1
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Patel R, Onyema A, Tang PK, Loverde SM. Conformational Dynamics of the Nucleosomal Histone H2B Tails Revealed by Molecular Dynamics Simulations. J Chem Inf Model 2024; 64:4709-4726. [PMID: 38865599 PMCID: PMC11200259 DOI: 10.1021/acs.jcim.4c00059] [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: 01/11/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/14/2024]
Abstract
Epigenetic modifications of histone N-terminal tails play a critical role in regulating the chromatin structure and biological processes such as transcription and DNA repair. One of the key post-translational modifications (PTMs) is the acetylation of lysine residues on histone tails. Epigenetic modifications are ubiquitous in the development of diseases, such as cancer and neurological disorders. Histone H2B tails are critical regulators of nucleosome dynamics, biological processes, and certain diseases. Here, we report all-atomistic molecular dynamics (MD) simulations of the nucleosome to demonstrate that acetylation of the histone tails changes their conformational space and interaction with DNA. We perform simulations of H2B tails, critical regulators of gene regulation, in both the lysine-acetylated (ACK) and unacetylated wild type (WT) states. To explore the effects of salt concentration, we use two different NaCl concentrations to perform simulations at microsecond time scales. Salt can modulate the effects of electrostatic interactions between the DNA phosphate backbone and histone tails. Upon acetylation, H2B tails shift their secondary structure helical propensity. The number of contacts between the DNA and the H2B tail decreases. We characterize the conformational dynamics of the H2B tails by principal component analysis (PCA). The ACK tails become more compact at increased salt concentrations, but conformations from the WT tails display the most contacts with DNA at both salt concentrations. Mainly, H2B acetylation may increase the DNA accessibility for regulatory proteins to bind, which can aid in gene regulation and NCP stability.
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Affiliation(s)
- Rutika Patel
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New
York, New York 10314, United States
| | - Augustine Onyema
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New
York, New York 10314, United States
| | - Phu K. Tang
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New
York, New York 10314, United States
| | - Sharon M. Loverde
- Ph.D.
Program in Biochemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Department
of Chemistry, College of Staten Island, The City University of New York, 2800 Victory Boulevard, Staten Island, New
York, New York 10314, United States
- Ph.D.
Program in Chemistry, The Graduate Center
of the City University of New York, New York, New York 10016, United States
- Ph.D.
Program in Physics, The Graduate Center
of the City University of New York, New York, New York 10016, United States
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2
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Chang YJ, Lin S, Kang ZF, Shen BJ, Tsai WH, Chen WC, Lu HP, Su YL, Chou SJ, Lin SY, Lin SW, Huang YJ, Wang HH, Chang CJ. Acetylation-Mimic Mutation of TRIM28-Lys304 to Gln Attenuates the Interaction with KRAB-Zinc-Finger Proteins and Affects Gene Expression in Leukemic K562 Cells. Int J Mol Sci 2023; 24:9830. [PMID: 37372979 DOI: 10.3390/ijms24129830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
TRIM28/KAP1/TIF1β is a crucial epigenetic modifier. Genetic ablation of trim28 is embryonic lethal, although RNAi-mediated knockdown in somatic cells yields viable cells. Reduction in TRIM28 abundance at the cellular or organismal level results in polyphenism. Posttranslational modifications such as phosphorylation and sumoylation have been shown to regulate TRIM28 activity. Moreover, several lysine residues of TRIM28 are subject to acetylation, but how acetylation of TRIM28 affects its functions remains poorly understood. Here, we report that, compared with wild-type TRIM28, the acetylation-mimic mutant TRIM28-K304Q has an altered interaction with Krüppel-associated box zinc-finger proteins (KRAB-ZNFs). The TRIM28-K304Q knock-in cells were created in K562 erythroleukemia cells by CRISPR-Cas9 (Clustered regularly interspaced short palindromic repeats/CRISPR-associated protein nuclease 9) gene editing method. Transcriptome analysis revealed that TRIM28-K304Q and TRIM28 knockout K562 cells had similar global gene expression profiles, yet the profiles differed considerably from wild-type K562 cells. The expression levels of embryonic-related globin gene and a platelet cell marker integrin-beta 3 were increased in TRIM28-K304Q mutant cells, indicating the induction of differentiation. In addition to the differentiation-related genes, many zinc-finger-proteins genes and imprinting genes were activated in TRIM28-K304Q cells; they were inhibited by wild-type TRIM28 via binding with KRAB-ZNFs. These results suggest that acetylation/deacetylation of K304 in TRIM28 constitutes a switch for regulating its interaction with KRAB-ZNFs and alters the gene regulation as demonstrated by the acetylation mimic TRIM28-K304Q.
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Affiliation(s)
- Yao-Jen Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Steven Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Zhi-Fu Kang
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Bin-Jon Shen
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Wen-Hai Tsai
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Wen-Ching Chen
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Hsin-Pin Lu
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
| | - Yu-Lun Su
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Shu-Jen Chou
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei 11529, Taiwan
| | - Shu-Yu Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Sheng-Wei Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Yin-Jung Huang
- Department of Pediatrics, Division of Pediatric Immunology and Nephrology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
| | - Hsin-Hui Wang
- Department of Pediatrics, Division of Pediatric Immunology and Nephrology, Taipei Veterans General Hospital, Taipei 11217, Taiwan
- Department of Pediatrics, Faculty of Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
- Institute of Emergency and Critical Care Medicine, School of Medicine, National Yang Ming Chiao Tung University, Taipei 112304, Taiwan
| | - Ching-Jin Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Graduate Institute of Biochemical Sciences, College of Life Science, National Taiwan University, Taipei 10617, Taiwan
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3
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Liu Q, Pillus L, Petty EL. Functional tug of war between kinases, phosphatases, and the Gcn5 acetyltransferase in chromatin and cell cycle checkpoint controls. G3 (BETHESDA, MD.) 2023; 13:jkad021. [PMID: 36772957 PMCID: PMC10085806 DOI: 10.1093/g3journal/jkad021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/13/2023] [Indexed: 02/09/2023]
Abstract
Covalent modifications of chromatin regulate genomic structure and accessibility in diverse biological processes such as transcriptional regulation, cell cycle progression, and DNA damage repair. Many histone modifications have been characterized, yet understanding the interactions between these and their combinatorial effects remains an active area of investigation, including dissecting functional interactions between enzymes mediating these modifications. In budding yeast, the histone acetyltransferase Gcn5 interacts with Rts1, a regulatory subunit of protein phosphatase 2A (PP2A). Implicated in the interaction is the potential for the dynamic phosphorylation of conserved residues on histone H2B and the Cse4 centromere-specific histone H3 variant. To probe these dynamics, we sought to identify kinases which contribute to the phosphorylated state. In a directed screen beginning with in silico analysis of the 127 members of yeast kinome, we have now identified 16 kinases with genetic interactions with GCN5 and specifically found distinct roles for the Hog1 stress-activated protein kinase. Deletion of HOG1 (hog1Δ) rescues gcn5Δ sensitivity to the microtubule poison nocodazole and the lethality of the gcn5Δ rts1Δ double mutant. The Hog1-Gcn5 interaction requires the conserved H2B-T91 residue, which is phosphorylated in vertebrate species. Furthermore, deletion of HOG1 decreases aneuploidy and apoptotic populations in gcn5Δ cells. Together, these results introduce Hog1 as a kinase that functionally opposes Gcn5 and Rts1 in the context of the spindle assembly checkpoint and suggest further kinases may also influence GCN5's functions.
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Affiliation(s)
- Qihao Liu
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-034, USA
| | - Lorraine Pillus
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-034, USA
| | - Emily L Petty
- Department of Molecular Biology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093-034, USA
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4
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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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5
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Hao F, Mishra LN, Jaya P, Jones R, Hayes JJ. Identification and Analysis of Six Phosphorylation Sites Within the Xenopus laevis Linker Histone H1.0 C-Terminal Domain Indicate Distinct Effects on Nucleosome Structure. Mol Cell Proteomics 2022; 21:100250. [PMID: 35618225 PMCID: PMC9243160 DOI: 10.1016/j.mcpro.2022.100250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 05/01/2022] [Accepted: 05/20/2022] [Indexed: 11/25/2022] Open
Abstract
As a key structural component of the chromatin of higher eukaryotes, linker histones (H1s) are involved in stabilizing the folding of extended nucleosome arrays into higher-order chromatin structures and function as a gene-specific regulator of transcription in vivo. The H1 C-terminal domain (CTD) is essential for high-affinity binding of linker histones to chromatin and stabilization of higher-order chromatin structure. Importantly, the H1 CTD is an intrinsically disordered domain that undergoes a drastic condensation upon binding to nucleosomes. Moreover, although phosphorylation is a prevalent post-translational modification within the H1 CTD, exactly where this modification is installed and how phosphorylation influences the structure of the H1 CTD remains unclear for many H1s. Using novel mass spectrometry techniques, we identified six phosphorylation sites within the CTD of the archetypal linker histone Xenopus H1.0. We then analyzed nucleosome-dependent CTD condensation and H1-dependent linker DNA organization for H1.0 in which the phosphorylated serine residues were replaced by glutamic acid residues (phosphomimics) in six independent mutants. We find that phosphomimetics at residues S117E, S155E, S181E, S188E, and S192E resulted in a significant reduction in nucleosome-bound H1.0 CTD condensation compared with unphosphorylated H1.0, whereas S130E did not alter CTD structure. Furthermore, we found distinct effects among the phosphomimetics on H1-dependent linker DNA trajectory, indicating unique mechanisms by which this modification can influence H1 CTD condensation. These results bring to light a novel role for linker histone phosphorylation in directly altering the structure of nucleosome-bound H1 and a potential novel mechanism for its effects on chromatin structure and function.
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Affiliation(s)
- Fanfan Hao
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, USA
| | - Laxmi N Mishra
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, USA
| | - Prasoon Jaya
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, USA; Department of Developmental and Molecular Biology, Albert Einstein College of Medicine, Bronx, New York, USA
| | | | - Jeffrey J Hayes
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York, USA.
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6
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Hao C, Shao X, Song J, Peng M, Lao Y, Mack R, Zhang L, Wei W, Liu N, Wang T, Wu Y, Feng L, Yin L, Wang S, Sun X, Chen S, Zhang J, Li B. SIRT2 regulates proliferation and chemotherapy response of MLL-ENL-driven acute myeloid leukemia. Biochem Biophys Res Commun 2022; 596:36-42. [PMID: 35108652 PMCID: PMC9052174 DOI: 10.1016/j.bbrc.2022.01.081] [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: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 11/15/2022]
Abstract
Both MLL-AF9 and MLL-ENL leukemia fusion proteins drive oncogenic transformation of hematopoietic cells through their N-terminal DNA/histone binding mixed-lineage leukemia 1 domain and C-terminal fragment of AF9 or ENL containing an unstructured linker region and the ANC1 homology domain, which recruits transcription factors. Despite of their structural similarity, acute myeloid leukemia (AML) patients bearing MLL-ENL show more adverse outcomes compared to those with MLL-AF9. We recapitulated the clinical patterns of these two MLL-fusions driven AMLs using murine models and found that MLL-ENL AML cells showed slower cell cycle progression and more resistance to standard chemotherapy than MLL-AF9 cells. These phenotypes were primarily controlled by the linker regions of ENL and a highly conserved lysine residue K469 within. Substitution of K469 with an acetylated mimic glutamine abolished the ability of MLL-ENL to suppress proliferation and promote chemo-resistance. We showed that deacetylase Sirt2 might act as an upstream regulator of MLL-ENL. Deletion of Sirt2 promoted proliferation of AML cells with either MLL fusions. Importantly, loss of Sirt2 greatly enhanced the sensitivity of the MLL-ENL AML cells to chemo-treatment. Taken together, our study uncovered a unique regulatory role of Sirt2 in leukemogenesis and suggested targeting SIRT2 as a new way to sensitize MLL-ENL AML patience for chemotherapy.
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MESH Headings
- Acute Disease
- Amino Acid Sequence
- Animals
- Antineoplastic Combined Chemotherapy Protocols/pharmacology
- Carcinogenesis/genetics
- Carcinogenesis/metabolism
- Carcinogenesis/pathology
- Cell Proliferation/genetics
- Cytarabine/administration & dosage
- Doxorubicin/administration & dosage
- Gene Expression Regulation, Leukemic/drug effects
- Gene Expression Regulation, Leukemic/genetics
- Kaplan-Meier Estimate
- Leukemia, Myeloid/drug therapy
- Leukemia, Myeloid/genetics
- Leukemia, Myeloid/metabolism
- Mice, Inbred C57BL
- Mice, Knockout
- Myeloid-Lymphoid Leukemia Protein/genetics
- Myeloid-Lymphoid Leukemia Protein/metabolism
- Oncogene Proteins, Fusion/genetics
- Oncogene Proteins, Fusion/metabolism
- Sequence Homology, Amino Acid
- Sirtuin 2/genetics
- Sirtuin 2/metabolism
- Tumor Cells, Cultured
- Mice
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Affiliation(s)
- Caiqing Hao
- Department of Life Science and Biotechnology, Shanghai Jiao Tong University School, 800 Dongchuan Road, Shanghai, 200240, China; Department of Biology, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China; Department of Biochemistry and Molecular Cell Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 280 S. Chongqing Road, Shanghai, 200025, China
| | - Xianyu Shao
- Department of Biology, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Juan Song
- Department of Biochemistry and Molecular Cell Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 280 S. Chongqing Road, Shanghai, 200025, China
| | - Mengyuan Peng
- Department of Biochemistry and Molecular Cell Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 280 S. Chongqing Road, Shanghai, 200025, China
| | - Yimin Lao
- Department of Biochemistry and Molecular Cell Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 280 S. Chongqing Road, Shanghai, 200025, China
| | - Ryan Mack
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Lei Zhang
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA; Cyrus Tang Hematology Center, National Clinical Research Center for Hematologic Diseases, Soochow University, 215123, Suzhou, China
| | - Wei Wei
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA
| | - Na Liu
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Road II, Shanghai, 200025, China
| | - Tian Wang
- Department of Biology, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Yuanyuan Wu
- Department of Biology, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Lanyao Feng
- Department of Biology, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Lijun Yin
- Department of Biology, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Shouxin Wang
- Department of Biology, College of Life Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xiaojian Sun
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Road II, Shanghai, 200025, China
| | - Saijuan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine (Shanghai), Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, 197 Rui Jin Road II, Shanghai, 200025, China; Key Laboratory of Ministry of Education for Systems Biomedicine, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, China
| | - Jiwang Zhang
- Department of Cancer Biology, Oncology Institute, Cardinal Bernardin Cancer Center, Loyola University Medical Center, Maywood, IL, 60153, USA.
| | - Bing Li
- Department of Biochemistry and Molecular Cell Biology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 280 S. Chongqing Road, Shanghai, 200025, China.
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7
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Whole-genome methods to define DNA and histone accessibility and long-range interactions in chromatin. Biochem Soc Trans 2022; 50:199-212. [PMID: 35166326 PMCID: PMC9847230 DOI: 10.1042/bst20210959] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 12/30/2021] [Accepted: 01/24/2022] [Indexed: 02/08/2023]
Abstract
Defining the genome-wide chromatin landscape has been a goal of experimentalists for decades. Here we review highlights of these efforts, from seminal experiments showing discontinuities in chromatin structure related to gene activation to extensions of these methods elucidating general features of chromatin related to gene states by exploiting deep sequencing methods. We also review chromatin conformational capture methods to identify patterns in long-range interactions between genomic loci.
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8
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Shvedunova M, Akhtar A. Modulation of cellular processes by histone and non-histone protein acetylation. Nat Rev Mol Cell Biol 2022; 23:329-349. [PMID: 35042977 DOI: 10.1038/s41580-021-00441-y] [Citation(s) in RCA: 253] [Impact Index Per Article: 126.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2021] [Indexed: 12/12/2022]
Abstract
Lysine acetylation is a widespread and versatile protein post-translational modification. Lysine acetyltransferases and lysine deacetylases catalyse the addition or removal, respectively, of acetyl groups at both histone and non-histone targets. In this Review, we discuss several features of acetylation and deacetylation, including their diversity of targets, rapid turnover, exquisite sensitivity to the concentrations of the cofactors acetyl-CoA, acyl-CoA and NAD+, and tight interplay with metabolism. Histone acetylation and non-histone protein acetylation influence a myriad of cellular and physiological processes, including transcription, phase separation, autophagy, mitosis, differentiation and neural function. The activity of lysine acetyltransferases and lysine deacetylases can, in turn, be regulated by metabolic states, diet and specific small molecules. Histone acetylation has also recently been shown to mediate cellular memory. These features enable acetylation to integrate the cellular state with transcriptional output and cell-fate decisions.
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Affiliation(s)
- Maria Shvedunova
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany
| | - Asifa Akhtar
- Department of Chromatin Regulation, Max Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.
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9
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Rico T, Gilles M, Chauderlier A, Comptdaer T, Magnez R, Chwastyniak M, Drobecq H, Pinet F, Thuru X, Buée L, Galas MC, Lefebvre B. Tau Stabilizes Chromatin Compaction. Front Cell Dev Biol 2021; 9:740550. [PMID: 34722523 PMCID: PMC8551707 DOI: 10.3389/fcell.2021.740550] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
An extensive body of literature suggested a possible role of the microtubule-associated protein Tau in chromatin functions and/or organization in neuronal, non-neuronal, and cancer cells. How Tau functions in these processes remains elusive. Here we report that Tau expression in breast cancer cell lines causes resistance to the anti-cancer effects of histone deacetylase inhibitors, by preventing histone deacetylase inhibitor-inducible gene expression and remodeling of chromatin structure. We identify Tau as a protein recognizing and binding to core histone when H3 and H4 are devoid of any post-translational modifications or acetylated H4 that increases the Tau's affinity. Consistent with chromatin structure alterations in neurons found in frontotemporal lobar degeneration, Tau mutations did not prevent histone deacetylase-inhibitor-induced higher chromatin structure remodeling by suppressing Tau binding to histones. In addition, we demonstrate that the interaction between Tau and histones prevents further histone H3 post-translational modifications induced by histone deacetylase-inhibitor treatment by maintaining a more compact chromatin structure. Altogether, these results highlight a new cellular role for Tau as a chromatin reader, which opens new therapeutic avenues to exploit Tau biology in neuronal and cancer cells.
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Affiliation(s)
- Thomas Rico
- Univ. Lille, INSERM, CHU-Lille, Lille Neuroscience and Cognition, UMR-S1172, Alzheimer and Tauopathies, Lille, France
| | - Melissa Gilles
- Univ. Lille, INSERM, CHU-Lille, Lille Neuroscience and Cognition, UMR-S1172, Alzheimer and Tauopathies, Lille, France
| | - Alban Chauderlier
- Univ. Lille, INSERM, CHU-Lille, Lille Neuroscience and Cognition, UMR-S1172, Alzheimer and Tauopathies, Lille, France
| | - Thomas Comptdaer
- Univ. Lille, INSERM, CHU-Lille, Lille Neuroscience and Cognition, UMR-S1172, Alzheimer and Tauopathies, Lille, France
| | - Romain Magnez
- Univ. Lille, CNRS, INSERM, CHU Lille, UMR 9020, UMR 1277, Canther, Platform of Integrative Chemical Biology, Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France
| | - Maggy Chwastyniak
- Univ. Lille, INSERM, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de Risque et Déterminants Moléculaires des Maladies Liées Au Vieillissement, Lille, France
| | - Herve Drobecq
- Univ. Lille, CNRS UMR 9017, INSERM U1019, CHRU Lille, Institut Pasteur de Lille, Center for Infection and Immunity of Lille, Lille, France
| | - Florence Pinet
- Univ. Lille, INSERM, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Facteurs de Risque et Déterminants Moléculaires des Maladies Liées Au Vieillissement, Lille, France
| | - Xavier Thuru
- Univ. Lille, CNRS, INSERM, CHU Lille, UMR 9020, UMR 1277, Canther, Platform of Integrative Chemical Biology, Cancer Heterogeneity, Plasticity and Resistance to Therapies, Lille, France
| | - Luc Buée
- Univ. Lille, INSERM, CHU-Lille, Lille Neuroscience and Cognition, UMR-S1172, Alzheimer and Tauopathies, Lille, France
| | - Marie-Christine Galas
- Univ. Lille, INSERM, CHU-Lille, Lille Neuroscience and Cognition, UMR-S1172, Alzheimer and Tauopathies, Lille, France
| | - Bruno Lefebvre
- Univ. Lille, INSERM, CHU-Lille, Lille Neuroscience and Cognition, UMR-S1172, Alzheimer and Tauopathies, Lille, France
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10
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Hansen JC, Maeshima K, Hendzel MJ. The solid and liquid states of chromatin. Epigenetics Chromatin 2021; 14:50. [PMID: 34717733 PMCID: PMC8557566 DOI: 10.1186/s13072-021-00424-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 10/22/2021] [Indexed: 12/14/2022] Open
Abstract
The review begins with a concise description of the principles of phase separation. This is followed by a comprehensive section on phase separation of chromatin, in which we recount the 60 years history of chromatin aggregation studies, discuss the evidence that chromatin aggregation intrinsically is a physiologically relevant liquid-solid phase separation (LSPS) process driven by chromatin self-interaction, and highlight the recent findings that under specific solution conditions chromatin can undergo liquid-liquid phase separation (LLPS) rather than LSPS. In the next section of the review, we discuss how certain chromatin-associated proteins undergo LLPS in vitro and in vivo. Some chromatin-binding proteins undergo LLPS in purified form in near-physiological ionic strength buffers while others will do so only in the presence of DNA, nucleosomes, or chromatin. The final section of the review evaluates the solid and liquid states of chromatin in the nucleus. While chromatin behaves as an immobile solid on the mesoscale, nucleosomes are mobile on the nanoscale. We discuss how this dual nature of chromatin, which fits well the concept of viscoelasticity, contributes to genome structure, emphasizing the dominant role of chromatin self-interaction.
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Affiliation(s)
- Jeffrey C Hansen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO, 80523, USA.
| | - Kazuhiro Maeshima
- Genome Dynamics Laboratory, National Institute of Genetics, and Department of Genetics, Sokendai (Graduate University for Advanced Studies), Mishima, Shizuoka, 411-8540, Japan.
| | - Michael J Hendzel
- Department of Cell Biology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada.
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11
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Ackermann BE, Debelouchina GT. Emerging Contributions of Solid-State NMR Spectroscopy to Chromatin Structural Biology. Front Mol Biosci 2021; 8:741581. [PMID: 34708075 PMCID: PMC8544521 DOI: 10.3389/fmolb.2021.741581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
The eukaryotic genome is packaged into chromatin, a polymer of DNA and histone proteins that regulates gene expression and the spatial organization of nuclear content. The repetitive character of chromatin is diversified into rich layers of complexity that encompass DNA sequence, histone variants and post-translational modifications. Subtle molecular changes in these variables can often lead to global chromatin rearrangements that dictate entire gene programs with far reaching implications for development and disease. Decades of structural biology advances have revealed the complex relationship between chromatin structure, dynamics, interactions, and gene expression. Here, we focus on the emerging contributions of magic-angle spinning solid-state nuclear magnetic resonance spectroscopy (MAS NMR), a relative newcomer on the chromatin structural biology stage. Unique among structural biology techniques, MAS NMR is ideally suited to provide atomic level information regarding both the rigid and dynamic components of this complex and heterogenous biological polymer. In this review, we highlight the advantages MAS NMR can offer to chromatin structural biologists, discuss sample preparation strategies for structural analysis, summarize recent MAS NMR studies of chromatin structure and dynamics, and close by discussing how MAS NMR can be combined with state-of-the-art chemical biology tools to reconstitute and dissect complex chromatin environments.
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Affiliation(s)
| | - Galia T. Debelouchina
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, United States
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12
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Histone H3K4me1 strongly activates the DNase I hypersensitive sites in super-enhancers than those in typical enhancers. Biosci Rep 2021; 41:229109. [PMID: 34195788 PMCID: PMC8264496 DOI: 10.1042/bsr20210691] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/21/2021] [Accepted: 06/23/2021] [Indexed: 01/02/2023] Open
Abstract
Super-enhancers (SEs), which consist of multiple enhancer elements, are occupied by master transcription factors and co-activators, such as Mediator, and are highly acetylated at histone H3K27. Here, we have characterized the SEs in terms of DNase I hypersensitive sites (DHSs) by analyzing publicly available chromatin immunoprecipitation (ChIP)-seq and DNase-seq data of K562 cells and compared with the DHSs in typical enhancers (TEs). DHSs in the SEs were highly marked by histone H3K4me1 than DHSs in TEs. Loss of H3K4me1 by the deletion of catalytic domains in histone methyltransferases MLL3 and MLL4 remarkably decreased histone H3K27ac and histone H3 depletion at SE DHSs than at TE DHSs. The levels of enhancer RNA (eRNA) transcripts and mRNA transcripts from the putative target genes were notably reduced at and near SE DHSs than TE DHSs following H3K4me1 loss. These results indicate that histone H3K4me1 is a marker for DHSs in SEs and that this modification has a more significant impact on the activation of SE DHSs than TE DHSs.
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13
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Peng Y, Li S, Landsman D, Panchenko AR. Histone tails as signaling antennas of chromatin. Curr Opin Struct Biol 2021; 67:153-160. [PMID: 33279866 PMCID: PMC8096652 DOI: 10.1016/j.sbi.2020.10.018] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 10/07/2020] [Accepted: 10/18/2020] [Indexed: 12/19/2022]
Abstract
Histone tails, representing the N-terminal or C-terminal regions flanking the histone core, play essential roles in chromatin signaling networks. Intrinsic disorder of histone tails and their propensity for post-translational modifications allow them to serve as hubs in coordination of epigenetic processes within the nucleosomal context. Deposition of histone variants with distinct histone tail properties further enriches histone tails' repertoire in epigenetic signaling. Given the advances in experimental techniques and in silico modelling, we review the most recent data on histone tails' effects on nucleosome stability and dynamics, their function in regulating chromatin accessibility and folding. Finally, we discuss different molecular mechanisms to understand how histone tails are involved in nucleosome recognition by binding partners and formation of higher-order chromatin structures.
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Affiliation(s)
- Yunhui Peng
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Shuxiang Li
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, ON, Canada
| | - David Landsman
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, ON, Canada.
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14
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Mechanistic insights into KDM4A driven genomic instability. Biochem Soc Trans 2021; 49:93-105. [PMID: 33492339 PMCID: PMC7925003 DOI: 10.1042/bst20191219] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 12/19/2022]
Abstract
Alterations in global epigenetic signatures on chromatin are well established to contribute to tumor initiation and progression. Chromatin methylation status modulates several key cellular processes that maintain the integrity of the genome. KDM4A, a demethylase that belongs to the Fe-II dependent dioxygenase family that uses α-ketoglutarate and molecular oxygen as cofactors, is overexpressed in several cancers and is associated with an overall poor prognosis. KDM4A demethylates lysine 9 (H3K9me2/3) and lysine 36 (H3K36me3) methyl marks on histone H3. Given the complexity that exists with these marks on chromatin and their effects on transcription and proliferation, it naturally follows that demethylation serves an equally important role in these cellular processes. In this review, we highlight the role of KDM4A in transcriptional modulation, either dependent or independent of its enzymatic activity, arising from the amplification of this demethylase in cancer. KDM4A modulates re-replication of distinct genomic loci, activates cell cycle inducers, and represses proteins involved in checkpoint control giving rise to proliferative damage, mitotic disturbances and chromosomal breaks, ultimately resulting in genomic instability. In parallel, emerging evidence of non-nuclear substrates of epigenetic modulators emphasize the need to investigate the role of KDM4A in regulating non-nuclear substrates and evaluate their contribution to genomic instability in this context. The existence of promising KDM-specific inhibitors makes these demethylases an attractive target for therapeutic intervention in cancers.
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15
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Willcockson MA, Healton SE, Weiss CN, Bartholdy BA, Botbol Y, Mishra LN, Sidhwani DS, Wilson TJ, Pinto HB, Maron MI, Skalina KA, Toro LN, Zhao J, Lee CH, Hou H, Yusufova N, Meydan C, Osunsade A, David Y, Cesarman E, Melnick AM, Sidoli S, Garcia BA, Edelmann W, Macian F, Skoultchi AI. H1 histones control the epigenetic landscape by local chromatin compaction. Nature 2021; 589:293-298. [PMID: 33299182 PMCID: PMC8110206 DOI: 10.1038/s41586-020-3032-z] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 10/06/2020] [Indexed: 01/29/2023]
Abstract
H1 linker histones are the most abundant chromatin-binding proteins1. In vitro studies indicate that their association with chromatin determines nucleosome spacing and enables arrays of nucleosomes to fold into more compact chromatin structures. However, the in vivo roles of H1 are poorly understood2. Here we show that the local density of H1 controls the balance of repressive and active chromatin domains by promoting genomic compaction. We generated a conditional triple-H1-knockout mouse strain and depleted H1 in haematopoietic cells. H1 depletion in T cells leads to de-repression of T cell activation genes, a process that mimics normal T cell activation. Comparison of chromatin structure in normal and H1-depleted CD8+ T cells reveals that H1-mediated chromatin compaction occurs primarily in regions of the genome containing higher than average levels of H1: the chromosome conformation capture (Hi-C) B compartment and regions of the Hi-C A compartment marked by PRC2. Reduction of H1 stoichiometry leads to decreased H3K27 methylation, increased H3K36 methylation, B-to-A-compartment shifting and an increase in interaction frequency between compartments. In vitro, H1 promotes PRC2-mediated H3K27 methylation and inhibits NSD2-mediated H3K36 methylation. Mechanistically, H1 mediates these opposite effects by promoting physical compaction of the chromatin substrate. Our results establish H1 as a critical regulator of gene silencing through localized control of chromatin compaction, 3D genome organization and the epigenetic landscape.
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Affiliation(s)
| | - Sean E Healton
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Cary N Weiss
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Boris A Bartholdy
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Yair Botbol
- Department of Pathology, Albert Einstein College of Medicine, New York, NY, USA
| | - Laxmi N Mishra
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Dhruv S Sidhwani
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Tommy J Wilson
- Department of Neurology, Columbia University College of Physicians and Surgeons, Columbia University Medical Center, New York Presbyterian Hospital, New York, NY, USA
| | - Hugo B Pinto
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Maxim I Maron
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Karin A Skalina
- Department of Pathology, Albert Einstein College of Medicine, New York, NY, USA
| | - Laura Norwood Toro
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jie Zhao
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Chul-Hwan Lee
- Department of Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Pharmacology, Seoul National University College of Medicine, Seoul, Korea
| | - Harry Hou
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Nevin Yusufova
- Cell & Molecular Biology Graduate Program, Weill Cornell Medicine, New York, NY, USA
- Division of Hematology/Oncology, Department of Medicine, Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Cem Meydan
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
| | - Adewola Osunsade
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Yael David
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Biochemistry, Weill Cornell Medicine, New York, NY, USA
| | - Simone Sidoli
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, Philadelphia, PA, USA
- Department of Biochemistry, Albert Einstein College of Medicine, New York, NY, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Smilow Center for Translational Research, Philadelphia, PA, USA
| | - Winfried Edelmann
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA
| | - Fernando Macian
- Department of Pathology, Albert Einstein College of Medicine, New York, NY, USA
| | - Arthur I Skoultchi
- Department of Cell Biology, Albert Einstein College of Medicine, New York, NY, USA.
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16
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Louphrasitthiphol P, Siddaway R, Loffreda A, Pogenberg V, Friedrichsen H, Schepsky A, Zeng Z, Lu M, Strub T, Freter R, Lisle R, Suer E, Thomas B, Schuster-Böckler B, Filippakopoulos P, Middleton M, Lu X, Patton EE, Davidson I, Lambert JP, Wilmanns M, Steingrímsson E, Mazza D, Goding CR. Tuning Transcription Factor Availability through Acetylation-Mediated Genomic Redistribution. Mol Cell 2020; 79:472-487.e10. [PMID: 32531202 PMCID: PMC7427332 DOI: 10.1016/j.molcel.2020.05.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 04/01/2020] [Accepted: 05/19/2020] [Indexed: 11/06/2022]
Abstract
It is widely assumed that decreasing transcription factor DNA-binding affinity reduces transcription initiation by diminishing occupancy of sequence-specific regulatory elements. However, in vivo transcription factors find their binding sites while confronted with a large excess of low-affinity degenerate motifs. Here, using the melanoma lineage survival oncogene MITF as a model, we show that low-affinity binding sites act as a competitive reservoir in vivo from which transcription factors are released by mitogen-activated protein kinase (MAPK)-stimulated acetylation to promote increased occupancy of their regulatory elements. Consequently, a low-DNA-binding-affinity acetylation-mimetic MITF mutation supports melanocyte development and drives tumorigenesis, whereas a high-affinity non-acetylatable mutant does not. The results reveal a paradoxical acetylation-mediated molecular clutch that tunes transcription factor availability via genome-wide redistribution and couples BRAF to tumorigenesis. Our results further suggest that p300/CREB-binding protein-mediated transcription factor acetylation may represent a common mechanism to control transcription factor availability. Reducing transcription factor DNA-binding affinity increases activity in vivo Acetylation is triggered by MAPK signaling Acetylation leads to genome-wide transcription factor redistribution Acetylation of MITF drives tumorigenesis and melanocyte development
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Affiliation(s)
- Pakavarin Louphrasitthiphol
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK; Department of Gastrointestinal and Hepato-Biliary-Pancreatic Surgery, Faculty of Medicine, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8575, Japan
| | - Robert Siddaway
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Alessia Loffreda
- Experimental Imaging Center, Cancer Imaging Unit, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy; Fondazione CEN, European Center for Nanomedicine, 20133 Milan, Italy
| | - Vivian Pogenberg
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 25a, 22607 Hamburg, Germany & University Hamburg Medical Centre Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Hans Friedrichsen
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Alexander Schepsky
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK; Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Zhiqiang Zeng
- MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit and Edinburgh Cancer Research UK Centre, Crewe Road South, Edinburgh EH4 2XR, UK
| | - Min Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Thomas Strub
- Institut de Génetique et Biologie Moléculaire et Cellulaire (IGBMC), Equipe labéllisée Ligue contre le Cancer, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Rasmus Freter
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Richard Lisle
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Eda Suer
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Benjamin Thomas
- Central Proteomics Facility, Sir William Dunn Pathology School, Oxford University, Oxford OX1 3RE, UK
| | - Benjamin Schuster-Böckler
- Ludwig Institute for Cancer Research, Big Data Institute, University of Oxford, Headington, Oxford OX3 7LF, UK
| | - Panagis Filippakopoulos
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - Mark Middleton
- Oxford NIHR Biomedical Research Centre, Department of Oncology, Churchill Hospital, Oxford OX3 7LE, UK
| | - Xin Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK
| | - E Elizabeth Patton
- MRC Institute of Genetics and Molecular Medicine, MRC Human Genetics Unit and Edinburgh Cancer Research UK Centre, Crewe Road South, Edinburgh EH4 2XR, UK
| | - Irwin Davidson
- Institut de Génetique et Biologie Moléculaire et Cellulaire (IGBMC), Equipe labéllisée Ligue contre le Cancer, 1 rue Laurent Fries, 67404 Illkirch Cedex, France
| | - Jean-Philippe Lambert
- Department of Molecular Medicine and Cancer Research Centre, Université Laval, Quebec, QC, Canada; CHU de Québec Research Center, CHUL, 2705 Boulevard Laurier, Quebec G1V 4G2, QC, Canada
| | - Matthias Wilmanns
- European Molecular Biology Laboratory, Hamburg Unit, Notkestrasse 25a, 22607 Hamburg, Germany & University Hamburg Medical Centre Hamburg-Eppendorf, Martinistrasse 52, 20246 Hamburg, Germany
| | - Eiríkur Steingrímsson
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland
| | - Davide Mazza
- Experimental Imaging Center, Cancer Imaging Unit, IRCCS San Raffaele Scientific Institute, Via Olgettina 58, 20132 Milan, Italy; Fondazione CEN, European Center for Nanomedicine, 20133 Milan, Italy.
| | - Colin R Goding
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford OX3 7DQ, UK.
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17
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Bozek M, Gompel N. Developmental Transcriptional Enhancers: A Subtle Interplay between Accessibility and Activity: Considering Quantitative Accessibility Changes between Different Regulatory States of an Enhancer Deconvolutes the Complex Relationship between Accessibility and Activity. Bioessays 2020; 42:e1900188. [PMID: 32142172 DOI: 10.1002/bies.201900188] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 01/16/2020] [Indexed: 12/21/2022]
Abstract
Measurements of open chromatin in specific cell types are widely used to infer the spatiotemporal activity of transcriptional enhancers. How reliable are these predictions? In this review, it is argued that the relationship between the accessibility and activity of an enhancer is insufficiently described by simply considering open versus closed chromatin, or active versus inactive enhancers. Instead, recent studies focusing on the quantitative nature of accessibility signal reveal subtle differences between active enhancers and their different inactive counterparts: the closed silenced state and the accessible primed and repressed states. While the open structure as such is not a specific indicator of enhancer activity, active enhancers display a higher degree of accessibility than the primed and repressed states. Molecular mechanisms that may account for these quantitative differences are discussed. A model that relates molecular events at an enhancer to changes in its activity and accessibility in a developing tissue is also proposed.
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Affiliation(s)
- Marta Bozek
- Department Biochemie, Ludwig-Maximilians Universität München, Genzentrum, 81377, München, Germany
| | - Nicolas Gompel
- Fakultät für Biologie, Ludwig-Maximilians Universität München, Biozentrum, 82152, Planegg-Martinsried, Germany
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18
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Cai Y, Geacintov NE, Broyde S. Variable impact of conformationally distinct DNA lesions on nucleosome structure and dynamics: Implications for nucleotide excision repair. DNA Repair (Amst) 2019; 87:102768. [PMID: 32018112 DOI: 10.1016/j.dnarep.2019.102768] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/14/2019] [Accepted: 12/08/2019] [Indexed: 12/26/2022]
Abstract
The packaging of DNA in nucleosomes presents a barrier for biological transactions including replication, transcription and repair. However, despite years of research, how the DNA is freed from the histone proteins and thereby allows the molecular machines to access the DNA remains poorly understood. We are interested in global genomic nucleotide excision repair (GG-NER). It is established that the histones are obstacles to this process, and DNA lesions are repaired less efficiently in nucleosomes than in free DNA. In the present study, we utilized molecular dynamics simulations to elucidate the nature of the distortions and dynamics imposed in the nucleosome by a set of three structually different lesions that vary in GG-NER efficiencies in free DNA, and in nucleosomes [Shafirovich, Geacintov, et. al, 2019]. Two of these are bulky lesions derived from metabolic activation of the environmental carcinogen benzo[a]pyrene, the 10R (+)-cis-anti-B[a]P-N2-dG and the stereoisomeric 10S (+)-trans-anti-B[a]P-N2-dG, which respectively adopt base-displaced/intercalated and minor groove-aligned conformations in DNA. The third is a non-bulky lesion, the 5'R-8-cyclo-2'-deoxyguanosine cross-link, produced by reactive oxygen and nitrogen species; cyclopurine lesions are highly mutagenic. These adducts are placed near the dyad axis, and rotationally with the lesion-containing strand facing towards or away from the histones. While each lesion has distinct conformational characteristics that are retained in the nucleosome, a spectrum of structural and dynamic disturbances, from slight to substantial, are displayed that depend on the lesion's structure and position in the nucleosome. We hypothesize that these intrinsic structural and dynamic distinctions provide different signals to initiate the cascade of chromatin-opening processes, including acetylation and other post translational modifications, remodeling by ATP-dependent complexes and spontaneous unwrapping that regulate the rate of access to the lesion; this may translate ultimately into varying GG-NER efficiencies, including repair resistance when signals for access are too weak.
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Affiliation(s)
- Yuqin Cai
- Department of Biology, New York University, 100 Washington Square East, New York, NY, 10003, USA
| | - Nicholas E Geacintov
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY, 10003, USA
| | - Suse Broyde
- Department of Biology, New York University, 100 Washington Square East, New York, NY, 10003, USA.
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19
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Banerjee DR, Deckard CE, Zeng Y, Sczepanski JT. Acetylation of the histone H3 tail domain regulates base excision repair on higher-order chromatin structures. Sci Rep 2019; 9:15972. [PMID: 31685935 PMCID: PMC6828659 DOI: 10.1038/s41598-019-52340-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Accepted: 10/15/2019] [Indexed: 02/07/2023] Open
Abstract
Despite recent evidence suggesting that histone lysine acetylation contributes to base excision repair (BER) in cells, their exact mechanistic role remains unclear. In order to examine the influence of histone acetylation on the initial steps of BER, we assembled nucleosome arrays consisting of homogeneously acetylated histone H3 (H3K18 and H3K27) and measured the repair of a site-specifically positioned 2′-deoxyuridine (dU) residue by uracil DNA glycosylase (UDG) and apurinic/apyrimidinic endonuclease 1 (APE1). We find that H3K18ac and H3K27ac differentially influence the combined activities of UDG/APE1 on compact chromatin, suggesting that acetylated lysine residues on the H3 tail domain play distinct roles in regulating the initial steps of BER. In addition, we show that the effects of H3 tail domain acetylation on UDG/APE1 activity are at the nucleosome level and do not influence higher-order chromatin folding. Overall, these results establish a novel regulatory role for histone H3 acetylation during the initiation of BER on chromatin.
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Affiliation(s)
- Deb Ranjan Banerjee
- Department of Chemistry, National Institute of Technology, Durgapur, West Bengal, India
| | - Charles E Deckard
- Department of Chemistry, Texas A&M University, College Station, Texas, 77843, United States
| | - Yu Zeng
- Department of Microbial Pathogenesis and Immunology, Texas A&M University, College Station, Texas, 77843, United States
| | - Jonathan T Sczepanski
- Department of Chemistry, Texas A&M University, College Station, Texas, 77843, United States.
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20
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Bozek M, Cortini R, Storti AE, Unnerstall U, Gaul U, Gompel N. ATAC-seq reveals regional differences in enhancer accessibility during the establishment of spatial coordinates in the Drosophila blastoderm. Genome Res 2019; 29:771-783. [PMID: 30962180 PMCID: PMC6499308 DOI: 10.1101/gr.242362.118] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 03/26/2019] [Indexed: 12/21/2022]
Abstract
Establishment of spatial coordinates during Drosophila embryogenesis relies on differential regulatory activity of axis patterning enhancers. Concentration gradients of activator and repressor transcription factors (TFs) provide positional information to each enhancer, which in turn promotes transcription of a target gene in a specific spatial pattern. However, the interplay between an enhancer regulatory activity and its accessibility as determined by local chromatin organization is not well understood. We profiled chromatin accessibility with ATAC-seq in narrow, genetically tagged domains along the antero-posterior axis in the Drosophila blastoderm. We demonstrate that one-quarter of the accessible genome displays significant regional variation in its ATAC-seq signal immediately after zygotic genome activation. Axis patterning enhancers are enriched among the most variable intervals, and their accessibility changes correlate with their regulatory activity. In an embryonic domain where an enhancer receives a net activating TF input and promotes transcription, it displays elevated accessibility in comparison to a domain where it receives a net repressive input. We propose that differential accessibility is a signature of patterning cis-regulatory elements in the Drosophila blastoderm and discuss potential mechanisms by which accessibility of enhancers may be modulated by activator and repressor TFs.
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Affiliation(s)
- Marta Bozek
- Ludwig-Maximilians-Universität München, Department Biochemie, Genzentrum, 81377 München, Germany
| | - Roberto Cortini
- Ludwig-Maximilians-Universität München, Department Biochemie, Genzentrum, 81377 München, Germany
| | - Andrea Ennio Storti
- Ludwig-Maximilians-Universität München, Department Biochemie, Genzentrum, 81377 München, Germany
| | - Ulrich Unnerstall
- Ludwig-Maximilians-Universität München, Department Biochemie, Genzentrum, 81377 München, Germany
| | - Ulrike Gaul
- Ludwig-Maximilians-Universität München, Department Biochemie, Genzentrum, 81377 München, Germany
| | - Nicolas Gompel
- Ludwig-Maximilians Universität München, Fakultät für Biologie, Biozentrum, 82152 Planegg-Martinsried, Germany
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21
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Post-translational modifications and chromatin dynamics. Essays Biochem 2019; 63:89-96. [DOI: 10.1042/ebc20180067] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 12/21/2022]
Abstract
Abstract
The dynamic structure of chromatin is linked to gene regulation and many other biological functions. Consequently, it is of importance to understand the factors that regulate chromatin dynamics. While the in vivo analysis of chromatin has verified that histone post-translational modifications play a role in modulating DNA accessibility, the complex nuclear environment and multiplicity of modifications prevents clear conclusions as to how individual modifications influence chromatin dynamics in the cell. For this reason, in vitro analyses of model reconstituted nucleosomal arrays has been pivotal in understanding the dynamic nature of chromatin compaction and the affects that specific post-translational modifications can have on the higher order chromatin structure. In this mini-review, we briefly describe the dynamic chromatin structures that have been observed in vitro and the environmental conditions that give rise to these various conformational states. Our focus then turns to a discussion of the specific histone post-translational modifications that have been shown to alter formation of these higher order chromatin structures in vitro and how this may relate to the biological state and accessibility of chromatin in vivo.
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Mishra LN, Hayes JJ. A nucleosome-free region locally abrogates histone H1-dependent restriction of linker DNA accessibility in chromatin. J Biol Chem 2018; 293:19191-19200. [PMID: 30373774 DOI: 10.1074/jbc.ra118.005721] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/16/2018] [Indexed: 12/20/2022] Open
Abstract
Eukaryotic genomes are packaged into linker-oligonucleosome assemblies, providing compaction of genomic DNA and contributing to gene regulation and genome integrity. To define minimal requirements for initial steps in the transition of compact, closed chromatin to a transcriptionally active, open state, we developed a model in vitro system containing a single, unique, "target" nucleosome in the center of a 25-nucleosome array and evaluated the accessibility of the linker DNA adjacent to this target nucleosome. We found that condensation of H1-lacking chromatin results in ∼60-fold reduction in linker DNA accessibility and that mimics of acetylation within all four core histone tail domains of the target nucleosome synergize to increase accessibility ∼3-fold. Notably, stoichiometric binding of histone H1 caused >2 orders of magnitude reduction in accessibility that was marginally diminished by histone acetylation mimics. Remarkably, a nucleosome-free region (NFR) in place of the target nucleosome completely abrogated H1-dependent restriction of linker accessibility in the immediate vicinity of the NFR. Our results suggest that linker DNA is as inaccessible as DNA within the nucleosome core in fully condensed, H1-containing chromatin. They further imply that an unrecognized function of NFRs in gene promoter regions is to locally abrogate the severe restriction of linker DNA accessibility imposed by H1s.
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Affiliation(s)
- Laxmi Narayan Mishra
- From the Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642
| | - Jeffrey J Hayes
- From the Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642
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Cai Y, Fu I, Geacintov NE, Zhang Y, Broyde S. Synergistic effects of H3 and H4 nucleosome tails on structure and dynamics of a lesion-containing DNA: Binding of a displaced lesion partner base to the H3 tail for GG-NER recognition. DNA Repair (Amst) 2018; 65:73-78. [PMID: 29631253 PMCID: PMC5911426 DOI: 10.1016/j.dnarep.2018.02.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/29/2018] [Accepted: 02/26/2018] [Indexed: 02/06/2023]
Abstract
How DNA lesions in nucleosomes are recognized for global genome nucleotide excision repair (GG-NER) remains poorly understood, and the roles that histone tails may play remains to be established. Histone H3 and H4 N-terminal tails are of particular interest as their acetylation states are important in regulating nucleosomal functions in transcription, replication and repair. In particular the H3 tail has been the focus of recent attention as a site for the interaction with XPC, the GG-NER lesion recognition factor. Here we have investigated how the structure and dynamics of the DNA lesion cis-B[a]P-dG, derived from the environmental carcinogen benzo[a]pyrene (B[a]P), is impacted by the presence of flanking H3 and H4 tails. This lesion is well-repaired by GG-NER, and adopts a base-displaced/intercalated conformation in which the lesion partner C is displaced into the major groove. We used molecular dynamics simulations to obtain structural and dynamic characterizations for this lesion positioned in nucleosomal DNA so that it is bracketed by the H3 and H4 tails. The H4 tail was studied in unacetylated and acetylated states, while the H3 tail was unacetylated, its state when it binds XPC (Kakumu, Nakanishi et al., 2017). Our results reveal that upon acetylation, the H4 tail is released from the DNA surface; the H3 tail then forms a pocket that induces flipping and capture of the displaced lesion partner base C. This reveals synergistic effects of the behavior of the two tails. We hypothesize that the dual capability of the H3 tail to sense the displaced lesion partner base and to bind XPC could foster recognition of this lesion by XPC for initiation of GG-NER in nucleosomes.
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Affiliation(s)
- Yuqin Cai
- Department of Biology, New York University, 100 Washington Square East, New York, NY, 10003, USA
| | - Iwen Fu
- Department of Biology, New York University, 100 Washington Square East, New York, NY, 10003, USA
| | - Nicholas E Geacintov
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY, 10003, USA
| | - Yingkai Zhang
- Department of Chemistry, New York University, 100 Washington Square East, New York, NY, 10003, USA; NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Suse Broyde
- Department of Biology, New York University, 100 Washington Square East, New York, NY, 10003, USA.
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Morrison EA, Bowerman S, Sylvers KL, Wereszczynski J, Musselman CA. The conformation of the histone H3 tail inhibits association of the BPTF PHD finger with the nucleosome. eLife 2018; 7:31481. [PMID: 29648537 PMCID: PMC5953545 DOI: 10.7554/elife.31481] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 04/11/2018] [Indexed: 01/08/2023] Open
Abstract
Histone tails harbor a plethora of post-translational modifications that direct the function of chromatin regulators, which recognize them through effector domains. Effector domain/histone interactions have been broadly studied, but largely using peptide fragments of histone tails. Here, we extend these studies into the nucleosome context and find that the conformation adopted by the histone H3 tails is inhibitory to BPTF PHD finger binding. Using NMR spectroscopy and MD simulations, we show that the H3 tails interact robustly but dynamically with nucleosomal DNA, substantially reducing PHD finger association. Altering the electrostatics of the H3 tail via modification or mutation increases accessibility to the PHD finger, indicating that PTM crosstalk can regulate effector domain binding by altering nucleosome conformation. Together, our results demonstrate that the nucleosome context has a dramatic impact on signaling events at the histone tails, and highlights the importance of studying histone binding in the context of the nucleosome.
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Affiliation(s)
- Emma A Morrison
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, United States
| | - Samuel Bowerman
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois.,Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois
| | - Kelli L Sylvers
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, United States
| | - Jeff Wereszczynski
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois.,Center for Molecular Study of Condensed Soft Matter, Illinois Institute of Technology, Chicago, Illinois
| | - Catherine A Musselman
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, United States
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The 10-nm chromatin fiber and its relationship to interphase chromosome organization. Biochem Soc Trans 2017; 46:67-76. [PMID: 29263138 PMCID: PMC5818668 DOI: 10.1042/bst20170101] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 10/25/2017] [Accepted: 10/27/2017] [Indexed: 01/09/2023]
Abstract
A chromosome is a single long DNA molecule assembled along its length with nucleosomes and proteins. During interphase, a mammalian chromosome exists as a highly organized supramolecular globule in the nucleus. Here, we discuss new insights into how genomic DNA is packaged and organized within interphase chromosomes. Our emphasis is on the structural principles that underlie chromosome organization, with a particular focus on the intrinsic contributions of the 10-nm chromatin fiber, but not the regular 30-nm fiber. We hypothesize that the hierarchical globular organization of an interphase chromosome is fundamentally established by the self-interacting properties of a 10-nm zig-zag array of nucleosomes, while histone post-translational modifications, histone variants, and chromatin-associated proteins serve to mold generic chromatin domains into specific structural and functional entities.
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Fu I, Cai Y, Geacintov NE, Zhang Y, Broyde S. Nucleosome Histone Tail Conformation and Dynamics: Impacts of Lysine Acetylation and a Nearby Minor Groove Benzo[a]pyrene-Derived Lesion. Biochemistry 2017; 56:1963-1973. [PMID: 28304160 DOI: 10.1021/acs.biochem.6b01208] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Histone tails in nucleosomes play critical roles in regulation of many biological processes, including chromatin compaction, transcription, and DNA repair. Moreover, post-translational modifications, notably lysine acetylation, are crucial to these functions. While the tails have been intensively studied, how the structures and dynamics of tails are impacted by the presence of a nearby bulky DNA lesion is a frontier research area, and how these properties are impacted by tail lysine acetylation remains unexplored. To obtain molecular insight, we have utilized all atom 3 μs molecular dynamics simulations of nucleosome core particles (NCPs) to determine the impact of a nearby DNA lesion, 10S (+)-trans-anti-B[a]P-N2-dG-the major adduct derived from the procarcinogen benzo[a]pyrene-on H2B tail behavior in unacetylated and acetylated states. We similarly studied lesion-free NCPs to investigate the normal properties of the H2B tail in both states. In the lesion-free NCPs, charge neutralization upon lysine acetylation causes release of the tail from the DNA. When the lesion is present, it stably engulfs part of the nearby tail, impairing the interactions between DNA and tail. With the tail in an acetylated state, the lesion still interacts with part of it, although unstably. The lesion's partial entrapment of the tail should hinder the tail from interacting with other nucleosomes, and other proteins such as acetylases, deacetylases, and acetyl-lysine binding proteins, and thus disrupt critical tail-governed processes. Hence, the lesion would impede tail functions modulated by acetylation or deacetylation, causing aberrant chromatin structures and impaired biological transactions such as transcription and DNA repair.
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Affiliation(s)
| | | | | | - Yingkai Zhang
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai , Shanghai 200062, China
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