1-mediated ubiquitin conjugation and by promoting Ubp8/Ubp10-mediated deubiquitination. In summary, absence of yeast deubiquitinases UBP8 and/or UBP10 allows uncovering the regulation of and requirements for ubiquitin addition and removal from their physiological substrates such as histone H2B or PCNA in vivo .
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27
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Mao X, Wu J, Zhang Q, Zhang S, Chen X, Liu X, Wei M, Wan X, Qiu L, Zeng M, Lei X, Liu C, Han J. Requirement of WDR70 for POLE3-mediated DNA double-strand breaks repair. SCIENCE ADVANCES 2023; 9:eadh2358. [PMID: 37682991 PMCID: PMC10491287 DOI: 10.1126/sciadv.adh2358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 08/08/2023] [Indexed: 09/10/2023]
Abstract
H2BK120ub1 triggers several prominent downstream histone modification pathways and changes in chromatin structure, therefore involving it into multiple critical cellular processes including DNA transcription and DNA damage repair. Although it has been reported that H2BK120ub1 is mediated by RNF20/40 and CRL4WDR70, less is known about the underlying regulation mechanism for H2BK120ub1 by WDR70. By using a series of biochemical and cell-based studies, we find that WDR70 promotes H2BK120ub1 by interacting with RNF20/40 complex, and deposition of H2BK120ub1 and H3K79me2 in POLE3 loci is highly sensitive to POLE3 transcription. Moreover, we demonstrate that POLE3 interacts CHRAC1 to promote DNA repair by regulation on the expression of homology-directed repair proteins and KU80 recruitment and identify CHRAC1 D121Y mutation in colorectal cancer, which leads to the defect in DNA repair due to attenuated the interaction with POLE3. These findings highlight a previously unknown role for WDR70 in maintenance of genomic stability and imply POLE3 and CHRAC1 as potential therapeutic targets in cancer.
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Affiliation(s)
- Xiaobing Mao
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jian Wu
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qin Zhang
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Su Zhang
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaoshuang Chen
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xueqin Liu
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Mingtian Wei
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaowen Wan
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lei Qiu
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ming Zeng
- Department of Pediatrics, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), West China Second University hospital, Sichuan University, Chengdu 610041, China
| | - Xue Lei
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Cong Liu
- Department of Pediatrics, Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), West China Second University hospital, Sichuan University, Chengdu 610041, China
| | - Junhong Han
- Department of Biotherapy, Cancer Center and State Laboratory of Biotherapy, and Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
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28
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Deng Z, Ai H, Sun M, Tong Z, Du Y, Qu Q, Zhang L, Xu Z, Tao S, Shi Q, Li JB, Pan M, Liu L. Mechanistic insights into nucleosomal H2B monoubiquitylation mediated by yeast Bre1-Rad6 and its human homolog RNF20/RNF40-hRAD6A. Mol Cell 2023; 83:3080-3094.e14. [PMID: 37633270 DOI: 10.1016/j.molcel.2023.08.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/27/2023] [Accepted: 08/02/2023] [Indexed: 08/28/2023]
Abstract
Histone H2B monoubiquitylation plays essential roles in chromatin-based transcriptional processes. A RING-type E3 ligase (yeast Bre1 or human RNF20/RNF40) and an E2 ubiquitin-conjugating enzyme (yeast Rad6 or human hRAD6A), together, precisely deposit ubiquitin on H2B K123 in yeast or K120 in humans. Here, we developed a chemical trapping strategy and successfully captured the transient structures of Bre1- or RNF20/RNF40-mediated ubiquitin transfer from Rad6 or hRAD6A to nucleosomal H2B. Our structures show that Bre1 and RNF40 directly bind nucleosomal DNA, exhibiting a conserved E3/E2/nucleosome interaction pattern from yeast to humans for H2B monoubiquitylation. We also find an uncanonical non-hydrophobic contact in the Bre1 RING-Rad6 interface, which positions Rad6 directly above the target H2B lysine residue. Our study provides mechanistic insights into the site-specific monoubiquitylation of H2B, reveals a critical role of nucleosomal DNA in mediating E3 ligase recognition, and provides a framework for understanding the cancer-driving mutations of RNF20/RNF40.
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Affiliation(s)
- Zhiheng Deng
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Huasong Ai
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China; Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Maoshen Sun
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Zebin Tong
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Yunxiang Du
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Qian Qu
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liying Zhang
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ziyu Xu
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Shixian Tao
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Qiang Shi
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jia-Bin Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China
| | - Man Pan
- Institute of Translational Medicine, National Center for Translational Medicine (Shanghai), School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Liu
- Tsinghua-Peking Joint Center for Life Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China.
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29
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Chakrabarty P, Sen R, Sengupta S. From parasites to partners: exploring the intricacies of host-transposon dynamics and coevolution. Funct Integr Genomics 2023; 23:278. [PMID: 37610667 DOI: 10.1007/s10142-023-01206-w] [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: 06/14/2023] [Revised: 08/01/2023] [Accepted: 08/07/2023] [Indexed: 08/24/2023]
Abstract
Transposable elements, often referred to as "jumping genes," have long been recognized as genomic parasites due to their ability to integrate and disrupt normal gene function and induce extensive genomic alterations, thereby compromising the host's fitness. To counteract this, the host has evolved a plethora of mechanisms to suppress the activity of the transposons. Recent research has unveiled the host-transposon relationships to be nuanced and complex phenomena, resulting in the coevolution of both entities. Transposition increases the mutational rate in the host genome, often triggering physiological pathways such as immune and stress responses. Current gene transfer technologies utilizing transposable elements have potential drawbacks, including off-target integration, induction of mutations, and modifications of cellular machinery, which makes an in-depth understanding of the host-transposon relationship imperative. This review highlights the dynamic interplay between the host and transposable elements, encompassing various factors and components of the cellular machinery. We provide a comprehensive discussion of the strategies employed by transposable elements for their propagation, as well as the mechanisms utilized by the host to mitigate their parasitic effects. Additionally, we present an overview of recent research identifying host proteins that act as facilitators or inhibitors of transposition. We further discuss the evolutionary outcomes resulting from the genetic interactions between the host and the transposable elements. Finally, we pose open questions in this field and suggest potential avenues for future research.
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Affiliation(s)
- Prayas Chakrabarty
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata, 700073, India
| | - Raneet Sen
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata, 700073, India
- Institute of Bioorganic Chemistry, Department of RNA Metabolism, Polish Academy of Sciences, Poznan, Poland
| | - Sugopa Sengupta
- Department of Life Sciences, Presidency University Kolkata, 86/1 College Street, Kolkata, 700073, India.
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30
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Sawade K, Marx A, Peter C, Kukharenko O. Combining molecular dynamics simulations and scoring method to computationally model ubiquitylated linker histones in chromatosomes. PLoS Comput Biol 2023; 19:e1010531. [PMID: 37527265 PMCID: PMC10442151 DOI: 10.1371/journal.pcbi.1010531] [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: 09/01/2022] [Revised: 08/21/2023] [Accepted: 06/15/2023] [Indexed: 08/03/2023] Open
Abstract
The chromatin in eukaryotic cells plays a fundamental role in all processes during a cell's life cycle. This nucleoprotein is normally tightly packed but needs to be unpacked for expression and division. The linker histones are critical for such packaging processes and while most experimental and simulation works recognize their crucial importance, the focus is nearly always set on the nucleosome as the basic chromatin building block. Linker histones can undergo several modifications, but only few studies on their ubiquitylation have been conducted. Mono-ubiquitylated linker histones (HUb), while poorly understood, are expected to influence DNA compaction. The size of ubiquitin and the globular domain of the linker histone are comparable and one would expect an increased disorder upon ubiquitylation of the linker histone. However, the formation of higher order chromatin is not hindered and ubiquitylation of the linker histone may even promote gene expression. Structural data on chromatosomes is rare and HUb has never been modeled in a chromatosome so far. Descriptions of the chromatin complex with HUb would greatly benefit from computational structural data. In this study we generate molecular dynamics simulation data for six differently linked HUb variants with the help of a sampling scheme tailored to drive the exploration of phase space. We identify conformational sub-states of the six HUb variants using the sketch-map algorithm for dimensionality reduction and iterative HDBSCAN for clustering on the excessively sampled, shallow free energy landscapes. We present a highly efficient geometric scoring method to identify sub-states of HUb that fit into the nucleosome. We predict HUb conformations inside a nucleosome using on-dyad and off-dyad chromatosome structures as reference and show that unbiased simulations of HUb produce significantly more fitting than non-fitting HUb conformations. A tetranucleosome array is used to show that ubiquitylation can even occur in chromatin without too much steric clashes.
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Affiliation(s)
- Kevin Sawade
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Andreas Marx
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Christine Peter
- Department of Chemistry, University of Konstanz, Konstanz, Germany
| | - Oleksandra Kukharenko
- Department of Chemistry, University of Konstanz, Konstanz, Germany
- Theory Department, Max-Planck Institute for Polymer Research, Mainz, Germany
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31
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Brickner JH. Inheritance of epigenetic transcriptional memory through read-write replication of a histone modification. Ann N Y Acad Sci 2023; 1526:50-58. [PMID: 37391188 PMCID: PMC11216120 DOI: 10.1111/nyas.15033] [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] [Indexed: 07/02/2023]
Abstract
Epigenetic transcriptional regulation frequently requires histone modifications. Some, but not all, of these modifications are able to template their own inheritance. Here, I discuss the molecular mechanisms by which histone modifications can be inherited and relate these ideas to new results about epigenetic transcriptional memory, a phenomenon that poises recently repressed genes for faster reactivation and has been observed in diverse organisms. Recently, we found that the histone H3 lysine 4 dimethylation that is associated with this phenomenon plays a critical role in sustaining memory and, when factors critical for the establishment of memory are inactivated, can be stably maintained through multiple mitoses. This chromatin-mediated inheritance mechanism may involve a physical interaction between an H3K4me2 reader, SET3C, and an H3K4me2 writer, Spp1- COMPASS. This is the first example of a chromatin-mediated inheritance of a mark that promotes transcription.
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Affiliation(s)
- Jason H Brickner
- Department of Molecular Biosciences, Northwestern University, Evanston, Illinois, USA
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32
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Currie MF, Singh SK, Ji M, Chatterjee C. The semisynthesis of site-specifically modified histones and histone-based probes of chromatin-modifying enzymes. Methods 2023; 215:28-37. [PMID: 37244506 PMCID: PMC10364803 DOI: 10.1016/j.ymeth.2023.05.004] [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: 02/17/2023] [Revised: 05/02/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023] Open
Abstract
Histone post-translational modifications (PTMs) on lysine residues, including methylation, ubiquitylation, and sumoylation, have been studied using semisynthetic histones reconstituted into nucleosomes. These studies have revealed the in vitro effects of histone PTMs on chromatin structure, gene transcription, and biochemical crosstalk. However, the dynamic and transient nature of most enzyme-chromatin interactions poses a challenge toward identifying specific enzyme-substrate interactions. To address this, we report methodology for the synthesis of two ubiquitylated activity-based probe histones, H2BK120ub(G76C) and H2BK120ub(G76Dha), that may be used to trap enzyme active-site cysteines as disulfides or in the form of thioether linkages, respectively. The general synthetic method we report for converting ubiquitylated nucleosomes into activity-based probes may also be applied to other histone sites of ubiquitylation in order to facilitate the identification of enzyme-chromatin interactions.
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Affiliation(s)
- Madeline F Currie
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
| | - Sumeet K Singh
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
| | - Meihuan Ji
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
| | - Champak Chatterjee
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States.
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33
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Deshpande N, Bryk M. Diverse and dynamic forms of gene regulation by the S. cerevisiae histone methyltransferase Set1. Curr Genet 2023; 69:91-114. [PMID: 37000206 DOI: 10.1007/s00294-023-01265-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 04/01/2023]
Abstract
Gene transcription is an essential and highly regulated process. In eukaryotic cells, the structural organization of nucleosomes with DNA wrapped around histone proteins impedes transcription. Chromatin remodelers, transcription factors, co-activators, and histone-modifying enzymes work together to make DNA accessible to RNA polymerase. Histone lysine methylation can positively or negatively regulate gene transcription. Methylation of histone 3 lysine 4 by SET-domain-containing proteins is evolutionarily conserved from yeast to humans. In higher eukaryotes, mutations in SET-domain proteins are associated with defects in the development and segmentation of embryos, skeletal and muscle development, and diseases, including several leukemias. Since histone methyltransferases are evolutionarily conserved, the mechanisms of gene regulation mediated by these enzymes are also conserved. Budding yeast Saccharomyces cerevisiae is an excellent model system to study the impact of histone 3 lysine 4 (H3K4) methylation on eukaryotic gene regulation. Unlike larger eukaryotes, yeast cells have only one enzyme that catalyzes H3K4 methylation, Set1. In this review, we summarize current knowledge about the impact of Set1-catalyzed H3K4 methylation on gene transcription in S. cerevisiae. We describe the COMPASS complex, factors that influence H3K4 methylation, and the roles of Set1 in gene silencing at telomeres and heterochromatin, as well as repression and activation at euchromatic loci. We also discuss proteins that "read" H3K4 methyl marks to regulate transcription and summarize alternate functions for Set1 beyond H3K4 methylation.
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Affiliation(s)
- Neha Deshpande
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA
| | - Mary Bryk
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
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34
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Yao L, Li J, Jiang B, Zhang Z, Li X, Ouyang X, Xiao Y, Liu G, Wang Z, Zhang G. RNF2 inhibits E-Cadherin transcription to promote hepatocellular carcinoma metastasis via inducing histone mono-ubiquitination. Cell Death Dis 2023; 14:261. [PMID: 37037816 PMCID: PMC10085990 DOI: 10.1038/s41419-023-05785-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/25/2023] [Accepted: 03/28/2023] [Indexed: 04/12/2023]
Abstract
RNF2 is a RING domain-containing E3 ubiquitin ligase that mediate histone H2A mono-ubiquitination to repress gene transcription, but its expression patterns and molecular function in hepatocellular carcinoma (HCC) remain unclear. Herein, we extracted data from TGCA database and validated RNF2 expression in our own cohort, which revealed that RNF2 was highly expressed in HCC and was associated with malignant characteristics and poor prognosis of HCC. Moreover, RNF2 was demonstrated to promote HCC metastasis via enhancing epithelial-mesenchymal transition (EMT) both in vitro and in vivo. Mechanistically, RNF2 repressed E-Cadherin transcription by increasing the deposition of H2K119ub at the E-Cadherin promoter region. In addition, RNF2-regulated crosstalk between H2AK119ub, H3K27me3 and H3K4me3 synergistically reduced E-Cadherin transcription, which promoted EMT and HCC metastasis. These results indicate that RNF2 played an oncogenic role in HCC progression via inducing EMT, and RNF2 could be a potential therapeutic target for HCC.
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Affiliation(s)
- Lei Yao
- Department of General Surgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, 410008, China
| | - Jun Li
- Department of General Surgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, 410008, China
| | - Bo Jiang
- Department of thyroid surgery, First Affiliated Hospital of Zhengzhou University, No.1, East Construction Road, Zhengzhou, 450052, Henan, China
| | - Zeyu Zhang
- Department of General Surgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, 410008, China
| | - Xinying Li
- Department of General Surgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, No. 87, Xiangya Road, Changsha, 410008, China
| | - Xiwu Ouyang
- Department of General Surgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, No. 87, Xiangya Road, Changsha, 410008, China
| | - Yao Xiao
- Department of General Surgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, No. 87, Xiangya Road, Changsha, 410008, China
| | - Guodong Liu
- Department of General Surgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, 410008, China
- National Clinical Research Center for Geriatric Disorders, No. 87, Xiangya Road, Changsha, 410008, China
| | - Zhiming Wang
- Department of General Surgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, 410008, China.
- National Clinical Research Center for Geriatric Disorders, No. 87, Xiangya Road, Changsha, 410008, China.
| | - Gewen Zhang
- Department of General Surgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, 410008, China.
- National Clinical Research Center for Geriatric Disorders, No. 87, Xiangya Road, Changsha, 410008, China.
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35
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Nakamura R, Nakayama JI. Regulation of the SUV39H Family Methyltransferases: Insights from Fission Yeast. Biomolecules 2023; 13:biom13040593. [PMID: 37189341 DOI: 10.3390/biom13040593] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/22/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Histones, which make up nucleosomes, undergo various post-translational modifications, such as acetylation, methylation, phosphorylation, and ubiquitylation. In particular, histone methylation serves different cellular functions depending on the location of the amino acid residue undergoing modification, and is tightly regulated by the antagonistic action of histone methyltransferases and demethylases. The SUV39H family of histone methyltransferases (HMTases) are evolutionarily conserved from fission yeast to humans and play an important role in the formation of higher-order chromatin structures called heterochromatin. The SUV39H family HMTases catalyzes the methylation of histone H3 lysine 9 (H3K9), and this modification serves as a binding site for heterochromatin protein 1 (HP1) to form a higher-order chromatin structure. While the regulatory mechanism of this family of enzymes has been extensively studied in various model organisms, Clr4, a fission yeast homologue, has made an important contribution. In this review, we focus on the regulatory mechanisms of the SUV39H family of proteins, in particular, the molecular mechanisms revealed by the studies of the fission yeast Clr4, and discuss their generality in comparison to other HMTases.
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36
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Shukla PK, Bissell JE, Kumar S, Pokhrel S, Palani S, Radmall K, Obidi O, Parnell TJ, Brasch J, Shrieve D, Chandrasekharan M. Structure and functional determinants of Rad6-Bre1 subunits in the histone H2B ubiquitin-conjugating complex. Nucleic Acids Res 2023; 51:2117-2136. [PMID: 36715322 PMCID: PMC10018343 DOI: 10.1093/nar/gkad012] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 12/28/2022] [Accepted: 01/04/2023] [Indexed: 01/31/2023] Open
Abstract
The conserved complex of the Rad6 E2 ubiquitin-conjugating enzyme and the Bre1 E3 ubiquitin ligase catalyzes histone H2B monoubiquitination (H2Bub1), which regulates chromatin dynamics during transcription and other nuclear processes. Here, we report a crystal structure of Rad6 and the non-RING domain N-terminal region of Bre1, which shows an asymmetric homodimer of Bre1 contacting a conserved loop on the Rad6 'backside'. This contact is distant from the Rad6 catalytic site and is the location of mutations that impair telomeric silencing in yeast. Mutational analyses validated the importance of this contact for the Rad6-Bre1 interaction, chromatin-binding dynamics, H2Bub1 formation and gene expression. Moreover, the non-RING N-terminal region of Bre1 is sufficient to confer nucleosome binding ability to Rad6 in vitro. Interestingly, Rad6 P43L protein, an interaction interface mutant and equivalent to a cancer mutation in the human homolog, bound Bre1 5-fold more tightly than native Rad6 in vitro, but showed reduced chromatin association of Bre1 and reduced levels of H2Bub1 in vivo. These surprising observations imply conformational transitions of the Rad6-Bre1 complex during its chromatin-associated functional cycle, and reveal the differential effects of specific disease-relevant mutations on the chromatin-bound and unbound states. Overall, our study provides structural insights into Rad6-Bre1 interaction through a novel interface that is important for their biochemical and biological responses.
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Affiliation(s)
- Prakash K Shukla
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Jesse E Bissell
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Sanjit Kumar
- Centre for Bioseparation Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India
| | - Srijana Pokhrel
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Sowmiya Palani
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kaitlin S Radmall
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Onyeka Obidi
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Timothy J Parnell
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Julia Brasch
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Dennis C Shrieve
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Mahesh B Chandrasekharan
- Department of Radiation Oncology, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
- Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
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37
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Shi M, Zhao J, Zhang S, Huang W, Li M, Bai X, Zhang W, Zhang K, Chen X, Xiang S. Structural basis for the Rad6 activation by the Bre1 N-terminal domain. eLife 2023; 12:84157. [PMID: 36912886 PMCID: PMC10036116 DOI: 10.7554/elife.84157] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/10/2023] [Indexed: 03/14/2023] Open
Abstract
The mono-ubiquitination of the histone protein H2B (H2Bub1) is a highly conserved histone post-translational modification that plays critical roles in many fundamental processes. In yeast, this modification is catalyzed by the conserved Bre1-Rad6 complex. Bre1 contains a unique N-terminal Rad6-binding domain (RBD), how it interacts with Rad6 and contributes to the H2Bub1 catalysis is unclear. Here, we present crystal structure of the Bre1 RBD-Rad6 complex and structure-guided functional studies. Our structure provides a detailed picture of the interaction between the dimeric Bre1 RBD and a single Rad6 molecule. We further found that the interaction stimulates Rad6's enzymatic activity by allosterically increasing its active site accessibility and likely contribute to the H2Bub1 catalysis through additional mechanisms. In line with these important functions, we found that the interaction is crucial for multiple H2Bub1-regulated processes. Our study provides molecular insights into the H2Bub1 catalysis.
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Affiliation(s)
- Meng Shi
- Department of Biochemistry and Molecular Biology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The province and ministry co-sponsored collaborative innovation center for medical epigenetics, Tianjin Medical University, Tianjin, China
| | - Jiaqi Zhao
- Department of Biochemistry and Molecular Biology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The province and ministry co-sponsored collaborative innovation center for medical epigenetics, Tianjin Medical University, Tianjin, China
| | - Simin Zhang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, The Institute of Advanced Studies, Wuhan University, Wuhan, China
| | - Wei Huang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The province and ministry co-sponsored collaborative innovation center for medical epigenetics, Tianjin Medical University, Tianjin, China
| | - Mengfei Li
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, The Institute of Advanced Studies, Wuhan University, Wuhan, China
| | - Xue Bai
- Department of Biochemistry and Molecular Biology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The province and ministry co-sponsored collaborative innovation center for medical epigenetics, Tianjin Medical University, Tianjin, China
| | - Wenxue Zhang
- Department of Radiation Oncology, Tianjin Medical University General Hospital, Tianjin, China
| | - Kai Zhang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The province and ministry co-sponsored collaborative innovation center for medical epigenetics, Tianjin Medical University, Tianjin, China
| | - Xuefeng Chen
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Frontier Science Centre of Immunology and Metabolism, The Institute of Advanced Studies, Wuhan University, Wuhan, China
| | - Song Xiang
- Department of Biochemistry and Molecular Biology, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The province and ministry co-sponsored collaborative innovation center for medical epigenetics, Tianjin Medical University, Tianjin, China
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38
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Structural insights on the KMT2-NCP interaction. Biochem Soc Trans 2023; 51:427-434. [PMID: 36695549 DOI: 10.1042/bst20221155] [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: 11/28/2022] [Revised: 01/13/2023] [Accepted: 01/16/2023] [Indexed: 01/26/2023]
Abstract
The MLL/KMT2 family enzymes are frequently mutated in human cancers and congenital diseases. They deposit the majority of histone 3 lysine 4 (H3K4) mono-, di-, or tri-methylation in mammals and are tightly associated with gene activation. Structural and biochemical studies in recent years provide in-depth understanding of how the MLL1 and homologous yeast SET1 complexes interact with the nucleosome core particle (NCP) and how their activities for H3K4 methylation are regulated by the conserved core components. Here, we will discuss the recent single molecule cryo-EM studies on the MLL1 and ySET1 complexes bound on the NCP. These studies highlight the dynamic regulation of the MLL/SET1 family lysine methyltransferases with unique features as compared with other histone lysine methyltransferases. These studies provide insights for loci-specific regulation of H3K4 methylation states in cells. The mechanistic studies on the MLL1 complex have already led to the development of the MLL1 inhibitors that show efficacy in acute leukemia and metastatic breast cancers. Future studies on the MLL/SET1 family enzymes will continue to bring to light potential therapeutic opportunities.
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Park J, Park S, Lee JS. Role of the Paf1 complex in the maintenance of stem cell pluripotency and development. FEBS J 2023; 290:951-961. [PMID: 35869661 DOI: 10.1111/febs.16582] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 06/26/2022] [Accepted: 07/21/2022] [Indexed: 11/30/2022]
Abstract
Cell identity is determined by the transcriptional regulation of a cell-type-specific gene group. The Paf1 complex (Paf1C), an RNA polymerase II-associating factor, is an important transcriptional regulator that not only participates in transcription elongation and termination but also affects transcription-coupled histone modifications and chromatin organisation. Recent studies have shown that Paf1C is involved in the expression of genes required for self-renewal and pluripotency in stem cells and tumorigenesis. In this review, we focused on the role of Paf1C as a critical transcriptional regulator in cell fate decisions. Paf1C affects the pluripotency of stem cells by regulating the expression of core transcription factors such as Oct4 and Nanog. In addition, Paf1C directly binds to the promoters or distant elements of target genes, thereby maintaining the pluripotency in embryonic stem cells derived from an early stage of the mammalian embryo. Paf1C is upregulated in cancer stem cells, as compared with that in cancer cells, suggesting that Paf1C may be a target for cancer therapy. Interestingly, Paf1C is involved in multiple developmental stages in Drosophila, zebrafish, mice and even humans, thereby displaying a trend for the correlation between Paf1C and cell fate. Thus, we propose that Paf1C is a critical contributor to cell differentiation, cell specification and its characteristics and could be employed as a therapeutic target in developmental diseases.
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Affiliation(s)
- Jiyeon Park
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon-si, Korea
| | - Shinae Park
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon-si, Korea
| | - Jung-Shin Lee
- Department of Molecular Bioscience, College of Biomedical Science, Kangwon National University, Chuncheon-si, Korea
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40
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Characterizing crosstalk in epigenetic signaling to understand disease physiology. Biochem J 2023; 480:57-85. [PMID: 36630129 PMCID: PMC10152800 DOI: 10.1042/bcj20220550] [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: 11/07/2022] [Revised: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 01/12/2023]
Abstract
Epigenetics, the inheritance of genomic information independent of DNA sequence, controls the interpretation of extracellular and intracellular signals in cell homeostasis, proliferation and differentiation. On the chromatin level, signal transduction leads to changes in epigenetic marks, such as histone post-translational modifications (PTMs), DNA methylation and chromatin accessibility to regulate gene expression. Crosstalk between different epigenetic mechanisms, such as that between histone PTMs and DNA methylation, leads to an intricate network of chromatin-binding proteins where pre-existing epigenetic marks promote or inhibit the writing of new marks. The recent technical advances in mass spectrometry (MS) -based proteomic methods and in genome-wide DNA sequencing approaches have broadened our understanding of epigenetic networks greatly. However, further development and wider application of these methods is vital in developing treatments for disorders and pathologies that are driven by epigenetic dysregulation.
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41
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Jezek M, Sun W, Negesse MY, Smith ZM, Orosz A, Green EM. Set1 regulates telomere function via H3K4 methylation-dependent and -independent pathways and calibrates the abundance of telomere maintenance factors. Mol Biol Cell 2023; 34:ar6. [PMID: 36416860 PMCID: PMC9816643 DOI: 10.1091/mbc.e22-06-0213] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/05/2022] [Accepted: 11/17/2022] [Indexed: 11/24/2022] Open
Abstract
Set1 is an H3K4 methyltransferase that comprises the catalytic subunit of the COMPASS complex and has been implicated in transcription, DNA repair, cell cycle control, and numerous other genomic functions. Set1 also promotes proper telomere maintenance, as cells lacking Set1 have short telomeres and disrupted subtelomeric gene repression; however, the precise role for Set1 in these processes has not been fully defined. In this study, we have tested mutants of Set1 and the COMPASS complex that differentially alter H3K4 methylation status, and we have attempted to separate catalytic and noncatalytic functions of Set1. Our data reveal that Set1-dependent subtelomeric gene repression relies on its catalytic activity toward H3K4, whereas telomere length is regulated by Set1 catalytic activity but likely independent of the H3K4 substrate. Furthermore, we uncover a role for Set1 in calibrating the abundance of critical telomere maintenance proteins, including components of the telomerase holoenzyme and members of the telomere capping CST (Cdc13-Stn1-Ten1) complex, through both transcriptional and posttranscriptional pathways. Altogether, our data provide new insights into the H3K4 methylation-dependent and -independent roles for Set1 in telomere maintenance in yeast and shed light on possible roles for Set1-related methyltransferases in other systems.
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Affiliation(s)
- Meagan Jezek
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250
| | - Winny Sun
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250
| | - Maraki Y. Negesse
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250
| | - Zachary M. Smith
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250
| | - Alexander Orosz
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250
| | - Erin M. Green
- Department of Biological Sciences, University of Maryland Baltimore County, Baltimore, MD 21250
- Marlene and Stewart Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, Baltimore, MD 21201
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42
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Mechanisms of DNA methylation and histone modifications. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 197:51-92. [PMID: 37019597 DOI: 10.1016/bs.pmbts.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
The field of genetics has expanded a lot in the past few decades due to the accessibility of human genome sequences, but still, the regulation of transcription cannot be explicated exclusively by the sequence of DNA of an individual. The coordination and crosstalk between chromatin factors which are conserved is indispensable for all living creatures. The regulation of gene expression has been dependent on the methylation of DNA, post-translational modifications of histones, effector proteins, chromatin remodeler enzymes that affect the chromatin structure and function, and other cellular activities such as DNA replication, DNA repair, proliferation and growth. The mutation and deletion of these factors can lead to human diseases. Various studies are being performed to identify and understand the gene regulatory mechanisms in the diseased state. The information from these high throughput screening studies is able to aid the treatment developments based on the epigenetics regulatory mechanisms. This book chapter will discourse on various modifications and their mechanisms that take place on histones and DNA that regulate the transcription of genes.
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43
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Asimaki E, Petriukov K, Renz C, Meister C, Ulrich HD. Fast friends - Ubiquitin-like modifiers as engineered fusion partners. Semin Cell Dev Biol 2022; 132:132-145. [PMID: 34840080 PMCID: PMC9703124 DOI: 10.1016/j.semcdb.2021.11.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 11/08/2021] [Accepted: 11/12/2021] [Indexed: 12/15/2022]
Abstract
Ubiquitin and its relatives are major players in many biological pathways, and a variety of experimental tools based on biological chemistry or protein engineering is available for their manipulation. One popular approach is the use of linear fusions between the modifier and a protein of interest. Such artificial constructs can facilitate the understanding of the role of ubiquitin in biological processes and can be exploited to control protein stability, interactions and degradation. Here we summarize the basic design considerations and discuss the advantages as well as limitations associated with their use. Finally, we will refer to several published case studies highlighting the principles of how they provide insight into pathways ranging from membrane protein trafficking to the control of epigenetic modifications.
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44
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Cobos SN, Janani C, Cruz G, Rana N, Son E, Frederic R, Paredes Casado J, Khan M, Bennett SA, Torrente MP. [PRION +] States Are Associated with Specific Histone H3 Post-Translational Modification Changes. Pathogens 2022; 11:pathogens11121436. [PMID: 36558770 PMCID: PMC9786042 DOI: 10.3390/pathogens11121436] [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: 08/26/2022] [Revised: 11/23/2022] [Accepted: 11/25/2022] [Indexed: 11/30/2022] Open
Abstract
Prions are proteins able to take on alternative conformations and propagate them in a self-templating process. In Saccharomyces cerevisiae, prions enable heritable responses to environmental conditions through bet-hedging mechanisms. Hence, [PRION+] states may serve as an atypical form of epigenetic control, producing heritable phenotypic change via protein folding. However, the connections between prion states and the epigenome remain unknown. Do [PRION+] states link to canonical epigenetic channels, such as histone post-translational modifications? Here, we map out the histone H3 modification landscape in the context of the [SWI+] and [PIN+] prion states. [SWI+] is propagated by Swi1, a subunit of the SWI/SNF chromatin remodeling complex, while [PIN+] is propagated by Rnq1, a protein of unknown function. We find [SWI+] yeast display decreases in the levels of H3K36me2 and H3K56ac compared to [swi-] yeast. In contrast, decreases in H3K4me3, H3K36me2, H3K36me3 and H3K79me3 are connected to the [PIN+] state. Curing of the prion state by treatment with guanidine hydrochloride restored histone PTM to [prion-] state levels. We find histone PTMs in the [PRION+] state do not match those in loss-of-function models. Our findings shed light into the link between prion states and histone modifications, revealing novel insight into prion function in yeast.
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Affiliation(s)
- Samantha N. Cobos
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Chaim Janani
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Gabriel Cruz
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Navin Rana
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Elizaveta Son
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Rania Frederic
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
| | | | - Maliha Khan
- Biology Department, Brooklyn College, Brooklyn, NY 11210, USA
| | - Seth A. Bennett
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
- Graduate Program in Biochemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| | - Mariana P. Torrente
- Chemistry Department, Brooklyn College, Brooklyn, NY 11210, USA
- Ph.D. Programs in Chemistry, Biochemistry, and Biology, The Graduate Center of the City University of New York, New York, NY 10016, USA
- Correspondence:
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45
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Quantitative Assessment of Histone H2B Monoubiquitination in Yeast Using Immunoblotting. Methods Protoc 2022; 5:mps5050074. [PMID: 36287046 PMCID: PMC9609377 DOI: 10.3390/mps5050074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/20/2022] [Accepted: 09/22/2022] [Indexed: 02/07/2023] Open
Abstract
Studies in Saccharomyces cerevisiae and Schizosaccharomyces pombe have enhanced our understanding of the regulation and functions of histone H2B monoubiquitination (H2Bub1), a key epigenetic marker with important roles in transcription and other processes. The detection of H2Bub1 in yeasts using immunoblotting has been greatly facilitated by the commercial availability of antibodies against yeast histone H2B and the cross-reactivity of an antibody raised against monoubiquitinated human H2BK120. These antibodies have obviated the need to express epitope-tagged histone H2B to detect H2Bub1 in yeasts. Here, we provide a step-by-step protocol and best practices for the quantification of H2Bub1 in yeast systems, from cell extract preparation to immunoblotting using the commercially available antibodies. We demonstrate that the commercial antibodies can effectively and accurately detect H2Bub1 in S. cerevisiae and S. pombe. Further, we show that the C-terminal epitope-tagging of histone H2B alters the steady-state levels of H2Bub1 in yeast systems. We report a sectioned blot probing approach combined with the serial dilution of protein lysates and the use of reversibly stained proteins as loading controls that together provide a cost-effective and sensitive method for the quantitative evaluation of H2Bub1 in yeast.
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46
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Shukla PK, Sinha D, Leng AM, Bissell JE, Thatipamula S, Ganguly R, Radmall KS, Skalicky JJ, Shrieve DC, Chandrasekharan MB. Mutations of Rad6 E2 ubiquitin-conjugating enzymes at alanine-126 affect ubiquitination activity and decrease enzyme stability. J Biol Chem 2022; 298:102524. [PMID: 36162503 PMCID: PMC9630792 DOI: 10.1016/j.jbc.2022.102524] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 11/28/2022] Open
Abstract
Rad6, an E2 ubiquitin-conjugating enzyme conserved from yeast to humans, functions in transcription, genome maintenance, and proteostasis. The contributions of many conserved secondary structures of Rad6 and its human homologs UBE2A and UBE2B to their biological functions are not understood. A mutant RAD6 allele with a missense substitution at alanine-126 (A126) of helix-3 that causes defects in telomeric gene silencing, DNA repair, and protein degradation was reported over 2 decades ago. Here, using a combination of genetics, biochemical, biophysical, and computational approaches, we discovered that helix-3 A126 mutations compromise the ability of Rad6 to ubiquitinate target proteins without disrupting interactions with partner E3 ubiquitin-ligases that are required for their various biological functions in vivo. Explaining the defective in vitro or in vivo ubiquitination activities, molecular dynamics simulations and NMR showed that helix-3 A126 mutations cause local disorder of the catalytic pocket of Rad6 in addition to disorganizing the global structure of the protein to decrease its stability in vivo. We also show that helix-3 A126 mutations deform the structures of UBE2A and UBE2B, the human Rad6 homologs, and compromise the in vitro ubiquitination activity and folding of UBE2B. Providing insights into their ubiquitination defects, we determined helix-3 A126 mutations impair the initial ubiquitin charging and the final discharging steps during substrate ubiquitination by Rad6. In summary, our studies reveal that the conserved helix-3 is a crucial structural constituent that controls the organization of catalytic pockets, enzymatic activities, and biological functions of the Rad6-family E2 ubiquitin-conjugating enzymes.
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Affiliation(s)
- Prakash K Shukla
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Dhiraj Sinha
- IHU, Aix Marseille University, Marseille, France
| | - Andrew M Leng
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Jesse E Bissell
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Shravya Thatipamula
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Rajarshi Ganguly
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Kaitlin S Radmall
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Jack J Skalicky
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Dennis C Shrieve
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA
| | - Mahesh B Chandrasekharan
- Department of Radiation Oncology and Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
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47
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Rahman S, Hoffmann NA, Worden EJ, Smith ML, Namitz KEW, Knutson BA, Cosgrove MS, Wolberger C. Multistate structures of the MLL1-WRAD complex bound to H2B-ubiquitinated nucleosome. Proc Natl Acad Sci U S A 2022; 119:e2205691119. [PMID: 36095189 PMCID: PMC9499523 DOI: 10.1073/pnas.2205691119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/09/2022] [Indexed: 11/18/2022] Open
Abstract
The human Mixed Lineage Leukemia-1 (MLL1) complex methylates histone H3K4 to promote transcription and is stimulated by monoubiquitination of histone H2B. Recent structures of the MLL1-WRAD core complex, which comprises the MLL1 methyltransferase, WDR5, RbBp5, Ash2L, and DPY-30, have revealed variability in the docking of MLL1-WRAD on nucleosomes. In addition, portions of the Ash2L structure and the position of DPY30 remain ambiguous. We used an integrated approach combining cryoelectron microscopy (cryo-EM) and mass spectrometry cross-linking to determine a structure of the MLL1-WRAD complex bound to ubiquitinated nucleosomes. The resulting model contains the Ash2L intrinsically disordered region (IDR), SPRY insertion region, Sdc1-DPY30 interacting region (SDI-motif), and the DPY30 dimer. We also resolved three additional states of MLL1-WRAD lacking one or more subunits, which may reflect different steps in the assembly of MLL1-WRAD. The docking of subunits in all four states differs from structures of MLL1-WRAD bound to unmodified nucleosomes, suggesting that H2B-ubiquitin favors assembly of the active complex. Our results provide a more complete picture of MLL1-WRAD and the role of ubiquitin in promoting formation of the active methyltransferase complex.
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Affiliation(s)
- Sanim Rahman
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Niklas A. Hoffmann
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Evan J. Worden
- Department of Structural Biology, Van Andel Research Institute, Grand Rapids, MI 49503
| | - Marissa L. Smith
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Kevin E. W. Namitz
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Bruce A. Knutson
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Michael S. Cosgrove
- Department of Biochemistry and Molecular Biology, State University of New York Upstate Medical University, Syracuse, NY 13210
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, The Johns Hopkins University School of Medicine, Baltimore, MD 21205
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El-Saafin F, Devys D, Johnsen SA, Vincent SD, Tora L. SAGA-Dependent Histone H2Bub1 Deubiquitination Is Essential for Cellular Ubiquitin Balance during Embryonic Development. Int J Mol Sci 2022; 23:ijms23137459. [PMID: 35806465 PMCID: PMC9267394 DOI: 10.3390/ijms23137459] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 12/24/2022] Open
Abstract
Ubiquitin (ub) is a small, highly conserved protein widely expressed in eukaryotic cells. Ubiquitination is a post-translational modification catalyzed by enzymes that activate, conjugate, and ligate ub to proteins. Substrates can be modified either by addition of a single ubiquitin molecule (monoubiquitination), or by conjugation of several ubs (polyubiquitination). Monoubiquitination acts as a signaling mark to control diverse biological processes. The cellular and spatial distribution of ub is determined by the opposing activities of ub ligase enzymes, and deubiquitinases (DUBs), which remove ub from proteins to generate free ub. In mammalian cells, 1–2% of total histone H2B is monoubiquitinated. The SAGA (Spt Ada Gcn5 Acetyl-transferase) is a transcriptional coactivator and its DUB module removes ub from H2Bub1. The mammalian SAGA DUB module has four subunits, ATXN7, ATXN7L3, USP22, and ENY2. Atxn7l3−/− mouse embryos, lacking DUB activity, have a five-fold increase in H2Bub1 retention, and die at mid-gestation. Interestingly, embryos lacking the ub encoding gene, Ubc, have a similar phenotype. Here we provide a current overview of data suggesting that H2Bub1 retention on the chromatin in Atxn7l3−/− embryos may lead to an imbalance in free ub distribution. Thus, we speculate that ATXN7L3-containing DUBs impact the free cellular ub pool during development.
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Affiliation(s)
- Farrah El-Saafin
- Olivia Newton-John Cancer Research Institute, Melbourne 3095, Australia;
| | - Didier Devys
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
| | | | - Stéphane D. Vincent
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
- Correspondence: (S.D.V.); (L.T.); Tel.: +33-3-88653425 (S.D.V.); +33-3-88653444 (L.T.)
| | - László Tora
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique (CNRS), UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), U1258, 67404 Illkirch, France
- Université de Strasbourg, 67404 Illkirch, France
- Correspondence: (S.D.V.); (L.T.); Tel.: +33-3-88653425 (S.D.V.); +33-3-88653444 (L.T.)
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Zhang M, Berk JM, Mehrtash AB, Kanyo J, Hochstrasser M. A versatile new tool derived from a bacterial deubiquitylase to detect and purify ubiquitylated substrates and their interacting proteins. PLoS Biol 2022; 20:e3001501. [PMID: 35771886 PMCID: PMC9278747 DOI: 10.1371/journal.pbio.3001501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 07/13/2022] [Accepted: 05/30/2022] [Indexed: 01/07/2023] Open
Abstract
Protein ubiquitylation is an important posttranslational modification affecting a wide range of cellular processes. Due to the low abundance of ubiquitylated species in biological samples, considerable effort has been spent on methods to purify and detect ubiquitylated proteins. We have developed and characterized a novel tool for ubiquitin detection and purification based on OtUBD, a high-affinity ubiquitin-binding domain (UBD) derived from an Orientia tsutsugamushi deubiquitylase (DUB). We demonstrate that OtUBD can be used to purify both monoubiquitylated and polyubiquitylated substrates from yeast and human tissue culture samples and compare their performance with existing methods. Importantly, we found conditions for either selective purification of covalently ubiquitylated proteins or co-isolation of both ubiquitylated proteins and their interacting proteins. As proof of principle for these newly developed methods, we profiled the ubiquitylome and ubiquitin-associated proteome of the budding yeast Saccharomyces cerevisiae. Combining OtUBD affinity purification with quantitative proteomics, we identified potential substrates for the E3 ligases Bre1 and Pib1. OtUBD provides a versatile, efficient, and economical tool for ubiquitin research with specific advantages over certain other methods, such as in efficiently detecting monoubiquitylation or ubiquitin linkages to noncanonical sites. This study presents OtUBD, a new tool derived from a bacterial deubiquitylase, for the purification and analysis of a broad range of endogenous ubiquitylated proteins, including monoubiquitylation, polyubiquitylation, non-lysine ubiquitylation and potentially other macromolecules.
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Affiliation(s)
- Mengwen Zhang
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America
| | - Jason M. Berk
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Adrian B. Mehrtash
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
| | - Jean Kanyo
- W.M. Keck Foundation Biotechnology Resource Laboratory, Yale University, New Haven, Connecticut, United States of America
| | - Mark Hochstrasser
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
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50
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Molenaar TM, van Leeuwen F. SETD2: from chromatin modifier to multipronged regulator of the genome and beyond. Cell Mol Life Sci 2022; 79:346. [PMID: 35661267 PMCID: PMC9167812 DOI: 10.1007/s00018-022-04352-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/09/2022] [Accepted: 05/05/2022] [Indexed: 12/13/2022]
Abstract
Histone modifying enzymes play critical roles in many key cellular processes and are appealing proteins for targeting by small molecules in disease. However, while the functions of histone modifying enzymes are often linked to epigenetic regulation of the genome, an emerging theme is that these enzymes often also act by non-catalytic and/or non-epigenetic mechanisms. SETD2 (Set2 in yeast) is best known for associating with the transcription machinery and methylating histone H3 on lysine 36 (H3K36) during transcription. This well-characterized molecular function of SETD2 plays a role in fine-tuning transcription, maintaining chromatin integrity, and mRNA processing. Here we give an overview of the various molecular functions and mechanisms of regulation of H3K36 methylation by Set2/SETD2. These fundamental insights are important to understand SETD2’s role in disease, most notably in cancer in which SETD2 is frequently inactivated. SETD2 also methylates non-histone substrates such as α-tubulin which may promote genome stability and contribute to the tumor-suppressor function of SETD2. Thus, to understand its role in disease, it is important to understand and dissect the multiple roles of SETD2 within the cell. In this review we discuss how histone methylation by Set2/SETD2 has led the way in connecting histone modifications in active regions of the genome to chromatin functions and how SETD2 is leading the way to showing that we also have to look beyond histones to truly understand the physiological role of an ‘epigenetic’ writer enzyme in normal cells and in disease.
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