51
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Sakamoto M, Abe S, Miki Y, Miyanari Y, Sasaki H, Ishiuchi T. Dynamic nucleosome remodeling mediated by YY1 underlies early mouse development. Genes Dev 2023; 37:590-604. [PMID: 37532472 PMCID: PMC10499016 DOI: 10.1101/gad.350376.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 07/12/2023] [Indexed: 08/04/2023]
Abstract
Nucleosome positioning can alter the accessibility of DNA-binding proteins to their cognate DNA elements, and thus its precise control is essential for cell identity and function. Mammalian preimplantation embryos undergo temporal changes in gene expression and cell potency, suggesting the involvement of dynamic epigenetic control during this developmental phase. However, the dynamics of nucleosome organization during early development are poorly understood. In this study, using a low-input MNase-seq method, we show that nucleosome positioning is globally obscure in zygotes but becomes well defined during subsequent development. Down-regulation of the chromatin assembly in embryonic stem cells can partially reverse nucleosome organization into a zygote-like pattern, suggesting a possible link between the chromatin assembly pathway and fuzzy nucleosomes in zygotes. We also reveal that YY1, a zinc finger-containing transcription factor expressed upon zygotic genome activation, regulates the de novo formation of well-positioned nucleosome arrays at the regulatory elements through identifying YY1-binding sites in eight-cell embryos. The YY1-binding regions acquire H3K27ac enrichment around the eight-cell and morula stages, and YY1 depletion impairs the morula-to-blastocyst transition. Thus, our study delineates the remodeling of nucleosome organization and its underlying mechanism during early mouse development.
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Affiliation(s)
- Mizuki Sakamoto
- Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi 400-8510, Japan
| | - Shusaku Abe
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Yuka Miki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Yusuke Miyanari
- NanoLSI, Cancer Research Institute, Kanazawa University, Kanazawa 920-1192, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, Fukuoka 812-8582, Japan
| | - Takashi Ishiuchi
- Faculty of Life and Environmental Sciences, University of Yamanashi, Yamanashi 400-8510, Japan;
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52
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Yu W, Zhou R, Li N, Lei ZC, Guo D, Peng F, Li Y, Bai X, Feng S, Wang Y, He J, Yin S, Zeng X, He L, Gao Y, Li M, Guo YR, Liu K, Wang Y. Histone tyrosine sulfation by SULT1B1 regulates H4R3me2a and gene transcription. Nat Chem Biol 2023; 19:855-864. [PMID: 36805701 DOI: 10.1038/s41589-023-01267-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 01/16/2023] [Indexed: 02/22/2023]
Abstract
Tyrosine sulfation is a common posttranslational modification in mammals. To date, it has been thought to be limited to secreted and transmembrane proteins, but little is known about tyrosine sulfation on nuclear proteins. Here we report that SULT1B1 is a histone sulfotransferase that can sulfate the tyrosine 99 residue of nascent histone H3 in cytosol. The sulfated histone H3 can be transported into the nucleus and majorly deposited in the promoter regions of genes in chromatin. While the H3Y99 residue is buried inside octameric nucleosome, dynamically regulated subnucleosomal structures provide chromatin-H3Y99sulf the opportunity of being recognized and bound by PRMT1, which deposits H4R3me2a in chromatin. Disruption of H3Y99sulf reduces PRMT1 binding to chromatin, H4R3me2a level and gene transcription. These findings reveal the mechanisms underlying H3Y99 sulfation and its cross-talk with H4R3me2a to regulate gene transcription. This study extends the spectrum of tyrosine sulfation on nuclear proteins and the repertoire of histone modifications regulating chromatin functions.
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Affiliation(s)
- Weixing Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Runxin Zhou
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Nan Li
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhi-Chao Lei
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dingyuan Guo
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Fei Peng
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yan Li
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xue Bai
- Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Center for Research Equipment and Facilities, Westlake University, Hangzhou, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Shan Feng
- Mass Spectrometry & Metabolomics Core Facility, The Biomedical Research Core Facility, Center for Research Equipment and Facilities, Westlake University, Hangzhou, China
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Yu Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jie He
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Department of Neurosurgery, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Sibi Yin
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiao Zeng
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Leya He
- Department of Gastrointestinal Surgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yuan Gao
- Institute of Precision Medicine, Jining Medical University, Jining, China
| | - Mingchang Li
- Department of Neurosurgery, Renmin Hospital of Wuhan University, Wuhan, China
| | - Yusong R Guo
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ke Liu
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China.
| | - Yugang Wang
- Department of Biochemistry and Molecular Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
- Cell Architecture Research Center, Huazhong University of Science and Technology, Wuhan, China.
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53
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Nagae F, Takada S, Terakawa T. Histone chaperone Nap1 dismantles an H2A/H2B dimer from a partially unwrapped nucleosome. Nucleic Acids Res 2023; 51:5351-5363. [PMID: 37177996 PMCID: PMC10287947 DOI: 10.1093/nar/gkad396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 04/22/2023] [Accepted: 05/05/2023] [Indexed: 05/15/2023] Open
Abstract
DNA translocases, such as RNA polymerases, inevitably collide with nucleosomes on eukaryotic chromatin. Upon these collisions, histone chaperones are suggested to facilitate nucleosome disassembly and re-assembly. In this study, by performing in vitro transcription assays and molecular simulations, we found that partial unwrapping of a nucleosome by an RNA polymerase dramatically facilitates an H2A/H2B dimer dismantling from the nucleosome by Nucleosome Assembly Protein 1 (Nap1). Furthermore, the results uncovered molecular mechanisms of Nap1 functions in which the highly acidic C-terminal flexible tails of Nap1 contribute to the H2A/H2B binding by associating with the binding interface buried and not accessible to Nap1 globular domains, supporting the penetrating fuzzy binding mechanism seemingly shared across various histone chaperones. These findings have broad implications for the mechanisms by which histone chaperones process nucleosomes upon collisions with translocases in transcription, histone recycling and nucleosomal DNA repair.
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Affiliation(s)
- Fritz Nagae
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Tsuyoshi Terakawa
- Department of Biophysics, Graduate School of Science, Kyoto University, Kyoto, Japan
- PREST, Japan Science and Technology Agency (JST), Kawaguchi, Japan
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54
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Gòdia M, Lian Y, Naval-Sanchez M, Ponte I, Rodríguez-Gil JE, Sanchez A, Clop A. Micrococcal nuclease sequencing of porcine sperm suggests enriched co-location between retained histones and genomic regions related to semen quality and early embryo development. PeerJ 2023; 11:e15520. [PMID: 37361042 PMCID: PMC10290446 DOI: 10.7717/peerj.15520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 05/16/2023] [Indexed: 06/28/2023] Open
Abstract
The mammalian spermatozoon has a unique chromatin structure in which the majority of histones are replaced by protamines during spermatogenesis and a small fraction of nucleosomes are retained at specific locations of the genome. The sperm's chromatin structure remains unresolved in most animal species, including the pig. However, mapping the genomic locations of retained nucleosomes in sperm could help understanding the molecular basis of both sperm development and function as well as embryo development. This information could then be useful to identify molecular markers for sperm quality and fertility traits. Here, micrococcal nuclease digestion coupled with high throughput sequencing was performed on pig sperm to map the genomic location of mono- and sub-nucleosomal chromatin fractions in relation to a set of diverse functional elements of the genome, some of which were related to semen quality and early embryogenesis. In particular, the investigated elements were promoters, the different sections of the gene body, coding and non-coding RNAs present in the pig sperm, potential transcription factor binding sites, genomic regions associated to semen quality traits and repeat elements. The analysis yielded 25,293 and 4,239 peaks in the mono- and sub-nucleosomal fractions, covering 0.3% and 0.02% of the porcine genome, respectively. A cross-species comparison revealed positional conservation of the nucleosome retention in sperm between the pig data and a human dataset that found nucleosome enrichment in genomic regions of importance in development. Both gene ontology analysis of the genes mapping nearby the mono-nucleosomal peaks and the identification of putative transcription factor binding motifs within the mono- and the sub- nucleosomal peaks showed enrichment for processes related to sperm function and embryo development. There was significant motif enrichment for Znf263, which in humans was suggested to be a key regulator of genes with paternal preferential expression during early embryogenesis. Moreover, enriched positional intersection was found in the genome between the mono-nucleosomal peaks and both the RNAs present in pig sperm and the RNAs related to sperm quality. There was no co-location between GWAS hits for semen quality in swine and the nucleosomal sites. Finally, the data evidenced depletion of mono-nucleosomes in long interspersed nuclear elements and enrichment of sub-nucleosomes in short interspersed repeat elements.These results suggest that retained nucleosomes in sperm could both mark regulatory elements or genes expressed during spermatogenesis linked to semen quality and fertility and act as transcriptional guides during early embryogenesis. The results of this study support the undertaking of ambitious research using a larger number of samples to robustly assess the positional relationship between histone retention in sperm and the reproductive ability of boars.
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Affiliation(s)
- Marta Gòdia
- Centre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB-UB), Cerdanyola del Vallés, Catalonia, Spain
- Animal Breeding and Genomics, Wageningen University and Research, Wageninger, Netherlands
| | - Yu Lian
- Centre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB-UB), Cerdanyola del Vallés, Catalonia, Spain
| | | | - Inma Ponte
- Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, Catalonia, Spain
| | - Joan Enric Rodríguez-Gil
- Animal Medicine and Surgery, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, Catalonia, Spain
| | - Armand Sanchez
- Centre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB-UB), Cerdanyola del Vallés, Catalonia, Spain
- Animal and food sciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallés, Catalonia, Spain
| | - Alex Clop
- Centre for Research in Agricultural Genomics CRAG (CSIC-IRTA-UAB-UB), Cerdanyola del Vallés, Catalonia, Spain
- Consejo Superior de Investigaciones Científicas, Barcelona, Catalonia, Spain
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55
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Haase MAB, Lazar-Stefanita L, Ólafsson G, Wudzinska A, Shen MJ, Truong DM, Boeke JD. Human macroH2A1 drives nucleosome dephasing and genome instability in histone-humanized yeast. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.06.538725. [PMID: 37205538 PMCID: PMC10187286 DOI: 10.1101/2023.05.06.538725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In addition to replicative histones, eukaryotic genomes encode a repertoire of non-replicative variant histones providing additional layers of structural and epigenetic regulation. Here, we systematically replaced individual replicative human histones with non-replicative human variant histones using a histone replacement system in yeast. Variants H2A.J, TsH2B, and H3.5 complemented for their respective replicative counterparts. However, macroH2A1 failed to complement and its expression was toxic in yeast, negatively interacting with native yeast histones and kinetochore genes. To isolate yeast with "macroH2A1 chromatin" we decoupled the effects of its macro and histone fold domains, which revealed that both domains sufficed to override native yeast nucleosome positioning. Furthermore, both modified constructs of macroH2A1 exhibited lower nucleosome occupancy that correlated with decreased short-range chromatin interactions (<20 Kb), disrupted centromeric clustering, and increased chromosome instability. While supporting viability, macroH2A1 dramatically alters chromatin organization in yeast, leading to genome instability and massive fitness defects.
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Affiliation(s)
- Max A. B. Haase
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
- Vilcek Institute of Graduate Biomedical Sciences, NYU School of Medicine, New York, NY, 10016, USA
| | - Luciana Lazar-Stefanita
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
| | - Guðjón Ólafsson
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
| | - Aleksandra Wudzinska
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
| | - Michael J. Shen
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
| | - David M. Truong
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, 11201, USA
- Department of Pathology, NYU Langone Health, New York, NY 10016, USA
| | - Jef D. Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, 430 East 29th Street, New York, 10016, USA
- Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY 10016, USA
- Department of Biomedical Engineering, NYU Tandon School of Engineering, Brooklyn, NY, 11201, USA
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56
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Abril-Garrido J, Dienemann C, Grabbe F, Velychko T, Lidschreiber M, Wang H, Cramer P. Structural basis of transcription reduction by a promoter-proximal +1 nucleosome. Mol Cell 2023:S1097-2765(23)00255-1. [PMID: 37148879 DOI: 10.1016/j.molcel.2023.04.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/16/2023] [Accepted: 04/11/2023] [Indexed: 05/08/2023]
Abstract
At active human genes, the +1 nucleosome is located downstream of the RNA polymerase II (RNA Pol II) pre-initiation complex (PIC). However, at inactive genes, the +1 nucleosome is found further upstream, at a promoter-proximal location. Here, we establish a model system to show that a promoter-proximal +1 nucleosome can reduce RNA synthesis in vivo and in vitro, and we analyze its structural basis. We find that the PIC assembles normally when the edge of the +1 nucleosome is located 18 base pairs (bp) downstream of the transcription start site (TSS). However, when the nucleosome edge is located further upstream, only 10 bp downstream of the TSS, the PIC adopts an inhibited state. The transcription factor IIH (TFIIH) shows a closed conformation and its subunit XPB contacts DNA with only one of its two ATPase lobes, inconsistent with DNA opening. These results provide a mechanism for nucleosome-dependent regulation of transcription initiation.
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Affiliation(s)
- Julio Abril-Garrido
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Christian Dienemann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Frauke Grabbe
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Taras Velychko
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Michael Lidschreiber
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Haibo Wang
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
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57
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Hirashima S, Park S, Sugiyama H. Evaluation by Experimentation and Simulation of a FRET Pair Comprising Fluorescent Nucleobase Analogs in Nucleosomes. Chemistry 2023; 29:e202203961. [PMID: 36700521 PMCID: PMC10332638 DOI: 10.1002/chem.202203961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/25/2023] [Accepted: 01/25/2023] [Indexed: 01/27/2023]
Abstract
Förster resonance energy transfer (FRET) is an attractive tool for understanding biomolecular dynamics. FRET-based analysis of nucleosomes has the potential to fill the knowledge gaps between static structures and dynamic cellular behaviors. Compared with typical FRET pairs using bulky fluorophores introduced by flexible linkers, fluorescent nucleoside-based FRET pair has great potential since it can be fitted within the helical structures of nucleic acids. Herein we report on the construction of nucleosomes containing a nucleobase FRET pair and the investigation of experimental and theoretical FRET efficiencies through steady-state fluorescence spectroscopy and calculation based on molecular dynamics simulations, respectively. Distinguishable experimental FRET efficiencies were observed depending on the positions of FRET pairs in nucleosomal DNA. The tendency could be supported by theoretical study. This work suggests the possibility of our approach to analyze structural changes of nucleosomes by epigenetic modifications or internucleosomal interactions.
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Affiliation(s)
- Shingo Hirashima
- Department of Chemistry Graduate School of Science, Kyoto University Sakyo, Kyoto, 606-8502, Japan
| | - Soyoung Park
- Immunology Frontier Research Center (iFReC), Osaka University Yamadaoka, Suita, 565-0871, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry Graduate School of Science, Kyoto University Sakyo, Kyoto, 606-8502, Japan
- Institute for Integrated Cell-Material Science (iCeMS), Kyoto University Sakyo, Kyoto, 606-8501, Japan
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58
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Boulasiki P, Tan XW, Spinelli M, Riccio A. The NuRD Complex in Neurodevelopment and Disease: A Case of Sliding Doors. Cells 2023; 12:cells12081179. [PMID: 37190088 DOI: 10.3390/cells12081179] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 04/12/2023] [Accepted: 04/14/2023] [Indexed: 05/17/2023] Open
Abstract
The Nucleosome Remodelling and Deacetylase (NuRD) complex represents one of the major chromatin remodelling complexes in mammalian cells, uniquely coupling the ability to "open" the chromatin by inducing nucleosome sliding with histone deacetylase activity. At the core of the NuRD complex are a family of ATPases named CHDs that utilise the energy produced by the hydrolysis of the ATP to induce chromatin structural changes. Recent studies have highlighted the prominent role played by the NuRD in regulating gene expression during brain development and in maintaining neuronal circuitry in the adult cerebellum. Importantly, components of the NuRD complex have been found to carry mutations that profoundly affect neurological and cognitive development in humans. Here, we discuss recent literature concerning the molecular structure of NuRD complexes and how the subunit composition and numerous permutations greatly determine their functions in the nervous system. We will also discuss the role of the CHD family members in an array of neurodevelopmental disorders. Special emphasis will be given to the mechanisms that regulate the NuRD complex composition and assembly in the cortex and how subtle mutations may result in profound defects of brain development and the adult nervous system.
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Affiliation(s)
- Paraskevi Boulasiki
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Xiao Wei Tan
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Matteo Spinelli
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
- Neuroscience Department, Catholic University of the Sacred Heart, 00168 Rome, Italy
| | - Antonella Riccio
- UCL Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
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59
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Carraro M, Hendriks IA, Hammond CM, Solis-Mezarino V, Völker-Albert M, Elsborg JD, Weisser MB, Spanos C, Montoya G, Rappsilber J, Imhof A, Nielsen ML, Groth A. DAXX adds a de novo H3.3K9me3 deposition pathway to the histone chaperone network. Mol Cell 2023; 83:1075-1092.e9. [PMID: 36868228 PMCID: PMC10114496 DOI: 10.1016/j.molcel.2023.02.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 11/29/2022] [Accepted: 02/08/2023] [Indexed: 03/05/2023]
Abstract
A multitude of histone chaperones are required to support histones from their biosynthesis until DNA deposition. They cooperate through the formation of histone co-chaperone complexes, but the crosstalk between nucleosome assembly pathways remains enigmatic. Using exploratory interactomics, we define the interplay between human histone H3-H4 chaperones in the histone chaperone network. We identify previously uncharacterized histone-dependent complexes and predict the structure of the ASF1 and SPT2 co-chaperone complex, expanding the role of ASF1 in histone dynamics. We show that DAXX provides a unique functionality to the histone chaperone network, recruiting histone methyltransferases to promote H3K9me3 catalysis on new histone H3.3-H4 prior to deposition onto DNA. Hereby, DAXX provides a molecular mechanism for de novo H3K9me3 deposition and heterochromatin assembly. Collectively, our findings provide a framework for understanding how cells orchestrate histone supply and employ targeted deposition of modified histones to underpin specialized chromatin states.
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Affiliation(s)
- Massimo Carraro
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ivo A Hendriks
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Colin M Hammond
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | | | | | - Jonas D Elsborg
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Melanie B Weisser
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christos Spanos
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK; Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany
| | - Guillermo Montoya
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK; Technische Universität Berlin, Chair of Bioanalytics, Berlin, Germany
| | - Axel Imhof
- EpiQMAx GmbH, Planegg, Germany; Faculty of Medicine, Biomedical Center, Protein Analysis Unit, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Michael L Nielsen
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Anja Groth
- Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark; Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
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60
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Hu Y, Ma S, Kartha VK, Duarte FM, Horlbeck M, Zhang R, Shrestha R, Labade A, Kletzien H, Meliki A, Castillo A, Durand N, Mattei E, Anderson LJ, Tay T, Earl AS, Shoresh N, Epstein CB, Wagers A, Buenrostro JD. Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.28.533945. [PMID: 37034577 PMCID: PMC10081223 DOI: 10.1101/2023.03.28.533945] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Cis-regulatory elements control gene expression and are dynamic in their structure, reflecting changes to the composition of diverse effector proteins over time1-3. Here we sought to connect the structural changes at cis-regulatory elements to alterations in cellular fate and function. To do this we developed PRINT, a computational method that uses deep learning to correct sequence bias in chromatin accessibility data and identifies multi-scale footprints of DNA-protein interactions. We find that multi-scale footprints enable more accurate inference of TF and nucleosome binding. Using PRINT with single-cell multi-omics, we discover wide-spread changes to the structure and function of candidate cis-regulatory elements (cCREs) across hematopoiesis, wherein nucleosomes slide, expose DNA for TF binding, and promote gene expression. Activity segmentation using the co-variance across cell states identifies "sub-cCREs" as modular cCRE subunits of regulatory DNA. We apply this single-cell and PRINT approach to characterize the age-associated alterations to cCREs within hematopoietic stem cells (HSCs). Remarkably, we find a spectrum of aging alterations among HSCs corresponding to a global gain of sub-cCRE activity while preserving cCRE accessibility. Collectively, we reveal the functional importance of cCRE structure across cell states, highlighting changes to gene regulation at single-cell and single-base-pair resolution.
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Affiliation(s)
- Yan Hu
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Sai Ma
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
- Current address: Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029 USA
| | - Vinay K. Kartha
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Fabiana M. Duarte
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Max Horlbeck
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Ruochi Zhang
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Rojesh Shrestha
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Ajay Labade
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Heidi Kletzien
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
- Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA 02115
| | - Alia Meliki
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Andrew Castillo
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Neva Durand
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
| | - Eugenio Mattei
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
| | - Lauren J. Anderson
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
| | - Tristan Tay
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Andrew S. Earl
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
| | - Noam Shoresh
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
| | - Charles B. Epstein
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
| | - Amy Wagers
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
- Paul F. Glenn Center for the Biology of Aging, Harvard Medical School, Boston, MA 02115
| | - Jason D. Buenrostro
- Gene Regulation Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142 USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138 USA
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Jie L, Sanagi M, Luo Y, Maeda H, Fukao Y, Chiba Y, Yanagisawa S, Yamaguchi J, Takagi J, Sato T. Histone chaperone NUCLEOSOME ASSEMBLY PROTEIN 1 proteins affect plant growth under nitrogen deficient conditions in Arabidopsis thaliana. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2023; 40:93-98. [PMID: 38439935 PMCID: PMC10910346 DOI: 10.5511/plantbiotechnology.22.1219a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/19/2022] [Indexed: 03/06/2024]
Abstract
Nitrogen (N) availability is one of the most important factors regulating plant metabolism and growth as it affects global gene expression profiles. Dynamic changes in chromatin structure, including histone modifications and nucleosome assembly/disassembly, have been extensively shown to regulate gene expression under various environmental stresses in plants. However, the involvement of chromatin related changes in plant nutrient responses has been demonstrated only in a few studies to date. In this study, we investigated the function of histone chaperone NUCLEOSOME ASSEMBLY PROTEIN1 (NAP1) proteins under N deficient conditions in Arabidopsis. In the nap1;1 nap1;2 nap1;3 triple mutant (m123-1), the expression of N-responsive marker genes and growth of lateral roots were decreased under N deficient conditions. In addition, the m123-1 plants showed a delay in N deficiency-induced leaf senescence. Taken together, these results suggest that NAP1s affect plant growth under N deficient conditions in Arabidopsis.
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Affiliation(s)
- Linnan Jie
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Miho Sanagi
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Yongming Luo
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Haruna Maeda
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Yoichiro Fukao
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Yukako Chiba
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Shuichi Yanagisawa
- Plant Functional Biotechnology, Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Junji Yamaguchi
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Junpei Takagi
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Takeo Sato
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
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62
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Nucleosome Remodeling at the Yeast PHO8 and PHO84 Promoters without the Putatively Essential SWI/SNF Remodeler. Int J Mol Sci 2023; 24:ijms24054949. [PMID: 36902382 PMCID: PMC10003099 DOI: 10.3390/ijms24054949] [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: 12/05/2022] [Revised: 02/14/2023] [Accepted: 02/19/2023] [Indexed: 03/08/2023] Open
Abstract
Chromatin remodeling by ATP-dependent remodeling enzymes is crucial for all genomic processes, like transcription or replication. Eukaryotes harbor many remodeler types, and it is unclear why a given chromatin transition requires more or less stringently one or several remodelers. As a classical example, removal of budding yeast PHO8 and PHO84 promoter nucleosomes upon physiological gene induction by phosphate starvation essentially requires the SWI/SNF remodeling complex. This dependency on SWI/SNF may indicate specificity in remodeler recruitment, in recognition of nucleosomes as remodeling substrate or in remodeling outcome. By in vivo chromatin analyses of wild type and mutant yeast under various PHO regulon induction conditions, we found that overexpression of the remodeler-recruiting transactivator Pho4 allowed removal of PHO8 promoter nucleosomes without SWI/SNF. For PHO84 promoter nucleosome removal in the absence of SWI/SNF, an intranucleosomal Pho4 site, which likely altered the remodeling outcome via factor binding competition, was required in addition to such overexpression. Therefore, an essential remodeler requirement under physiological conditions need not reflect substrate specificity, but may reflect specific recruitment and/or remodeling outcomes.
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De Sarkar N, Patton RD, Doebley AL, Hanratty B, Adil M, Kreitzman AJ, Sarthy JF, Ko M, Brahma S, Meers MP, Janssens DH, Ang LS, Coleman IM, Bose A, Dumpit RF, Lucas JM, Nunez TA, Nguyen HM, McClure HM, Pritchard CC, Schweizer MT, Morrissey C, Choudhury AD, Baca SC, Berchuck JE, Freedman ML, Ahmad K, Haffner MC, Montgomery RB, Corey E, Henikoff S, Nelson PS, Ha G. Nucleosome Patterns in Circulating Tumor DNA Reveal Transcriptional Regulation of Advanced Prostate Cancer Phenotypes. Cancer Discov 2023; 13:632-653. [PMID: 36399432 PMCID: PMC9976992 DOI: 10.1158/2159-8290.cd-22-0692] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 10/01/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022]
Abstract
Advanced prostate cancers comprise distinct phenotypes, but tumor classification remains clinically challenging. Here, we harnessed circulating tumor DNA (ctDNA) to study tumor phenotypes by ascertaining nucleosome positioning patterns associated with transcription regulation. We sequenced plasma ctDNA whole genomes from patient-derived xenografts representing a spectrum of androgen receptor active (ARPC) and neuroendocrine (NEPC) prostate cancers. Nucleosome patterns associated with transcriptional activity were reflected in ctDNA at regions of genes, promoters, histone modifications, transcription factor binding, and accessible chromatin. We identified the activity of key phenotype-defining transcriptional regulators from ctDNA, including AR, ASCL1, HOXB13, HNF4G, and GATA2. To distinguish NEPC and ARPC in patient plasma samples, we developed prediction models that achieved accuracies of 97% for dominant phenotypes and 87% for mixed clinical phenotypes. Although phenotype classification is typically assessed by IHC or transcriptome profiling from tumor biopsies, we demonstrate that ctDNA provides comparable results with diagnostic advantages for precision oncology. SIGNIFICANCE This study provides insights into the dynamics of nucleosome positioning and gene regulation associated with cancer phenotypes that can be ascertained from ctDNA. New methods for classification in phenotype mixtures extend the utility of ctDNA beyond assessments of somatic DNA alterations with important implications for molecular classification and precision oncology. This article is highlighted in the In This Issue feature, p. 517.
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Affiliation(s)
- Navonil De Sarkar
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Pathology and Prostate Cancer Center of Excellence, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Robert D. Patton
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Anna-Lisa Doebley
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, Washington
- Medical Scientist Training Program, University of Washington, Seattle, Washington
| | - Brian Hanratty
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Mohamed Adil
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Adam J. Kreitzman
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Jay F. Sarthy
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Minjeong Ko
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Sandipan Brahma
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Michael P. Meers
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Derek H. Janssens
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Lisa S. Ang
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Ilsa M. Coleman
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Arnab Bose
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Ruth F. Dumpit
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Jared M. Lucas
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Talina A. Nunez
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Holly M. Nguyen
- Department of Urology, University of Washington, Seattle, Washington
| | | | - Colin C. Pritchard
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
| | - Michael T. Schweizer
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington
| | - Colm Morrissey
- Department of Urology, University of Washington, Seattle, Washington
| | - Atish D. Choudhury
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Sylvan C. Baca
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Matthew L. Freedman
- Dana-Farber Cancer Institute, Boston, Massachusetts
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Kami Ahmad
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Michael C. Haffner
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - R. Bruce Montgomery
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington
| | - Eva Corey
- Department of Urology, University of Washington, Seattle, Washington
| | - Steven Henikoff
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Howard Hughes Medical Institute, Chevy Chase, Maryland
| | - Peter S. Nelson
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Urology, University of Washington, Seattle, Washington
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Division of Oncology, Department of Medicine, University of Washington, Seattle, Washington
- Corresponding Authors: Gavin Ha, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109. Phone: 206-667-2802; E-mail: ; and Peter S. Nelson, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109. Phone: 206-667-3377; E-mail:
| | - Gavin Ha
- Division of Public Health Sciences, Fred Hutchinson Cancer Center, Seattle, Washington
- Division of Human Biology, Fred Hutchinson Cancer Center, Seattle, Washington
- Brotman Baty Institute for Precision Medicine, Seattle, Washington
- Department of Genome Sciences, University of Washington, Seattle, Washington
- Corresponding Authors: Gavin Ha, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109. Phone: 206-667-2802; E-mail: ; and Peter S. Nelson, Fred Hutchinson Cancer Center, 1100 Fairview Avenue North, Seattle, WA 98109. Phone: 206-667-3377; E-mail:
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64
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Singha R, Aggarwal R, Sanyal K. Negative regulation of biofilm development by the CUG-Ser1 clade-specific histone H3 variant is dependent on the canonical histone chaperone CAF-1 complex in Candida albicans. Mol Microbiol 2023; 119:574-585. [PMID: 36855815 DOI: 10.1111/mmi.15050] [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: 06/25/2022] [Revised: 02/21/2023] [Accepted: 02/26/2023] [Indexed: 03/02/2023]
Abstract
The CUG-Ser1 clade-specific histone H3 variant (H3VCTG ) has been reported to be a negative regulator of planktonic to biofilm growth transition in Candida albicans. The preferential binding of H3VCTG at the biofilm gene promoters makes chromatin repressive for the biofilm mode of growth. The two evolutionarily conserved chaperone complexes involved in incorporating histone H3 are CAF-1 and HIRA. In this study, we sought to identify the chaperone complex(es) involved in loading H3VCTG . We demonstrate that C. albicans cells lacking either Cac1 or Cac2 subunit of the CAF-1 chaperone complex, exhibit a hyper-filamentation phenotype on solid surfaces and form more robust biofilms than wild-type cells, thereby mimicking the phenotype of the H3VCTG null mutant. None of the subunits of the HIRA chaperone complex shows any significant difference in biofilm growth as compared to the wild type. The occupancy of H3VCTG is found to be significantly reduced at the promoters of biofilm genes in the absence of CAF-1 subunits. Hence, we provide evidence that CAF-1, a chaperone known to load canonical histone H3 in mammalian cells, is involved in chaperoning of variant histone H3VCTG at the biofilm gene promoters in C. albicans. Our findings also illustrate the acquisition of an unconventional role of the CAF-1 chaperone complex in morphogenesis in C. albicans.
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Affiliation(s)
- Rima Singha
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Rashi Aggarwal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
| | - Kaustuv Sanyal
- Molecular Mycology Laboratory, Molecular Biology and Genetics Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore, India
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65
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Simultaneous Measurement of DNA Methylation and Nucleosome Occupancy in Single Cells Using scNOMe-Seq. Methods Mol Biol 2023; 2611:231-247. [PMID: 36807071 DOI: 10.1007/978-1-0716-2899-7_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Single-cell Nucleosome Occupancy and Methylome sequencing (scNOMe-seq) is a multimodal assay that simultaneously measures endogenous DNA methylation and nucleosome occupancy (i.e., chromatin accessibility) in single cells. scNOMe-seq combines the activity of a GpC Methyltransferase, an enzyme which methylates cytosines in GpC dinucleotides, with bisulfite conversion, whereby unmethylated cytosines are converted into thymines. Because GpC Methyltransferase acts only on cytosines present in non-nucleosomal regions of the genome, the subsequent bisulfite conversion step not only detects the endogenous DNA methylation, but also reveals the genome-wide pattern of chromatin accessibility. Implementing this technology at the single-cell level helps to capture the dynamics governing methylation and accessibility vary across individual cells and cell types. Here, we provide a scalable plate-based protocol for preparing scNOMe-seq libraries from single nucleus suspensions.
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66
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Wang H, Schilbach S, Ninov M, Urlaub H, Cramer P. Structures of transcription preinitiation complex engaged with the +1 nucleosome. Nat Struct Mol Biol 2023; 30:226-232. [PMID: 36411341 PMCID: PMC9935396 DOI: 10.1038/s41594-022-00865-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 10/07/2022] [Indexed: 11/22/2022]
Abstract
The preinitiation complex (PIC) assembles on promoters of protein-coding genes to position RNA polymerase II (Pol II) for transcription initiation. Previous structural studies revealed the PIC on different promoters, but did not address how the PIC assembles within chromatin. In the yeast Saccharomyces cerevisiae, PIC assembly occurs adjacent to the +1 nucleosome that is located downstream of the core promoter. Here we present cryo-EM structures of the yeast PIC bound to promoter DNA and the +1 nucleosome located at three different positions. The general transcription factor TFIIH engages with the incoming downstream nucleosome and its translocase subunit Ssl2 (XPB in human TFIIH) drives the rotation of the +1 nucleosome leading to partial detachment of nucleosomal DNA and intimate interactions between TFIIH and the nucleosome. The structures provide insights into how transcription initiation can be influenced by the +1 nucleosome and may explain why the transcription start site is often located roughly 60 base pairs upstream of the dyad of the +1 nucleosome in yeast.
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Affiliation(s)
- Haibo Wang
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Cancer Institute of the Second Affiliated Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China
| | - Sandra Schilbach
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Momchil Ninov
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.,Institute of Clinical Chemistry, Bioanalytics Group, University Medical Center Göttingen, Göttingen, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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67
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Wang F, Feng X, He Q, Li H, Li H. The Saccharomyces cerevisiae Yta7 ATPase hexamer contains a unique bromodomain tier that functions in nucleosome disassembly. J Biol Chem 2023; 299:102852. [PMID: 36592926 PMCID: PMC9898759 DOI: 10.1016/j.jbc.2022.102852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 01/01/2023] Open
Abstract
The Saccharomyces cerevisiae Yta7 is a chromatin remodeler harboring a histone-interacting bromodomain (BRD) and two AAA+ modules. It is not well understood how Yta7 recognizes the histone H3 tail to promote nucleosome disassembly for DNA replication or RNA transcription. By cryo-EM analysis, here we show that Yta7 assembles a three-tiered hexamer with a top BRD tier, a middle AAA1 tier, and a bottom AAA2 tier. Unexpectedly, the Yta7 BRD stabilizes a four-stranded β-helix, termed BRD-interacting motif (BIM), of the largely disordered N-terminal region. The BIM motif is unique to the baker's yeast, and we show both BRD and BIM contribute to nucleosome recognition. We found that Yta7 binds both acetylated and nonacetylated H3 peptides but with a higher affinity for the unmodified peptide. This property is consistent with the absence of key residues of canonical BRDs involved in acetylated peptide recognition and the role of Yta7 in general nucleosome remodeling. Interestingly, the BRD tier exists in a spiral and a flat-ring form on top of the Yta7 AAA+ hexamer. The spiral is likely in a nucleosome-searching mode because the bottom BRD blocks the entry to the AAA+ chamber. The flat ring may be in a nucleosome disassembly state because the entry is unblocked and the H3 peptide has entered the AAA+ chamber and is stabilized by the AAA1 pore loops 1 and 2. Indeed, we show that the BRD tier is a flat ring when bound to the nucleosome. Overall, our study sheds light on the nucleosome disassembly by Yta7.
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Affiliation(s)
- Feng Wang
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Xiang Feng
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Qing He
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Hua Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, Michigan, USA.
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68
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Zhang M, Celis CD, Liu J, Bustamante C, Ren G. Conformational Change of Nucleosome Arrays prior to Phase Separation. RESEARCH SQUARE 2023:rs.3.rs-2460504. [PMID: 36711774 PMCID: PMC9882673 DOI: 10.21203/rs.3.rs-2460504/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Chromatin phase transition serves as a regulatory mechanism for eukaryotic transcription. Understanding this process requires the characterization of the nucleosome array structure in response to external stimuli prior to phase separation. However, the intrinsic flexibility and heterogeneity hinders the arrays' structure determination. Here we exploit advances in cryogenic electron tomography (cryo-ET) to determine the three-dimensional (3D) structure of each individual particle of mono-, di-, tri-, and tetranucleosome arrays. Statistical analysis reveals the ionic strength changes the angle between the DNA linker and nucleosome core particle (NCP), which regulate the overall morphology of nucleosome arrays. The finding that one-third of the arrays in the presence of H1 contain an NCP invaded by foreign DNA suggests an alternative function of H1 in constructing nucleosomal networks. The new insights into the nucleosome conformational changes prior to the intermolecular interaction stage extends our understanding of chromatin phase separation regulation.
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Affiliation(s)
- Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, USA
- Applied Science and Technology Graduate Group, University of California, Berkeley, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, USA
| | - César-Díaz Celis
- California Institute for Quantitative Biosciences, University of California, Berkeley, USA
- Howard Hughes Medical Institute, University of California, Berkeley, USA
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, USA
| | - Carlos Bustamante
- Applied Science and Technology Graduate Group, University of California, Berkeley, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, USA
- Howard Hughes Medical Institute, University of California, Berkeley, USA
- Department of Chemistry, University of California, Berkeley, USA
- Department of Physics, University of California, Berkeley, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, USA
- Molecular Biophysics and Integrative Bioimaging Division, Lawrence Berkeley National Laboratory, USA
- Kavli Energy Nanoscience Institute, University of California, Berkeley, USA
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, USA
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69
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Wu X, Xie Y, Zhao K, Lu J. Targeting the super elongation complex for oncogenic transcription driven tumor malignancies: Progress in structure, mechanisms and small molecular inhibitor discovery. Adv Cancer Res 2023; 158:387-421. [PMID: 36990537 DOI: 10.1016/bs.acr.2022.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Oncogenic transcription activation is associated with tumor development and resistance derived from chemotherapy or target therapy. The super elongation complex (SEC) is an important complex regulating gene transcription and expression in metazoans closely related to physiological activities. In normal transcriptional regulation, SEC can trigger promoter escape, limit proteolytic degradation of transcription elongation factors and increase the synthesis of RNA polymerase II (POL II), and regulate many normal human genes to stimulate RNA elongation. Dysregulation of SEC accompanied by multiple transcription factors in cancer promotes rapid transcription of oncogenes and induce cancer development. In this review, we summarized recent progress in understanding the mechanisms of SEC in regulating normal transcription, and importantly its roles in cancer development. We also highlighted the discovery of SEC complex target related inhibitors and their potential applications in cancer treatment.
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Affiliation(s)
- Xinyu Wu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yanqiu Xie
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China; Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China.
| | - Jing Lu
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China.
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70
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Zhao T, Lu J, Zhang H, Xue M, Pan J, Ma L, Berger F, Jiang D. Histone H3.3 deposition in seed is essential for the post-embryonic developmental competence in Arabidopsis. Nat Commun 2022; 13:7728. [PMID: 36513677 PMCID: PMC9747979 DOI: 10.1038/s41467-022-35509-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022] Open
Abstract
The acquisition of germination and post-embryonic developmental ability during seed maturation is vital for seed vigor, an important trait for plant propagation and crop production. How seed vigor is established in seeds is still poorly understood. Here, we report the crucial function of Arabidopsis histone variant H3.3 in endowing seeds with post-embryonic developmental potentials. H3.3 is not essential for seed formation, but loss of H3.3 results in severely impaired germination and post-embryonic development. H3.3 exhibits a seed-specific 5' gene end distribution and facilitates chromatin opening at regulatory regions in seeds. During germination, H3.3 is essential for proper gene transcriptional regulation. Moreover, H3.3 is constantly loaded at the 3' gene end, correlating with gene body DNA methylation and the restriction of chromatin accessibility and cryptic transcription at this region. Our results suggest a fundamental role of H3.3 in initiating chromatin accessibility at regulatory regions in seed and licensing the embryonic to post-embryonic transition.
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Affiliation(s)
- Ting Zhao
- grid.9227.e0000000119573309State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Jingyun Lu
- grid.9227.e0000000119573309State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Huairen Zhang
- grid.9227.e0000000119573309State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Mande Xue
- grid.9227.e0000000119573309State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Jie Pan
- grid.9227.e0000000119573309State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Lijun Ma
- grid.9227.e0000000119573309State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
| | - Frédéric Berger
- grid.24194.3a0000 0000 9669 8503Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Danhua Jiang
- grid.9227.e0000000119573309State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China ,grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, Beijing, China
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71
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Muñoz S, Jones A, Bouchoux C, Gilmore T, Patel H, Uhlmann F. Functional crosstalk between the cohesin loader and chromatin remodelers. Nat Commun 2022; 13:7698. [PMID: 36509793 PMCID: PMC9744909 DOI: 10.1038/s41467-022-35444-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022] Open
Abstract
The cohesin complex participates in many structural and functional aspects of genome organization. Cohesin recruitment onto chromosomes requires nucleosome-free DNA and the Scc2-Scc4 cohesin loader complex that catalyzes topological cohesin loading. Additionally, the cohesin loader facilitates promoter nucleosome clearance in a yet unknown way, and it recognizes chromatin receptors such as the RSC chromatin remodeler. Here, we explore the cohesin loader-RSC interaction. Amongst multi-pronged contacts by Scc2 and Scc4, we find that Scc4 contacts a conserved patch on the RSC ATPase motor module. The cohesin loader directly stimulates in vitro nucleosome sliding by RSC, providing an explanation how it facilitates promoter nucleosome clearance. Furthermore, we observe cohesin loader interactions with a wide range of chromatin remodelers. Our results provide mechanistic insight into how the cohesin loader recognizes, as well as influences, the chromatin landscape, with implications for our understanding of human developmental disorders including Cornelia de Lange and Coffin-Siris syndromes.
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Affiliation(s)
- Sofía Muñoz
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK.
- Cell Cycle Control and the Maintenance of Genomic Stability Laboratory, Cancer Research Center (CIC), University of Salamanca, Salamanca, Spain.
| | - Andrew Jones
- Proteomics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Céline Bouchoux
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK
| | - Tegan Gilmore
- Bioinformatics & Biostatistics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Harshil Patel
- Bioinformatics & Biostatistics Science Technology Platform, The Francis Crick Institute, London, UK
| | - Frank Uhlmann
- Chromosome Segregation Laboratory, The Francis Crick Institute, London, UK.
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72
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Barsoum M, Stenzel AT, Bochyńska A, Kuo CC, Tsompanidis A, Sayadi-Boroujeni R, Bussmann P, Lüscher-Firzlaff J, Costa IG, Lüscher B. Loss of the Ash2l subunit of histone H3K4 methyltransferase complexes reduces chromatin accessibility at promoters. Sci Rep 2022; 12:21506. [PMID: 36513698 PMCID: PMC9747801 DOI: 10.1038/s41598-022-25881-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Changes in gene expression programs are intimately linked to cell fate decisions. Post-translational modifications of core histones contribute to control gene expression. Methylation of lysine 4 of histone H3 (H3K4) correlates with active promoters and gene transcription. This modification is catalyzed by KMT2 methyltransferases, which require interaction with 4 core subunits, WDR5, RBBP5, ASH2L and DPY30, for catalytic activity. Ash2l is necessary for organismal development and for tissue homeostasis. In mouse embryo fibroblasts (MEFs), Ash2l loss results in gene repression, provoking a senescence phenotype. We now find that upon knockout of Ash2l both H3K4 mono- and tri-methylation (H3K4me1 and me3, respectively) were deregulated. In particular, loss of H3K4me3 at promoters correlated with gene repression, especially at CpG island promoters. Ash2l loss resulted in increased loading of histone H3 and reduced chromatin accessibility at promoters, accompanied by an increase of repressing and a decrease of activating histone marks. Moreover, we observed altered binding of CTCF upon Ash2l loss. Lost and gained binding was noticed at promoter-associated and intergenic sites, respectively. Thus, Ash2l loss and reduction of H3K4me3 correlate with altered chromatin accessibility and transcription factor binding. These findings contribute to a more detailed understanding of mechanistic consequences of H3K4me3 loss and associated repression of gene transcription and thus of the observed cellular consequences.
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Affiliation(s)
- Mirna Barsoum
- grid.1957.a0000 0001 0728 696XInstitute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Alexander T. Stenzel
- grid.1957.a0000 0001 0728 696XInstitute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Agnieszka Bochyńska
- grid.1957.a0000 0001 0728 696XInstitute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Chao-Chung Kuo
- grid.1957.a0000 0001 0728 696XInstitute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany ,grid.1957.a0000 0001 0728 696XInterdisciplinary Center for Clinical Research (IZKF), Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Alexander Tsompanidis
- grid.1957.a0000 0001 0728 696XInstitute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Roksaneh Sayadi-Boroujeni
- grid.1957.a0000 0001 0728 696XInstitute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Philip Bussmann
- grid.1957.a0000 0001 0728 696XInstitute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Juliane Lüscher-Firzlaff
- grid.1957.a0000 0001 0728 696XInstitute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Ivan G. Costa
- grid.1957.a0000 0001 0728 696XInstitute for Computational Genomics, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstrasse 30, 52074, Aachen, Germany.
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73
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Kunert F, Metzner FJ, Jung J, Höpfler M, Woike S, Schall K, Kostrewa D, Moldt M, Chen JX, Bantele S, Pfander B, Eustermann S, Hopfner KP. Structural mechanism of extranucleosomal DNA readout by the INO80 complex. SCIENCE ADVANCES 2022; 8:eadd3189. [PMID: 36490333 PMCID: PMC9733932 DOI: 10.1126/sciadv.add3189] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
The nucleosomal landscape of chromatin depends on the concerted action of chromatin remodelers. The INO80 remodeler specifically places nucleosomes at the boundary of gene regulatory elements, which is proposed to be the result of an ATP-dependent nucleosome sliding activity that is regulated by extranucleosomal DNA features. Here, we use cryo-electron microscopy and functional assays to reveal how INO80 binds and is regulated by extranucleosomal DNA. Structures of the regulatory A-module bound to DNA clarify the mechanism of linker DNA binding. The A-module is connected to the motor unit via an HSA/post-HSA lever element to chemomechanically couple the motor and linker DNA sensing. Two notable sites of curved DNA recognition by coordinated action of the four actin/actin-related proteins and the motor suggest how sliding by INO80 can be regulated by extranucleosomal DNA features. Last, the structures clarify the recruitment of YY1/Ies4 subunits and reveal deep architectural similarities between the regulatory modules of INO80 and SWI/SNF complexes.
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Affiliation(s)
- Franziska Kunert
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Felix J. Metzner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - James Jung
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Markus Höpfler
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Stephan Woike
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Kevin Schall
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Dirk Kostrewa
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Manuela Moldt
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jia-Xuan Chen
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Susanne Bantele
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Boris Pfander
- DNA Replication and Genome Integrity, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sebastian Eustermann
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Karl-Peter Hopfner
- Gene Center, Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany
- Corresponding author.
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74
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Milazzotto MP, Ispada J, de Lima CB. Metabolism-epigenetic interactions on in vitro produced embryos. Reprod Fertil Dev 2022; 35:84-97. [PMID: 36592974 DOI: 10.1071/rd22203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Metabolism and epigenetics, which reciprocally regulate each other in different cell types, are fundamental aspects of cellular adaptation to the environment. Evidence in cancer and stem cells has shown that the metabolic status modifies the epigenome while epigenetic mechanisms regulate the expression of genes involved in metabolic processes, thereby altering the metabolome. This crosstalk occurs as many metabolites serve as substrates or cofactors of chromatin-modifying enzymes. If we consider the intense metabolic dynamic and the epigenetic remodelling of the embryo, the comprehension of these regulatory networks will be important not only for understanding early embryonic development, but also to determine in vitro culture conditions that support embryo development and may insert positive regulatory marks that may persist until adult life. In this review, we focus on how metabolism may affect epigenetic reprogramming of the early stages of development, in particular acetylation and methylation of histone and DNA. We also present other metabolic modifications in bovine embryos, such as lactylation, highlighting the promising epigenetic and metabolic targets to improve conditions for in vitro embryo development.
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Affiliation(s)
- Marcella Pecora Milazzotto
- Laboratory of Embryo Metabolism and Epigenomic, Center of Natural and Human Science, Federal University of ABC, Santo Andre, SP, Brazil
| | - Jessica Ispada
- Laboratory of Embryo Metabolism and Epigenomic, Center of Natural and Human Science, Federal University of ABC, Santo Andre, SP, Brazil
| | - Camila Bruna de Lima
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des Sciences Animales, Faculté des Sciences de l'Agriculture et de l'Alimentation, Université Laval, Quebec City, QC, Canada
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75
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Brandani GB, Gopi S, Yamauchi M, Takada S. Molecular dynamics simulations for the study of chromatin biology. Curr Opin Struct Biol 2022; 77:102485. [PMID: 36274422 DOI: 10.1016/j.sbi.2022.102485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/05/2022] [Accepted: 09/18/2022] [Indexed: 12/14/2022]
Abstract
The organization of Eukaryotic DNA into chromatin has profound implications for the processing of genetic information. In the past years, molecular dynamics (MD) simulations proved to be a powerful tool to investigate the mechanistic basis of chromatin biology. We review recent all-atom and coarse-grained MD studies revealing how the structure and dynamics of chromatin underlie its biological functions. We describe the latest method developments; the structural fluctuations of nucleosomes and the various factors affecting them; the organization of chromatin fibers, with particular emphasis on its liquid-like character; the interactions and dynamics of transcription factors on chromatin; and how chromatin organization is modulated by molecular motors acting on DNA.
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Affiliation(s)
- Giovanni B Brandani
- Department of Biophysics, Graduate School of Science, Kyoto University, Japan.
| | - Soundhararajan Gopi
- Department of Biophysics, Graduate School of Science, Kyoto University, Japan
| | - Masataka Yamauchi
- Department of Biophysics, Graduate School of Science, Kyoto University, Japan
| | - Shoji Takada
- Department of Biophysics, Graduate School of Science, Kyoto University, Japan
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76
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Lizcano F, Bustamante L. Molecular perspectives in hypertrophic heart disease: An epigenetic approach from chromatin modification. Front Cell Dev Biol 2022; 10:1070338. [DOI: 10.3389/fcell.2022.1070338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 11/18/2022] [Indexed: 11/30/2022] Open
Abstract
Epigenetic changes induced by environmental factors are increasingly relevant in cardiovascular diseases. The most frequent molecular component in cardiac hypertrophy is the reactivation of fetal genes caused by various pathologies, including obesity, arterial hypertension, aortic valve stenosis, and congenital causes. Despite the multiple investigations performed to achieve information about the molecular components of this pathology, its influence on therapeutic strategies is relatively scarce. Recently, new information has been taken about the proteins that modify the expression of fetal genes reactivated in cardiac hypertrophy. These proteins modify the DNA covalently and induce changes in the structure of chromatin. The relationship between histones and DNA has a recognized control in the expression of genes conditioned by the environment and induces epigenetic variations. The epigenetic modifications that regulate pathological cardiac hypertrophy are performed through changes in genomic stability, chromatin architecture, and gene expression. Histone 3 trimethylation at lysine 4, 9, or 27 (H3-K4; -K9; -K27me3) and histone demethylation at lysine 9 and 79 (H3-K9; -K79) are mediators of reprogramming in pathologic hypertrophy. Within the chromatin architecture modifiers, histone demethylases are a group of proteins that have been shown to play an essential role in cardiac cell differentiation and may also be components in the development of cardiac hypertrophy. In the present work, we review the current knowledge about the influence of epigenetic modifications in the expression of genes involved in cardiac hypertrophy and its possible therapeutic approach.
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77
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Zhong Z, Wang Y, Wang M, Yang F, Thomas QA, Xue Y, Zhang Y, Liu W, Jami-Alahmadi Y, Xu L, Feng S, Marquardt S, Wohlschlegel JA, Ausin I, Jacobsen SE. Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis. Nat Commun 2022; 13:6970. [PMID: 36379930 PMCID: PMC9666630 DOI: 10.1038/s41467-022-34648-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 11/01/2022] [Indexed: 11/16/2022] Open
Abstract
Histone chaperones and chromatin remodelers control nucleosome dynamics, which are essential for transcription, replication, and DNA repair. The histone chaperone Anti-Silencing Factor 1 (ASF1) plays a central role in facilitating CAF-1-mediated replication-dependent H3.1 deposition and HIRA-mediated replication-independent H3.3 deposition in yeast and metazoans. Whether ASF1 function is evolutionarily conserved in plants is unknown. Here, we show that Arabidopsis ASF1 proteins display a preference for the HIRA complex. Simultaneous mutation of both Arabidopsis ASF1 genes caused a decrease in chromatin density and ectopic H3.1 occupancy at loci typically enriched with H3.3. Genetic, transcriptomic, and proteomic data indicate that ASF1 proteins strongly prefers the HIRA complex over CAF-1. asf1 mutants also displayed an increase in spurious Pol II transcriptional initiation and showed defects in the maintenance of gene body CG DNA methylation and in the distribution of histone modifications. Furthermore, ectopic targeting of ASF1 caused excessive histone deposition, less accessible chromatin, and gene silencing. These findings reveal the importance of ASF1-mediated histone deposition for proper epigenetic regulation of the genome.
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Affiliation(s)
- Zhenhui Zhong
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Yafei Wang
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences and Institute of Future Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Ming Wang
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Fan Yang
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences and Institute of Future Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Quentin Angelo Thomas
- grid.5254.60000 0001 0674 042XCopenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Yan Xue
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Yaxin Zhang
- grid.256111.00000 0004 1760 2876Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Wanlu Liu
- grid.512487.dZhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining, 314400 Zhejiang China
| | - Yasaman Jami-Alahmadi
- grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA 90095 USA
| | - Linhao Xu
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, 06466 Germany
| | - Suhua Feng
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los Angeles, CA 90095 USA
| | - Sebastian Marquardt
- grid.5254.60000 0001 0674 042XCopenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - James A. Wohlschlegel
- grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA 90095 USA
| | - Israel Ausin
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences and Institute of Future Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Steven E. Jacobsen
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095 USA
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Nozawa K, Takizawa Y, Pierrakeas L, Sogawa-Fujiwara C, Saikusa K, Akashi S, Luk E, Kurumizaka H. Cryo-electron microscopy structure of the H3-H4 octasome: A nucleosome-like particle without histones H2A and H2B. Proc Natl Acad Sci U S A 2022; 119:e2206542119. [PMID: 36322721 PMCID: PMC9659345 DOI: 10.1073/pnas.2206542119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 09/26/2022] [Indexed: 03/16/2023] Open
Abstract
The canonical nucleosome, which represents the major packaging unit of eukaryotic chromatin, has an octameric core composed of two histone H2A-H2B and H3-H4 dimers with ∼147 base pairs (bp) of DNA wrapped around it. Non-nucleosomal particles with alternative histone stoichiometries and DNA wrapping configurations have been found, and they could profoundly influence genome architecture and function. Using cryo-electron microscopy, we solved the structure of the H3-H4 octasome, a nucleosome-like particle with a di-tetrameric core consisting exclusively of the H3 and H4 histones. The core is wrapped by ∼120 bp of DNA in 1.5 negative superhelical turns, forming two stacked disks that are connected by a H4-H4' four-helix bundle. Three conformations corresponding to alternative interdisk angles were observed, indicating the flexibility of the H3-H4 octasome structure. In vivo crosslinking experiments detected histone-histone interactions consistent with the H3-H4 octasome model, suggesting that H3-H4 octasomes or related structural features exist in cells.
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Affiliation(s)
- Kayo Nozawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama, Kanagawa 226-8501, Japan
| | - Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Leonidas Pierrakeas
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794
| | - Chizuru Sogawa-Fujiwara
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
| | - Kazumi Saikusa
- National Metrology Institute of Japan, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8563, Japan
- Graduate School of Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Satoko Akashi
- Graduate School of Medical Life Science, Yokohama City University, Yokohama, Kanagawa 230-0045, Japan
| | - Ed Luk
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Tokyo 113-0032, Japan
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79
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Nagaraju GP, Dariya B, Kasa P, Peela S, El-Rayes BF. Epigenetics in hepatocellular carcinoma. Semin Cancer Biol 2022; 86:622-632. [PMID: 34324953 DOI: 10.1016/j.semcancer.2021.07.017] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/17/2021] [Accepted: 07/25/2021] [Indexed: 01/27/2023]
Abstract
Hepatocellular carcinoma (HCC) is the most common primary malignancy of the liver and has a high fatality rate. Genetic and epigenetic aberrations are commonly observed in HCC. The epigenetic processes include chromatin remodelling, histone alterations, DNA methylation, and noncoding RNA (ncRNA) expression and are connected with the progression and metastasis of HCC. Due to their potential reversibility, these epigenetic alterations are widely targeted for the development of biomarkers. In-depth understanding of the epigenetics of HCC is critical for developing rational clinical strategies that can provide a meaningful improvement in overall survival and prediction of therapeutic outcomes. In this article, we have summarised the epigenetic modifications involved in HCC progression and highlighted the potential biomarkers for diagnosis and drug development.
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Affiliation(s)
- Ganji Purnachandra Nagaraju
- Department of Hematology & Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Begum Dariya
- Department of Biosciences and Biotechnology, Banasthali University, Banasthali, 304022, Rajasthan, India
| | - Prameswari Kasa
- Dr. L.V. Prasad Diagnostics and Research Laboratory, Khairtabad, Hyderabad 500004, India
| | - Sujatha Peela
- Department of Biotechnology, Dr. B.R. Ambedkar University, Srikakulam, 532410 AP, India
| | - Bassel F El-Rayes
- Department of Hematology & Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA.
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80
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Yang ZK, Huang XL, Peng L. Transcriptome analysis reveals gene expression changes of the basidiomycetous yeast Apiotrichum mycotoxinivorans in response to ochratoxin A exposure. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 246:114146. [PMID: 36215880 DOI: 10.1016/j.ecoenv.2022.114146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 09/23/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Ochratoxin A (OTA) is one of the most common and deleterious mycotoxins found in food and feedstuffs worldwide; however, Apiotrichum mycotoxinivorans can detoxify OTA. Our results show that A. mycotoxinivorans GUM1709 efficiently degraded OTA, but it caused the accumulation of intracellular reactive oxygen species. The main aim of this study was to identify potential OTA-detoxifying enzymes and to explore the effects of OTA on A. mycotoxinivorans GMU1709. RNA-seq data revealed that 1643 and 1980 genes were significantly upregulated and downregulated, respectively, after OTA exposure. Functional enrichment analyses indicated that OTA exposure enhanced defense capability, protein transport, endocytosis, and energy metabolism; caused ribosomal stress; suppressed DNA replication and transcription; inhibited cell growth and division; and promoted cell death. The integration of secretome, gene expression, and molecular docking analyses revealed that two carboxypeptidase homologues (members of the metallocarboxypeptidase family) were most likely responsible for the detoxification of both extracellular and intracellular OTA. Superoxide dismutase and catalase were the main genes activated in response to oxidative stress. In addition, analysis of key genes associated with cell division and apoptosis showed that OTA exposure inhibited mitosis and promoted cell death. This study revealed the possible OTA response and detoxification mechanisms in A. mycotoxinivorans.
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Affiliation(s)
- Zhi-Kai Yang
- Innovation centre for Advanced Interdisciplinary Medicine, Key Laboratory of Biological Targeting Diagnosis, Therapy and Rehabilitation of Guangdong Higher Education Institutes, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Xue-Ling Huang
- Key Laboratory of Eutrophication and Red Tide Prevention of Guangdong Higher Education Institutes, College of Life Science and Technology, Jinan University, Guangzhou, China
| | - Liang Peng
- Department of Clinical Laboratory, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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81
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Characterizing and exploiting the many roles of aberrant H2B monoubiquitination in cancer pathogenesis. Semin Cancer Biol 2022; 86:782-798. [PMID: 34953650 DOI: 10.1016/j.semcancer.2021.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/08/2021] [Accepted: 12/19/2021] [Indexed: 01/27/2023]
Abstract
Monoubiquitination of histone H2B on lysine 120 (H2Bub1) is implicated in the control of multiple essential processes, including transcription, DNA damage repair and mitotic chromosome segregation. Accordingly, aberrant regulation of H2Bub1 can induce transcriptional reprogramming and genome instability that may promote oncogenesis. Remarkably, alterations of the ubiquitin ligases and deubiquitinating enzymes regulating H2Bub1 are emerging as ubiquitous features in cancer, further supporting the possibility that the misregulation of H2Bub1 is an underlying mechanism contributing to cancer pathogenesis. To date, aberrant H2Bub1 dynamics have been reported in multiple cancer types and are associated with transcriptional changes that promote oncogenesis in a cancer type-specific manner. Owing to the multi-functional nature of H2Bub1, misregulation of its writers and erasers may drive disease initiation and progression through additional synergistic processes. Accordingly, understanding the molecular determinants and pathogenic impacts associated with aberrant H2Bub1 regulation may reveal novel drug targets and therapeutic vulnerabilities that can be exploited to develop innovative precision medicine strategies that better combat cancer. In this review, we present the normal functions of H2Bub1 in the control of DNA-associated processes and describe the pathogenic implications associated with its misregulation in cancer. We further discuss the challenges coupled with the development of therapeutic strategies targeting H2Bub1 misregulation and expose the potential benefits of designing treatments that synergistically exploit the multiple functionalities of H2Bub1 to improve treatment selectivity and efficacy.
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82
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Chen X, Wang X, Liu W, Ren Y, Qu X, Li J, Yin X, Xu Y. Structures of +1 nucleosome-bound PIC-Mediator complex. Science 2022; 378:62-68. [PMID: 36201575 DOI: 10.1126/science.abn8131] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
RNA polymerase II-mediated eukaryotic transcription starts with the assembly of the preinitiation complex (PIC) on core promoters. The +1 nucleosome is well positioned about 40 base pairs downstream of the transcription start site (TSS) and is commonly known as a barrier of transcription. The +1 nucleosome-bound PIC-Mediator structures show that PIC-Mediator prefers binding to T40N nucleosome located 40 base pairs downstream of TSS and contacts T50N but not the T70N nucleosome. The nucleosome facilitates the organization of PIC-Mediator on the promoter by binding TFIIH subunit p52 and Mediator subunits MED19 and MED26 and may contribute to transcription initiation. PIC-Mediator exhibits multiple nucleosome-binding patterns, supporting a structural role of the +1 nucleosome in the coordination of PIC-Mediator assembly. Our study reveals the molecular mechanism of PIC-Mediator organization on chromatin and underscores the significance of the +1 nucleosome in regulating transcription initiation.
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Affiliation(s)
- Xizi Chen
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xinxin Wang
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Weida Liu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yulei Ren
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xuechun Qu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Jiabei Li
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Xiaotong Yin
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China
| | - Yanhui Xu
- Fudan University Shanghai Cancer Center, Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering, Department of Biochemistry and Biophysics, School of Life Sciences, Shanghai Key Laboratory of Radiation Oncology, and Shanghai Key Laboratory of Medical Epigenetics, Shanghai Medical College of Fudan University, Shanghai 200032, China.,The International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, China, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai 200032, China.,Human Phenome Institute, Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China
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83
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Takizawa Y, Kurumizaka H. Chromatin structure meets cryo-EM: Dynamic building blocks of the functional architecture. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194851. [PMID: 35952957 DOI: 10.1016/j.bbagrm.2022.194851] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Chromatin is a dynamic molecular complex composed of DNA and proteins that package the DNA in the nucleus of eukaryotic cells. The basic structural unit of chromatin is the nucleosome core particle, composed of ~150 base pairs of genomic DNA wrapped around a histone octamer containing two copies each of four histones, H2A, H2B, H3, and H4. Individual nucleosome core particles are connected by short linker DNAs, forming a nucleosome array known as a beads-on-a-string fiber. Higher-order structures of chromatin are closely linked to nuclear events such as replication, transcription, recombination, and repair. Recently, a variety of chromatin structures have been determined by single-particle cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), and their structural details have provided clues about the chromatin architecture functions in the cell. In this review, we highlight recent cryo-EM structural studies of a fundamental chromatin unit to clarify the functions of chromatin.
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Affiliation(s)
- Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
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84
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Wan WT, Hu P, Chang Z, Ren YD, Dong ZW, Yang J, Pan XY, He JW, Liu W, Liu GC, Zhao RP, Mao CY, Li J, Wang W, Li XY. Genome-wide survey of open chromatin regions in two swallowtail butterflies Papilio machaon and P. bianor. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2022; 111:e21952. [PMID: 35909310 DOI: 10.1002/arch.21952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/20/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Papilio machaon was assigned as the type species for all butterflies by Linnaeus and P. bianor is a congener but exhibits a great difference in morphology (especially larva and adult color pattern) and larval host plants from P. machaon. Thus, they are the ideal models to investigate genetic mechanisms underlying morphology and plasticity between congeners. The reference genomes of both species were dissected in our previous studies, but little is known about their regulatory genome and the epigenetic regulation of gene expression throughout developmental stages. Here, we profiled the chromatin accessibility and gene expression of three developmental stages (the 4th instar larva [L4], the 5th instar larva [L5], and pupa [P]) using transposase accessible chromatin sequencing (ATAC-seq) and RNA-seq. Results showed that many accessible chromatin peaks were identified at three developmental stages (peak number, P. machaon: 44,977 [L4], 36,919 [L5], 47,147 [P]; P. bianor: 20,341 [L4], 44,668 [L5], 62,249 [P]). Moreover, the number of differentially accessible peaks and differentially expressed genes between larval stages of each butterfly species are significantly fewer than that between larval and pupal stages, suggesting a higher similarity within larvae and a significant difference between larvae and pupae. This study added the annotated information of chromatin accessibility genome-wide of the two papilionid species and will promote the investigation of gene regulation in butterfly evolution.
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Affiliation(s)
- Wen-Ting Wan
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Ping Hu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Zhou Chang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Yan-Dong Ren
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Zhi-Wei Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jie Yang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Xiang-Yu Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Jin-Wu He
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi, China
| | - Wei Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Gui-Chun Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Ruo-Ping Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Chu-Yang Mao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Jun Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shaanxi, China
- Center for Excellence in Animal Evolution and Genetics, Kunming, Yunnan, China
| | - Xue-Yan Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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85
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HIV-1 Preintegration Complex Preferentially Integrates the Viral DNA into Nucleosomes Containing Trimethylated Histone 3-Lysine 36 Modification and Flanking Linker DNA. J Virol 2022; 96:e0101122. [PMID: 36094316 PMCID: PMC9517705 DOI: 10.1128/jvi.01011-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
HIV-1 DNA is preferentially integrated into chromosomal hot spots by the preintegration complex (PIC). To understand the mechanism, we measured the DNA integration activity of PICs-extracted from infected cells-and intasomes, biochemically assembled PIC substructures using a number of relevant target substrates. We observed that PIC-mediated integration into human chromatin is preferred compared to genomic DNA. Surprisingly, nucleosomes lacking histone modifications were not preferred integration compared to the analogous naked DNA. Nucleosomes containing the trimethylated histone 3 lysine 36 (H3K36me3), an epigenetic mark linked to active transcription, significantly stimulated integration, but the levels remained lower than the naked DNA. Notably, H3K36me3-modified nucleosomes with linker DNA optimally supported integration mediated by the PIC but not by the intasome. Interestingly, optimal intasome-mediated integration required the cellular cofactor LEDGF. Unexpectedly, LEDGF minimally affected PIC-mediated integration into naked DNA but blocked integration into nucleosomes. The block for the PIC-mediated integration was significantly relieved by H3K36me3 modification. Mapping the integration sites in the preferred substrates revealed that specific features of the nucleosome-bound DNA are preferred for integration, whereas integration into naked DNA was random. Finally, biochemical and genetic studies demonstrate that DNA condensation by the H1 protein dramatically reduces integration, providing further evidence that features inherent to the open chromatin are preferred for HIV-1 integration. Collectively, these results identify the optimal target substrate for HIV-1 integration, report a mechanistic link between H3K36me3 and integration preference, and importantly, reveal distinct mechanisms utilized by the PIC for integration compared to the intasomes. IMPORTANCE HIV-1 infection is dependent on integration of the viral DNA into the host chromosomes. The preintegration complex (PIC) containing the viral DNA, the virally encoded integrase (IN) enzyme, and other viral/host factors carries out HIV-1 integration. HIV-1 integration is not dependent on the target DNA sequence, and yet the viral DNA is selectively inserted into specific "hot spots" of human chromosomes. A growing body of literature indicates that structural features of the human chromatin are important for integration targeting. However, the mechanisms that guide the PIC and enable insertion of the PIC-associated viral DNA into specific hot spots of the human chromosomes are not fully understood. In this study, we describe a biochemical mechanism for the preference of the HIV-1 DNA integration into open chromatin. Furthermore, our study defines a direct role for the histone epigenetic mark H3K36me3 in HIV-1 integration preference and identify an optimal substrate for HIV-1 PIC-mediated viral DNA integration.
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86
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Coakley-Youngs E, Ranatunga M, Richardson S, Getti G, Shorter S, Fivaz M. Autism-associated CHD8 keeps proliferation of human neural progenitors in check by lengthening the G1 phase of the cell cycle. Biol Open 2022; 11:276883. [PMID: 36222238 PMCID: PMC9548376 DOI: 10.1242/bio.058941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 07/28/2022] [Indexed: 01/17/2023] Open
Abstract
ABSTRACT
De novo mutations (DNMs) in chromodomain helicase DNA binding protein 8 (CHD8) are associated with a specific subtype of autism characterized by enlarged heads and distinct cranial features. The vast majority of these DNMs are heterozygous loss-of-function mutations with high penetrance for autism. CHD8 is a chromatin remodeler that preferentially regulates expression of genes implicated in early development of the cerebral cortex. How CHD8 haploinsufficiency alters the normal developmental trajectory of the brain is poorly understood and debated. Using long-term single-cell imaging, we show that disruption of a single copy of CHD8 in human neural precursor cells (NPCs) markedly shortens the G1 phase of the cell cycle. Consistent with faster progression of CHD8+/− NPCs through G1 and the G1/S checkpoint, we observed increased expression of E cyclins and elevated phosphorylation of Erk in these mutant cells – two central signaling pathways involved in S phase entry. Thus, CHD8 keeps proliferation of NPCs in check by lengthening G1, and mono-allelic disruption of this gene alters cell-cycle timing in a way that favors self-renewing over neurogenic cell divisions. Our findings further predict enlargement of the neural progenitor pool in CHD8+/− developing brains, providing a mechanistic basis for macrocephaly in this autism subtype.
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Affiliation(s)
- Emma Coakley-Youngs
- Stem Cell & Gene Editing Laboratory, University of Greenwich at Medway 1 , Faculty of Science and Engineering, Kent ME4 4TB , UK
| | - Medhavi Ranatunga
- University of Greenwich at Medway 2 , Faculty of Science and Engineering, Kent ME4 4TB , UK
| | - Simon Richardson
- Exogenics Laboratory, University of Greenwich at Medway 3 , Faculty of Science and Engineering, Kent ME4 4TB , UK
| | - Giulia Getti
- University of Greenwich at Medway 2 , Faculty of Science and Engineering, Kent ME4 4TB , UK
| | - Susan Shorter
- Stem Cell & Gene Editing Laboratory, University of Greenwich at Medway 1 , Faculty of Science and Engineering, Kent ME4 4TB , UK
| | - Marc Fivaz
- Stem Cell & Gene Editing Laboratory, University of Greenwich at Medway 1 , Faculty of Science and Engineering, Kent ME4 4TB , UK
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87
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Millán-Zambrano G, Burton A, Bannister AJ, Schneider R. Histone post-translational modifications - cause and consequence of genome function. Nat Rev Genet 2022; 23:563-580. [PMID: 35338361 DOI: 10.1038/s41576-022-00468-7] [Citation(s) in RCA: 282] [Impact Index Per Article: 141.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/28/2022] [Indexed: 12/16/2022]
Abstract
Much has been learned since the early 1960s about histone post-translational modifications (PTMs) and how they affect DNA-templated processes at the molecular level. This understanding has been bolstered in the past decade by the identification of new types of histone PTM, the advent of new genome-wide mapping approaches and methods to deposit or remove PTMs in a locally and temporally controlled manner. Now, with the availability of vast amounts of data across various biological systems, the functional role of PTMs in important processes (such as transcription, recombination, replication, DNA repair and the modulation of genomic architecture) is slowly emerging. This Review explores the contribution of histone PTMs to the regulation of genome function by discussing when these modifications play a causative (or instructive) role in DNA-templated processes and when they are deposited as a consequence of such processes, to reinforce and record the event. Important advances in the field showing that histone PTMs can exert both direct and indirect effects on genome function are also presented.
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Affiliation(s)
- Gonzalo Millán-Zambrano
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Adam Burton
- Institute of Epigenetics and Stem Cells, Helmholtz Center Munich, Munich, Germany
| | - Andrew J Bannister
- Gurdon Institute and Department of Pathology, University of Cambridge, Cambridge, UK.
| | - Robert Schneider
- Institute of Functional Epigenetics, Helmholtz Center Munich, Munich, Germany.
- Faculty of Biology, Ludwig Maximilian University (LMU) of Munich, Munich, Germany.
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88
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FACT modulates the conformations of histone H2A and H2B N-terminal tails within nucleosomes. Commun Biol 2022; 5:814. [PMID: 35963897 PMCID: PMC9376062 DOI: 10.1038/s42003-022-03785-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 08/01/2022] [Indexed: 11/09/2022] Open
Abstract
Gene expression is regulated by the modification and accessibility of histone tails within nucleosomes. The histone chaperone FACT (facilitate chromatin transcription), comprising SPT16 and SSRP1, interacts with nucleosomes through partial replacement of DNA with the phosphorylated acidic intrinsically disordered (pAID) segment of SPT16; pAID induces an accessible conformation of the proximal histone H3 N-terminal tail (N-tail) in the unwrapped nucleosome with FACT. Here, we use NMR to probe the histone H2A and H2B tails in the unwrapped nucleosome. Consequently, both the H2A and H2B N-tails on the pAID-proximal side bind to pAID with robust interactions, which are important for nucleosome assembly with FACT. Furthermore, the conformations of these N-tails on the distal DNA-contact site are altered from those in the canonical nucleosome. Our findings highlight that FACT both proximally and distally regulates the conformations of the H2A and H2B N-tails in the asymmetrically unwrapped nucleosome.
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89
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Hatazawa S, Liu J, Takizawa Y, Zandian M, Negishi L, Kutateladze TG, Kurumizaka H. Structural basis for binding diversity of acetyltransferase p300 to the nucleosome. iScience 2022; 25:104563. [PMID: 35754730 PMCID: PMC9218434 DOI: 10.1016/j.isci.2022.104563] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 05/12/2022] [Accepted: 06/02/2022] [Indexed: 11/22/2022] Open
Abstract
p300 is a human acetyltransferase that associates with chromatin and mediates vital cellular processes. We now report the cryo-electron microscopy structures of the p300 catalytic core in complex with the nucleosome core particle (NCP). In the most resolved structure, the HAT domain and bromodomain of p300 contact nucleosomal DNA at superhelical locations 2 and 3, and the catalytic site of the HAT domain are positioned near the N-terminal tail of histone H4. Mutations of the p300-DNA interfacial residues of p300 substantially decrease binding to NCP. Three additional classes of p300-NCP complexes show different modes of the p300-NCP complex formation. Our data provide structural details critical to our understanding of the mechanism by which p300 acetylates multiple sites on the nucleosome.
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Affiliation(s)
- Suguru Hatazawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Jiuyang Liu
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Yoshimasa Takizawa
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Mohamad Zandian
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Lumi Negishi
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Tatiana G. Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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90
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Farnung L, Ochmann M, Garg G, Vos SM, Cramer P. Structure of a backtracked hexasomal intermediate of nucleosome transcription. Mol Cell 2022; 82:3126-3134.e7. [PMID: 35858621 DOI: 10.1016/j.molcel.2022.06.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/17/2022] [Accepted: 06/21/2022] [Indexed: 10/17/2022]
Abstract
During gene transcription, RNA polymerase II (RNA Pol II) passes nucleosomes with the help of various elongation factors. Here, we show that RNA Pol II achieves efficient nucleosome passage when the human elongation factors DSIF, PAF1 complex (PAF), RTF1, SPT6, and TFIIS are present. The cryo-EM structure of an intermediate of the nucleosome passage shows a partially unraveled hexasome that lacks the proximal H2A-H2B dimer and interacts with the RNA Pol II jaw, DSIF, and the CTR9trestle helix. RNA Pol II adopts a backtracked state with the RNA 3' end dislodged from the active site and bound in the RNA Pol II pore. Additional structures and biochemical data show that human TFIIS enters the RNA Pol II pore and stimulates the cleavage of the backtracked RNA and nucleosome passage.
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Affiliation(s)
- Lucas Farnung
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Moritz Ochmann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Gaurika Garg
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Seychelle M Vos
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
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91
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Mattes RD, Rowe SB, Ohlhorst SD, Brown AW, Hoffman DJ, Liska DJ, Feskens EJM, Dhillon J, Tucker KL, Epstein LH, Neufeld LM, Kelley M, Fukagawa NK, Sunde RA, Zeisel SH, Basile AJ, Borth LE, Jackson E. Valuing the Diversity of Research Methods to Advance Nutrition Science. Adv Nutr 2022; 13:1324-1393. [PMID: 35802522 PMCID: PMC9340992 DOI: 10.1093/advances/nmac043] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 04/08/2022] [Indexed: 12/13/2022] Open
Abstract
The ASN Board of Directors appointed the Nutrition Research Task Force to develop a report on scientific methods used in nutrition science to advance discovery, interpretation, and application of knowledge in the field. The genesis of this report was growing concern about the tone of discourse among nutrition professionals and the implications of acrimony on the productive study and translation of nutrition science. Too often, honest differences of opinion are cast as conflicts instead of areas of needed collaboration. Recognition of the value (and limitations) of contributions from well-executed nutrition science derived from the various approaches used in the discipline, as well as appreciation of how their layering will yield the strongest evidence base, will provide a basis for greater productivity and impact. Greater collaborative efforts within the field of nutrition science will require an understanding that each method or approach has a place and function that should be valued and used together to create the nutrition evidence base. Precision nutrition was identified as an important emerging nutrition topic by the preponderance of task force members, and this theme was adopted for the report because it lent itself to integration of many approaches in nutrition science. Although the primary audience for this report is nutrition researchers and other nutrition professionals, a secondary aim is to develop a document useful for the various audiences that translate nutrition research, including journalists, clinicians, and policymakers. The intent is to promote accurate, transparent, verifiable evidence-based communication about nutrition science. This will facilitate reasoned interpretation and application of emerging findings and, thereby, improve understanding and trust in nutrition science and appropriate characterization, development, and adoption of recommendations.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Leonard H Epstein
- University at Buffalo Jacobs School of Medicine and Biomedical Sciences, Buffalo, NY, USA
| | | | - Michael Kelley
- Michael Kelley Nutrition Science Consulting, Wauwatosa, WI, USA
| | - Naomi K Fukagawa
- USDA Beltsville Human Nutrition Research Center, Beltsville, MD, USA
| | | | - Steven H Zeisel
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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92
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Asim MN, Ibrahim MA, Malik MI, Razzak I, Dengel A, Ahmed S. Histone-Net: a multi-paradigm computational framework for histone occupancy and modification prediction. COMPLEX INTELL SYST 2022. [DOI: 10.1007/s40747-022-00802-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
AbstractDeep exploration of histone occupancy and covalent post-translational modifications (e.g., acetylation, methylation) is essential to decode gene expression regulation, chromosome packaging, DNA damage, and transcriptional activation. Existing computational approaches are unable to precisely predict histone occupancy and modifications mainly due to the use of sub-optimal statistical representation of histone sequences. For the establishment of an improved histone occupancy and modification landscape for multiple histone markers, the paper in hand presents an end-to-end computational multi-paradigm framework “Histone-Net”. To learn local and global residue context aware sequence representation, Histone-Net generates unsupervised higher order residue embeddings (DNA2Vec) and presents a different application of language modelling, where it encapsulates histone occupancy and modification information while generating higher order residue embeddings (SuperDNA2Vec) in a supervised manner. We perform an intrinsic and extrinsic evaluation of both presented distributed representation learning schemes. A comprehensive empirical evaluation of Histone-Net over ten benchmark histone markers data sets for three different histone sequence analysis tasks indicates that SuperDNA2Vec sequence representation and softmax classifier-based approach outperforms state-of-the-art approach by an average accuracy of 7%. To eliminate the overhead of training separate binary classifiers for all ten histone markers, Histone-Net is evaluated in multi-label classification paradigm, where it produces decent performance for simultaneous prediction of histone occupancy, acetylation, and methylation.
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93
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A study of strong nucleosomes in the human genome. iScience 2022; 25:104593. [PMID: 35789840 PMCID: PMC9249913 DOI: 10.1016/j.isci.2022.104593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 03/03/2022] [Accepted: 06/08/2022] [Indexed: 11/30/2022] Open
Abstract
Micrococcal nuclease (MNase) is widely used to map nucleosomes. However, nucleosomes are highly dynamic and susceptible to experimental conditions, resulting in extreme variability across nucleosome maps, which complicates the generation of accurate nucleosome organization data. We mapped nucleosomes from different individuals using improved MNase-seq. The improvements included setting different digestion levels (low, medium, high) and naked DNA correction to remove the noise caused by experimental manipulation and comparing maps to obtain the accurate position and occupancy of strong nucleosomes (SNs) in the whole genome. In addition, the characteristics of SNs were further excavated. SNs were enriched in Alu elements and near the centromere of Chr12. SNs contain some specific sequences, and the GC content of SNs is different from that of dynamic nucleosomes. The findings suggest that nucleosome location in the genome and the DNA sequence may affect nucleosome stability. Naked DNA correction improved the accuracy of nucleosome map in partial digestion Level of MNase digestion has effects on nucleosome organization A type of strong nucleosomes (SNs) exist across different nucleosome maps Nucleosome stability may be related to its location and the DNA sequence
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94
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Dijkwel Y, Tremethick DJ. The Role of the Histone Variant H2A.Z in Metazoan Development. J Dev Biol 2022; 10:jdb10030028. [PMID: 35893123 PMCID: PMC9326617 DOI: 10.3390/jdb10030028] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/12/2022] [Accepted: 06/23/2022] [Indexed: 12/10/2022] Open
Abstract
During the emergence and radiation of complex multicellular eukaryotes from unicellular ancestors, transcriptional systems evolved by becoming more complex to provide the basis for this morphological diversity. The way eukaryotic genomes are packaged into a highly complex structure, known as chromatin, underpins this evolution of transcriptional regulation. Chromatin structure is controlled by a variety of different epigenetic mechanisms, including the major mechanism for altering the biochemical makeup of the nucleosome by replacing core histones with their variant forms. The histone H2A variant H2A.Z is particularly important in early metazoan development because, without it, embryos cease to develop and die. However, H2A.Z is also required for many differentiation steps beyond the stage that H2A.Z-knockout embryos die. H2A.Z can facilitate the activation and repression of genes that are important for pluripotency and differentiation, and acts through a variety of different molecular mechanisms that depend upon its modification status, its interaction with histone and nonhistone partners, and where it is deposited within the genome. In this review, we discuss the current knowledge about the different mechanisms by which H2A.Z regulates chromatin function at various developmental stages and the chromatin remodeling complexes that determine when and where H2A.Z is deposited.
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95
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Wang Y, Wu L, Yuen KWY. The roles of transcription, chromatin organisation and chromosomal processes in holocentromere establishment and maintenance. Semin Cell Dev Biol 2022; 127:79-89. [PMID: 35042676 DOI: 10.1016/j.semcdb.2022.01.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 01/09/2022] [Accepted: 01/09/2022] [Indexed: 12/15/2022]
Abstract
The centromere is a unique functional region on each eukaryotic chromosome where the kinetochore assembles and orchestrates microtubule attachment and chromosome segregation. Unlike monocentromeres that occupy a specific region on the chromosome, holocentromeres are diffused along the length of the chromosome. Despite being less common, holocentromeres have been verified in almost 800 nematode, insect, and plant species. Understanding of the molecular and epigenetic regulation of holocentromeres is lagging that of monocentromeres. Here we review how permissive locations for holocentromeres are determined across the genome, potentially by chromatin organisation, transcription, and non-coding RNAs, specifically in the nematode C. elegans. In addition, we discuss how holocentric CENP-A or CENP-T-containing nucleosomes are recruited and deposited, through the help of histone chaperones, licensing factors, and condensin complexes, both during de novo holocentromere establishment, and in each mitotic cell cycle. The process of resolving sister centromeres after DNA replication in holocentric organisms is also mentioned. Conservation and diversity between holocentric and monocentric organisms are highlighted, and outstanding questions are proposed.
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Affiliation(s)
- Yue Wang
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong
| | - Lillian Wu
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong; Epigenetics and Genome Stability Team, The Institute of Cancer Research, 237 Fulham Road, London SW3 6JB, United Kingdom
| | - Karen Wing Yee Yuen
- School of Biological Sciences, The University of Hong Kong, Kadoorie Biological Sciences Building, Pokfulam Road, Hong Kong.
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96
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Dalui S, Dasgupta A, Adhikari S, Das C, Roy S. Human testis-specific Y-encoded protein-like protein 5 is a histone H3/H4-specific chaperone that facilitates histone deposition in vitro. J Biol Chem 2022; 298:102200. [PMID: 35772497 PMCID: PMC9305336 DOI: 10.1016/j.jbc.2022.102200] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 11/20/2022] Open
Abstract
DNA and core histones are hierarchically packaged into a complex organization called chromatin. The nucleosome assembly protein (NAP) family of histone chaperones is involved in the deposition of histone complexes H2A/H2B and H3/H4 onto DNA and prevents nonspecific aggregation of histones. Testis-specific Y-encoded protein (TSPY)–like protein 5 (TSPYL5) is a member of the TSPY-like protein family, which has been previously reported to interact with ubiquitin-specific protease USP7 and regulate cell proliferation and is thus implicated in various cancers, but its interaction with chromatin has not been investigated. In this study, we characterized the chromatin association of TSPYL5 and found that it preferentially binds histone H3/H4 via its C-terminal NAP-like domain both in vitro and ex vivo. We identified the critical residues involved in the TSPYL5–H3/H4 interaction and further quantified the binding affinity of TSPYL5 toward H3/H4 using biolayer interferometry. We then determined the binding stoichiometry of the TSPYL5–H3/H4 complex in vitro using a chemical cross-linking assay and size-exclusion chromatography coupled with multiangle laser light scattering. Our results indicate that a TSPYL5 dimer binds to either two histone H3/H4 dimers or a single tetramer. We further demonstrated that TSPYL5 has a specific affinity toward longer DNA fragments and that the same histone-binding residues are also critically involved in its DNA binding. Finally, employing histone deposition and supercoiling assays, we confirmed that TSPYL5 is a histone chaperone responsible for histone H3/H4 deposition and nucleosome assembly. We conclude that TSPYL5 is likely a new member of the NAP histone chaperone family.
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Affiliation(s)
- Sambit Dalui
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India
| | - Anirban Dasgupta
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India
| | - Swagata Adhikari
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhaba National Institute, Mumbai, India
| | - Chandrima Das
- Biophysics and Structural Genomics Division, Saha Institute of Nuclear Physics, Kolkata, India; Homi Bhaba National Institute, Mumbai, India
| | - Siddhartha Roy
- Structural Biology and Bioinformatics Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Chemical Biology, Kolkata, India.
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97
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Jonas F, Yaakov G, Barkai N. Rtt109 promotes nucleosome replacement ahead of the replication fork. Genome Res 2022; 32:1089-1098. [PMID: 35609993 DOI: 10.1101/gr.276674.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 05/05/2022] [Indexed: 11/25/2022]
Abstract
DNA replication perturbs chromatin by triggering the eviction, replacement, and incorporation of nucleosomes. How this dynamic is orchestrated in time and space is poorly understood. Here, we apply a genetically encoded sensor for histone exchange to follow the time-resolved histone H3 exchange profile in budding yeast cells undergoing slow synchronous replication in nucleotide-limiting conditions. We find that new histones are incorporated not only behind, but also ahead of the replication fork. We provide evidence that Rtt109, the S-phase-induced acetyltransferase, stabilizes nucleosomes behind the fork but promotes H3 replacement ahead of the fork. Increased replacement ahead of the fork is independent of the primary Rtt109 acetylation target H3K56 and rather results from Vps75-dependent Rtt109 activity toward the H3 N terminus. Our results suggest that, at least under nucleotide-limiting conditions, selective incorporation of differentially modified H3s behind and ahead of the replication fork results in opposing effects on histone exchange, likely reflecting the distinct challenges for genome stability at these different regions.
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Affiliation(s)
- Felix Jonas
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Gilad Yaakov
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Naama Barkai
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
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98
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Kreienbaum C, Paasche LW, Hake SB. H2A.Z's 'social' network: functional partners of an enigmatic histone variant. Trends Biochem Sci 2022; 47:909-920. [PMID: 35606214 DOI: 10.1016/j.tibs.2022.04.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 04/14/2022] [Accepted: 04/26/2022] [Indexed: 11/25/2022]
Abstract
The histone variant H2A.Z has been extensively studied to understand its manifold DNA-based functions. In the past years, researchers identified its specific binding partners, the 'H2A.Z interactome', that convey H2A.Z-dependent chromatin changes. Here, we summarize the latest findings regarding vertebrate H2A.Z-associated factors and focus on their roles in gene activation and repression, cell cycle regulation, (neuro)development, and tumorigenesis. Additionally, we demonstrate how protein-protein interactions and post-translational histone modifications can fine-tune the complex interplay of H2A.Z-regulated gene expression. Last, we review the most recent results on interactors of the two isoforms H2A.Z.1 and H2A.Z.2.1, which differ in only three amino acids, and focus on cancer-associated mutations of H2A and H2A.Z, which reveal fascinating insights into the functional importance of such minuscule changes.
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Affiliation(s)
| | - Lena W Paasche
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany
| | - Sandra B Hake
- Institute for Genetics, Justus-Liebig-University Giessen, Giessen, Germany.
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99
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Ranjan R, Snedeker J, Wooten M, Chu C, Bracero S, Mouton T, Chen X. Differential condensation of sister chromatids acts with Cdc6 to ensure asynchronous S-phase entry in Drosophila male germline stem cell lineage. Dev Cell 2022; 57:1102-1118.e7. [PMID: 35483360 PMCID: PMC9134767 DOI: 10.1016/j.devcel.2022.04.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 01/16/2022] [Accepted: 04/05/2022] [Indexed: 01/06/2023]
Abstract
During Drosophila melanogaster male germline stem cell (GSC) asymmetric division, preexisting old versus newly synthesized histones H3 and H4 are asymmetrically inherited. However, the biological outcomes of this phenomenon have remained unclear. Here, we tracked old and new histones throughout the GSC cell cycle through the use of high spatial and temporal resolution microscopy. We found unique features that differ between old and new histone-enriched sister chromatids, including differences in nucleosome density, chromosomal condensation, and H3 Ser10 phosphorylation. These distinct chromosomal features lead to their differential association with Cdc6, a pre-replication complex component, and subsequent asynchronous DNA replication initiation in the resulting daughter cells. Disruption of asymmetric histone inheritance abolishes differential Cdc6 association and asynchronous S-phase entry, demonstrating that histone asymmetry acts upstream of these critical cell-cycle progression events. Furthermore, disruption of these GSC-specific chromatin features leads to GSC defects, indicating a connection between histone inheritance, cell-cycle progression, and cell fate determination.
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Affiliation(s)
- Rajesh Ranjan
- Howard Hughes Medical Institute, Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Jonathan Snedeker
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Matthew Wooten
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Carolina Chu
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Sabrina Bracero
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Taylar Mouton
- Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA
| | - Xin Chen
- Howard Hughes Medical Institute, Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA; Department of Biology, The Johns Hopkins University, Baltimore, MD 21218, USA.
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100
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Dombrowski M, Engeholm M, Dienemann C, Dodonova S, Cramer P. Histone H1 binding to nucleosome arrays depends on linker DNA length and trajectory. Nat Struct Mol Biol 2022; 29:493-501. [PMID: 35581345 PMCID: PMC9113941 DOI: 10.1038/s41594-022-00768-w] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 04/01/2022] [Indexed: 01/17/2023]
Abstract
Throughout the genome, nucleosomes often form regular arrays that differ in nucleosome repeat length (NRL), occupancy of linker histone H1 and transcriptional activity. Here, we report cryo-EM structures of human H1-containing tetranucleosome arrays with four physiologically relevant NRLs. The structures show a zig-zag arrangement of nucleosomes, with nucleosomes 1 and 3 forming a stack. H1 binding to stacked nucleosomes depends on the NRL, whereas H1 always binds to the non-stacked nucleosomes 2 and 4. Short NRLs lead to altered trajectories of linker DNA, and these altered trajectories sterically impair H1 binding to the stacked nucleosomes in our structures. As the NRL increases, linker DNA trajectories relax, enabling H1 contacts and binding. Our results provide an explanation for why arrays with short NRLs are depleted of H1 and suited for transcription, whereas arrays with long NRLs show full H1 occupancy and can form transcriptionally silent heterochromatin regions. Cryo-EM structures of human H1-containing tetranucleosome arrays with distinct, physiological nucleosome repeat lengths reveal that nucleosomes assume a zig-zag arrangement and H1 binds to stacked nucleosomes with longer linker DNA.
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Affiliation(s)
- Marco Dombrowski
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Maik Engeholm
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Christian Dienemann
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Svetlana Dodonova
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany. .,Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Multidisciplinary Sciences, Göttingen, Germany.
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