1
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Huang YC, Yuan W, Jacob Y. The Role of the TSK/TONSL-H3.1 Pathway in Maintaining Genome Stability in Multicellular Eukaryotes. Int J Mol Sci 2022; 23:9029. [PMID: 36012288 PMCID: PMC9409234 DOI: 10.3390/ijms23169029] [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: 07/22/2022] [Revised: 08/09/2022] [Accepted: 08/10/2022] [Indexed: 11/22/2022] Open
Abstract
Replication-dependent histone H3.1 and replication-independent histone H3.3 are nearly identical proteins in most multicellular eukaryotes. The N-terminal tails of these H3 variants, where the majority of histone post-translational modifications are made, typically differ by only one amino acid. Despite extensive sequence similarity with H3.3, the H3.1 variant has been hypothesized to play unique roles in cells, as it is specifically expressed and inserted into chromatin during DNA replication. However, identifying a function that is unique to H3.1 during replication has remained elusive. In this review, we discuss recent findings regarding the involvement of the H3.1 variant in regulating the TSK/TONSL-mediated resolution of stalled or broken replication forks. Uncovering this new function for the H3.1 variant has been made possible by the identification of the first proteins containing domains that can selectively bind or modify the H3.1 variant. The functional characterization of H3-variant-specific readers and writers reveals another layer of chromatin-based information regulating transcription, DNA replication, and DNA repair.
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Affiliation(s)
| | | | - Yannick Jacob
- Department of Molecular, Cellular and Developmental Biology, Faculty of Arts and Sciences, Yale University, 260 Whitney Avenue, New Haven, CT 06511, USA
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2
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Fraschilla I, Amatullah H, Jeffrey KL. One genome, many cell states: epigenetic control of innate immunity. Curr Opin Immunol 2022; 75:102173. [PMID: 35405493 PMCID: PMC9081230 DOI: 10.1016/j.coi.2022.102173] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 02/23/2022] [Accepted: 02/23/2022] [Indexed: 12/15/2022]
Abstract
A hallmark of the innate immune system is its ability to rapidly initiate short-lived or sustained transcriptional programs in a cell-specific and pathogen-specific manner that is dependent on dynamic chromatin states. Much of the epigenetic landscape is set during cellular differentiation; however, pathogens and other environmental cues also induce changes in chromatin that can either promote tolerance or 'train' innate immune cells for amplified secondary responses. We review chromatin processes that enable innate immune cell differentiation and functional transcriptional responses in naive or experienced cells, in concert with signal transduction and cellular metabolic shifts. We discuss how immune chromatin mechanisms are maladapted in disease and novel therapeutic approaches for cellular reprogramming.
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Affiliation(s)
- Isabella Fraschilla
- Division of Gastroenterology and Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA
| | - Hajera Amatullah
- Division of Gastroenterology and Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Kate L Jeffrey
- Division of Gastroenterology and Center for the Study of Inflammatory Bowel Disease, Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Program in Immunology, Harvard Medical School, Boston, MA 02115, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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3
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Petell CJ, Randene K, Pappas M, Sandoval D, Strahl BD, Harrison JS, Steimel JP. Mechanically transduced immunosorbent assay to measure protein-protein interactions. eLife 2021; 10:67525. [PMID: 34581668 PMCID: PMC8479797 DOI: 10.7554/elife.67525] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 08/28/2021] [Indexed: 12/16/2022] Open
Abstract
Measuring protein-protein interaction (PPI) affinities is fundamental to biochemistry. Yet, conventional methods rely upon the law of mass action and cannot measure many PPIs due to a scarcity of reagents and limitations in the measurable affinity ranges. Here, we present a novel technique that leverages the fundamental concept of friction to produce a mechanical signal that correlates to binding potential. The mechanically transduced immunosorbent (METRIS) assay utilizes rolling magnetic probes to measure PPI interaction affinities. METRIS measures the translational displacement of protein-coated particles on a protein-functionalized substrate. The translational displacement scales with the effective friction induced by a PPI, thus producing a mechanical signal when a binding event occurs. The METRIS assay uses as little as 20 pmols of reagents to measure a wide range of affinities while exhibiting a high resolution and sensitivity. We use METRIS to measure several PPIs that were previously inaccessible using traditional methods, providing new insights into epigenetic recognition.
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Affiliation(s)
- Christopher J Petell
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, United States.,UNC Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, United States
| | - Kathyrn Randene
- Department of Chemistry, University of the Pacific, Stockton, United States
| | - Michael Pappas
- Department of Biological Engineering, University of the Pacific, Stockton, United States
| | - Diego Sandoval
- Department of Biological Engineering, University of the Pacific, Stockton, United States
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, The University of North Carolina School of Medicine, Chapel Hill, United States.,UNC Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, United States
| | - Joseph S Harrison
- Department of Chemistry, University of the Pacific, Stockton, United States
| | - Joshua P Steimel
- Department of Mechanical Engineering, University of the Pacific, Stockton, United States
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4
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Papamokos GV, Tziatzos G, Papageorgiou DG, Georgatos S, Kaxiras E, Politou AS. Progressive Phosphorylation Modulates the Self-Association of a Variably Modified Histone H3 Peptide. Front Mol Biosci 2021; 8:698182. [PMID: 34179102 PMCID: PMC8226166 DOI: 10.3389/fmolb.2021.698182] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/31/2021] [Indexed: 11/19/2022] Open
Abstract
Protein phosphorylation is a key regulatory mechanism in eukaryotic cells. In the intrinsically disordered histone tails, phosphorylation is often a part of combinatorial post-translational modifications and an integral part of the “histone code” that regulates gene expression. Here, we study the association between two histone H3 tail peptides modified to different degrees, using fully atomistic molecular dynamics simulations. Assuming that the initial conformations are either α-helical or fully extended, we compare the propensity of the two peptides to associate with one another when both are unmodified, one modified and the other unmodified, or both modified. The simulations lead to the identification of distinct inter- and intramolecular interactions in the peptide dimer, highlighting a prominent role of a fine-tuned phosphorylation rheostat in peptide association. Progressive phosphorylation appears to modulate peptide charge, inducing strong and specific intermolecular interactions between the monomers, which do not result in the formation of amorphous or ordered aggregates, as documented by experimental evidence derived from Circular Dichroism and NMR spectroscopy. However, upon complete saturation of positive charges by phosphate groups, this effect is reversed: intramolecular interactions prevail and dimerization of zero-charge peptides is markedly reduced. These findings underscore the role of phosphorylation thresholds in the dynamics of intrinsically disordered proteins. Phosphorylation rheostats might account for the divergent effects of histone modifications on the modulation of chromatin structure.
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Affiliation(s)
- George V Papamokos
- Biomedical Division, The Institute of Molecular Biology and Biotechnology, FORTH-ITE, Ioannina, Greece.,Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, United States.,Laboratory of Biological Chemistry, Medical School, University of Ioannina, Ioannina, Greece
| | - George Tziatzos
- Department of Materials Science and Engineering, University of Ioannina, Ioannina, Greece
| | | | - Spyros Georgatos
- Biomedical Division, The Institute of Molecular Biology and Biotechnology, FORTH-ITE, Ioannina, Greece.,Laboratory of Biology, School of Medicine, University of Ioannina, Ioannina, Greece
| | - Efthimios Kaxiras
- Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, United States
| | - Anastasia S Politou
- Biomedical Division, The Institute of Molecular Biology and Biotechnology, FORTH-ITE, Ioannina, Greece.,Laboratory of Biological Chemistry, Medical School, University of Ioannina, Ioannina, Greece
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5
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Villaseñor R, Baubec T. Regulatory mechanisms governing chromatin organization and function. Curr Opin Cell Biol 2020; 70:10-17. [PMID: 33276273 DOI: 10.1016/j.ceb.2020.10.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 10/26/2020] [Accepted: 10/30/2020] [Indexed: 12/12/2022]
Abstract
Nucleosomes, the basic structures used to package genetic information into chromatin, are subject to a diverse array of chemical modifications. A large number of these marks serve as interaction hubs for many nuclear proteins and provide critical structural features for protein recruitment. Dynamic deposition and removal of chromatin modifications by regulatory proteins ensure their correct deposition to the genome, which is essential for DNA replication, transcription, chromatin compaction, or DNA damage repair. The spatiotemporal regulation and maintenance of chromatin marks relies on coordinated activities of writer, eraser, and reader enzymes and often depends on complex multicomponent regulatory circuits. In recent years, the field has made enormous advances in uncovering the mechanisms that regulate chromatin modifications. Here, we discuss well-established and emerging concepts in chromatin biology ranging from cooperativity and multivalent interactions to regulatory feedback loops and increased local concentration of chromatin-modifying enzymes.
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Affiliation(s)
- Rodrigo Villaseñor
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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6
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Arora S, Sappa S, Hinkelman K, Islam K. Engineering a methyllysine reader with photoactive amino acid in mammalian cells. Chem Commun (Camb) 2020; 56:12210-12213. [PMID: 32926023 DOI: 10.1039/d0cc03814h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Methyllysine sites in proteins are recognized by an array of reader domains that mediate protein-protein interactions for controlling cellular processes. Herein, we engineer a chromodomain, an essential methyllysine reader, to carry 4-azido-l-phenylalanine (AzF) via amber suppressor mutagenesis and demonstrate its potential to bind and crosslink methylated proteins in human cells. We further develop a first-of-its kind chromodomain variant bearing two AzF units with enhanced crosslinking potential suitable for profiling the transient methyllysine interactome.
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Affiliation(s)
- Simran Arora
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
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7
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Komar D, Juszczynski P. Rebelled epigenome: histone H3S10 phosphorylation and H3S10 kinases in cancer biology and therapy. Clin Epigenetics 2020; 12:147. [PMID: 33054831 PMCID: PMC7556946 DOI: 10.1186/s13148-020-00941-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 09/28/2020] [Indexed: 12/15/2022] Open
Abstract
Background With the discovery that more than half of human cancers harbor mutations in chromatin proteins, deregulation of epigenetic mechanisms has been recognized a hallmark of malignant transformation. Post-translational modifications (PTMs) of histone proteins, as main components of epigenetic regulatory machinery, are also broadly accepted as therapeutic target. Current “epigenetic” therapies target predominantly writers, erasers and readers of histone acetylation and (to a lesser extent) methylation, leaving other types of PTMs largely unexplored. One of them is the phosphorylation of serine 10 on histone H3 (H3S10ph). Main body H3S10ph is emerging as an important player in the initiation and propagation of cancer, as it facilitates cellular malignant transformation and participates in fundamental cellular functions. In normal cells this histone mark dictates the hierarchy of additional histone modifications involved in the formation of protein binding scaffolds, transcriptional regulation, blocking repressive epigenetic information and shielding gene regions from heterochromatin spreading. During cell division, this mark is essential for chromosome condensation and segregation. It is also involved in the function of specific DNA–RNA hybrids, called R-loops, which modulate transcription and facilitate chromosomal instability. Increase in H3S10ph is observed in numerous cancer types and its abundance has been associated with inferior prognosis. Many H3S10-kinases, including MSK1/2, PIM1, CDK8 and AURORA kinases, have been long considered targets in cancer therapy. However, since these proteins also participate in other critical processes, including signal transduction, apoptotic signaling, metabolic fitness and transcription, their chromatin functions are often neglected. Conclusions H3S10ph and enzymes responsible for deposition of this histone modification are important for chromatin activity and oncogenesis. Epigenetic-drugs targeting this axis of modifications, potentially in combination with conventional or targeted therapy, provide a promising angle in search for knowledge-driven therapeutic strategies in oncology.
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Affiliation(s)
- Dorota Komar
- Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine, Gandhi 14 Str, 02-776, Warsaw, Poland.
| | - Przemyslaw Juszczynski
- Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine, Gandhi 14 Str, 02-776, Warsaw, Poland
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8
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Armache A, Yang S, Martínez de Paz A, Robbins LE, Durmaz C, Cheong JQ, Ravishankar A, Daman AW, Ahimovic DJ, Klevorn T, Yue Y, Arslan T, Lin S, Panchenko T, Hrit J, Wang M, Thudium S, Garcia BA, Korb E, Armache KJ, Rothbart SB, Hake SB, Allis CD, Li H, Josefowicz SZ. Histone H3.3 phosphorylation amplifies stimulation-induced transcription. Nature 2020; 583:852-857. [PMID: 32699416 PMCID: PMC7517595 DOI: 10.1038/s41586-020-2533-0] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 05/05/2020] [Indexed: 01/07/2023]
Abstract
Complex organisms can rapidly induce select genes in response to diverse environmental cues. This regulation occurs in the context of large genomes condensed by histone proteins into chromatin. The sensing of pathogens by macrophages engages conserved signalling pathways and transcription factors to coordinate the induction of inflammatory genes1-3. Enriched integration of histone H3.3, the ancestral histone H3 variant, is a general feature of dynamically regulated chromatin and transcription4-7. However, how chromatin is regulated at induced genes, and what features of H3.3 might enable rapid and high-level transcription, are unknown. The amino terminus of H3.3 contains a unique serine residue (Ser31) that is absent in 'canonical' H3.1 and H3.2. Here we show that this residue, H3.3S31, is phosphorylated (H3.3S31ph) in a stimulation-dependent manner along rapidly induced genes in mouse macrophages. This selective mark of stimulation-responsive genes directly engages the histone methyltransferase SETD2, a component of the active transcription machinery, and 'ejects' the elongation corepressor ZMYND118,9. We propose that features of H3.3 at stimulation-induced genes, including H3.3S31ph, provide preferential access to the transcription apparatus. Our results indicate dedicated mechanisms that enable rapid transcription involving the histone variant H3.3, its phosphorylation, and both the recruitment and the ejection of chromatin regulators.
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Affiliation(s)
- Anja Armache
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
| | - Shuang Yang
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Alexia Martínez de Paz
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Lexi E Robbins
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ceyda Durmaz
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Jin Q Cheong
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Arjun Ravishankar
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andrew W Daman
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Dughan J Ahimovic
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Thaís Klevorn
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Yuan Yue
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China
| | - Tanja Arslan
- Adolf-Butenandt Institute, Ludwig-Maximilians University, Munich, Germany
| | - Shu Lin
- Epigenetics Institute, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Tanya Panchenko
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
- Perlmutter Cancer Center, New York University Langone Medical Center, New York, NY, USA
| | - Joel Hrit
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Miao Wang
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Samuel Thudium
- Department of Genetics, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Benjamin A Garcia
- Adolf-Butenandt Institute, Ludwig-Maximilians University, Munich, Germany
| | - Erica Korb
- Department of Genetics, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Karim-Jean Armache
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - Scott B Rothbart
- Center for Epigenetics, Van Andel Institute, Grand Rapids, MI, USA
| | - Sandra B Hake
- Adolf-Butenandt Institute, Ludwig-Maximilians University, Munich, Germany
- Institute for Genetics, Justus-Liebig-University, Giessen, Germany
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY, USA
| | - Haitao Li
- MOE Key Laboratory of Protein Sciences, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Tsinghua-Peking Joint Center for Life Sciences, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing, China.
| | - Steven Z Josefowicz
- Laboratory of Epigenetics and Immunity, Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
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9
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Schmitz ML, Higgins JMG, Seibert M. Priming chromatin for segregation: functional roles of mitotic histone modifications. Cell Cycle 2020; 19:625-641. [PMID: 31992120 DOI: 10.1080/15384101.2020.1719585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Posttranslational modifications (PTMs) of histone proteins are important for various cellular processes including regulation of gene expression and chromatin structure, DNA damage response and chromosome segregation. Here we comprehensively review mitotic histone PTMs, in particular phosphorylations, and discuss their interplay and functions in the control of dynamic protein-protein interactions as well as their contribution to centromere and chromosome structure and function during cell division. Histone phosphorylations can create binding sites for mitotic regulators such as the chromosomal passenger complex, which is required for correction of erroneous spindle attachments and chromosome bi-orientation. Other histone PTMs can alter the structural properties of nucleosomes and the accessibility of chromatin. Epigenetic marks such as lysine methylations are maintained during mitosis and may also be important for mitotic transcription as well as bookmarking of transcriptional states to ensure the transmission of gene expression programs through cell division. Additionally, histone phosphorylation can dissociate readers of methylated histones without losing epigenetic information. Through all of these processes, mitotic histone PTMs play a functional role in priming the chromatin for faithful chromosome segregation and preventing genetic instability, one of the characteristic hallmarks of cancer cells.
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Affiliation(s)
- M Lienhard Schmitz
- Institute of Biochemistry, Medical Faculty, Member of the German Center for Lung Research, Justus-Liebig-University, Giessen, Germany
| | - Jonathan M G Higgins
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Markus Seibert
- Institute of Biochemistry, Medical Faculty, Member of the German Center for Lung Research, Justus-Liebig-University, Giessen, Germany
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10
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The PHD finger of Spp1 mediates histone modification cross-talk. Biochem J 2019; 476:2351-2354. [PMID: 31462441 DOI: 10.1042/bcj20190492] [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: 07/24/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 11/17/2022]
Abstract
Binding of the Spp1 PHD finger to histone H3K4me3 is sensitive to adjacent post-translational modifications in the histone tail. This commentary discusses the findings of He and colleagues [Biochem. J. 476, 1957-1973] which show that the PHD finger binds to H3K4me3 in a selective manner which is conserved in the Saccharomyces pombe and mammalian orthologues of Spp1.
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11
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Thankam FG, Boosani CS, Dilisio MF, Agrawal DK. Epigenetic mechanisms and implications in tendon inflammation (Review). Int J Mol Med 2019; 43:3-14. [PMID: 30387824 PMCID: PMC6257858 DOI: 10.3892/ijmm.2018.3961] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 09/18/2018] [Indexed: 12/18/2022] Open
Abstract
Cellular inflammation is not just an immediate response following pathogenic infections or resulting from damage due to injury, it is also associated with normal physiological functions, including wound healing and tissue repair. The existence of such a definitive role in normal physiology and in disease pathology indicates the presence of a regulatory mechanism that is tightly controlled in normal cells. A tight control over gene expression is associated with regulatory mechanisms in the cells, which can be either inducible or epigenetic. Among other intracellular mechanisms that contribute to epigenetic gene regulation, DNA methylation has been shown to maintain a tight control over gene expression through the actions of DNA methyltransferases (DNMTs). With a clear role in developmental and tissue‑specific temporal gene regulation, the involvement of DNMTs is evident in normal and pathological conditions. In this review article, inflammation in tendons associated with disease pathology and tissue repair or regeneration at the musculoskeletal joints is critically reviewed. More specifically, the review focuses on known epigenetic mechanisms and their role in the clinical presentation of the disease in human joint disorders associated with tendon inflammation, with an emphasis on the gene regulatory mechanisms that are controlled through DNA methylation, histone deacetylation, and microRNAs.
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Affiliation(s)
| | | | - Matthew F. Dilisio
- Department of Orthopedic Surgery, Creighton University School of Medicine, Omaha, NE 68178, USA
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12
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Klein BJ, Krajewski K, Restrepo S, Lewis PW, Strahl BD, Kutateladze TG. Recognition of cancer mutations in histone H3K36 by epigenetic writers and readers. Epigenetics 2018; 13:683-692. [PMID: 30045670 DOI: 10.1080/15592294.2018.1503491] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Histone posttranslational modifications control the organization and function of chromatin. In particular, methylation of lysine 36 in histone H3 (H3K36me) has been shown to mediate gene transcription, DNA repair, cell cycle regulation, and pre-mRNA splicing. Notably, mutations at or near this residue have been causally linked to the development of several human cancers. These observations have helped to illuminate the role of histones themselves in disease and to clarify the mechanisms by which they acquire oncogenic properties. This perspective focuses on recent advances in discovery and characterization of histone H3 mutations that impact H3K36 methylation. We also highlight findings that the common cancer-related substitution of H3K36 to methionine (H3K36M) disturbs functions of not only H3K36me-writing enzymes but also H3K36me-specific readers. The latter case suggests that the oncogenic effects could also be linked to the inability of readers to engage H3K36M.
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Affiliation(s)
- Brianna J Klein
- a Department of Pharmacology , University of Colorado School of Medicine , Aurora , CO , USA
| | - Krzysztof Krajewski
- b Department of Biochemistry & Biophysics , The University of North Carolina School of Medicine , Chapel Hill , NC , USA
| | - Susana Restrepo
- a Department of Pharmacology , University of Colorado School of Medicine , Aurora , CO , USA
| | - Peter W Lewis
- c Wisconsin Institute for Discovery , University of Wisconsin , Madison , WI , USA
| | - Brian D Strahl
- b Department of Biochemistry & Biophysics , The University of North Carolina School of Medicine , Chapel Hill , NC , USA
| | - Tatiana G Kutateladze
- a Department of Pharmacology , University of Colorado School of Medicine , Aurora , CO , USA
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13
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O'Kane PT, Mrksich M. An Assay Based on SAMDI Mass Spectrometry for Profiling Protein Interaction Domains. J Am Chem Soc 2017; 139:10320-10327. [PMID: 28689418 DOI: 10.1021/jacs.7b03805] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
This paper describes an assay that can profile the binding of a protein to ligands and can rank the affinities of a library of ligands. The method is based on the enhanced rate of an enzyme-mediated reaction that follows from colocalization of the enzyme and substrate by a protein-ligand interaction. This assay uses a self-assembled monolayer that presents a candidate peptide ligand for a receptor and a peptide substrate for an enzyme. The receptor is prepared as a fusion to the relevant enzyme so that binding of the receptor to the immobilized ligand brings the enzyme to the surface, where it can more rapidly modify its substrate. The extent of conversion of the substrate to product is therefore a measure of the average time the ligand-receptor complex is present and is quantified using the SAMDI mass spectrometry technique. The approach is used to profile the binding of chromodomain proteins to methylated lysine peptides derived from the histone 3 protein. The relative affinities for the peptide ligands found in this work agreed with results from prior studies. Additionally, this work revealed cross-talk interactions whereby phosphorylation of certain residues impaired binding of chromodomains to the peptide ligands. The method presented here, which we term protein interaction by SAMDI (PI-SAMDI), has the advantages that it is applicable to low-affinity interactions because the complexes are not observed directly, but rather leave a "covalent record" of the interaction that is measured with mass spectrometry and because it is compatible with laboratory automation for high-throughput analysis.
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Affiliation(s)
- Patrick T O'Kane
- Department of Chemistry, Department of Biomedical Engineering, and Department of Cell & Molecular Biology, Northwestern University , Evanston, Illinois 60208, United States
| | - Milan Mrksich
- Department of Chemistry, Department of Biomedical Engineering, and Department of Cell & Molecular Biology, Northwestern University , Evanston, Illinois 60208, United States
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14
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Andrews FH, Strahl BD, Kutateladze TG. Insights into newly discovered marks and readers of epigenetic information. Nat Chem Biol 2017; 12:662-8. [PMID: 27538025 DOI: 10.1038/nchembio.2149] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 07/11/2016] [Indexed: 02/06/2023]
Abstract
The field of chromatin biology has been advancing at an accelerated pace. Recent discoveries of previously uncharacterized sites and types of post-translational modifications (PTMs) and the identification of new sets of proteins responsible for the deposition, removal, and reading of these marks continue raising the complexity of an already exceedingly complicated biological phenomenon. In this Perspective article we examine the biological importance of new types and sites of histone PTMs and summarize the molecular mechanisms of chromatin engagement by newly discovered epigenetic readers. We also highlight the imperative role of structural insights in understanding PTM-reader interactions and discuss future directions to enhance the knowledge of PTM readout.
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Affiliation(s)
- Forest H Andrews
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Brian D Strahl
- Department of Biochemistry and Biophysics, the University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA
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van Wely KHM, Mora Gallardo C, Vann KR, Kutateladze TG. Epigenetic countermarks in mitotic chromosome condensation. Nucleus 2017; 8:144-149. [PMID: 28045584 PMCID: PMC5403135 DOI: 10.1080/19491034.2016.1276144] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mitosis in metazoans is characterized by abundant phosphorylation of histone H3 and involves the recruitment of condensin complexes to chromatin. The relationship between the 2 phenomena and their respective contributions to chromosome condensation in vivo remain poorly understood. Recent studies have shown that H3T3 phosphorylation decreases binding of histone readers to methylated H3K4 in vitro and is essential to displace the corresponding proteins from mitotic chromatin in vivo. Together with previous observations, these data provide further evidence for a role of mitotic histone H3 phosphorylation in blocking transcriptional programs or preserving the ‘memory’ PTMs. Mitotic protein exclusion can also have a role in depopulating the chromatin template for subsequent condensin loading. H3 phosphorylation thus serves as an integral step in the condensation of chromosome arms.
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Affiliation(s)
- Karel H M van Wely
- a Department of Immunology and Oncology , Centro Nacional de Biotecnología/CSIC , Madrid , Spain
| | - Carmen Mora Gallardo
- a Department of Immunology and Oncology , Centro Nacional de Biotecnología/CSIC , Madrid , Spain
| | - Kendra R Vann
- b Department of Pharmacology , University of Colorado School of Medicine , Aurora , CO , USA
| | - Tatiana G Kutateladze
- b Department of Pharmacology , University of Colorado School of Medicine , Aurora , CO , USA
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