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Bhardwaj SK, Hailu SG, Olufemi L, Brahma S, Kundu S, Hota SK, Persinger J, Bartholomew B. Dinucleosome specificity and allosteric switch of the ISW1a ATP-dependent chromatin remodeler in transcription regulation. Nat Commun 2020; 11:5913. [PMID: 33219211 PMCID: PMC7680125 DOI: 10.1038/s41467-020-19700-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 10/27/2020] [Indexed: 01/22/2023] Open
Abstract
Over the last 3 decades ATP-dependent chromatin remodelers have been thought to recognize chromatin at the level of single nucleosomes rather than higher-order organization of more than one nucleosome. We show the yeast ISW1a remodeler has such higher-order structural specificity, as manifested by large allosteric changes that activate the nucleosome remodeling and spacing activities of ISW1a when bound to dinucleosomes. Although the ATPase domain of Isw1 docks at the SHL2 position when ISW1a is bound to either mono- or di-nucleosomes, there are major differences in the interactions of the catalytic subunit Isw1 with the acidic pocket of nucleosomes and the accessory subunit Ioc3 with nucleosomal DNA. By mutational analysis and uncoupling of ISW1a's dinucleosome specificity, we find that dinucleosome recognition is required by ISW1a for proper chromatin organization at promoters; as well as transcription regulation in combination with the histone acetyltransferase NuA4 and histone H2A.Z exchanger SWR1.
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Affiliation(s)
- Saurabh K Bhardwaj
- The University of Texas MD Anderson Cancer Center, Department of Epigenetics & Molecular Carcinogenesis, Science Park, Smithville, TX, 78957, USA
- Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, USA
- Worldwide Research and Development, Pfizer Inc, Houston, USA
| | - Solomon G Hailu
- The University of Texas MD Anderson Cancer Center, Department of Epigenetics & Molecular Carcinogenesis, Science Park, Smithville, TX, 78957, USA
- Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, USA
- EpiCypher, Inc., Durham, USA
| | - Lola Olufemi
- National Institute of Neurological Disorders and Stroke, Bethesda, USA
| | - Sandipan Brahma
- The University of Texas MD Anderson Cancer Center, Department of Epigenetics & Molecular Carcinogenesis, Science Park, Smithville, TX, 78957, USA
- Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, USA
- Division of Basic Sciences, Fred Hutchinson Cancer Center, Seattle, USA
| | - Soumyadipta Kundu
- The University of Texas MD Anderson Cancer Center, Department of Epigenetics & Molecular Carcinogenesis, Science Park, Smithville, TX, 78957, USA
- Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, USA
- ZS Associates, Evanston, USA
| | - Swetansu K Hota
- University of California-San Francisco, Gladstone Institutes, San Francisco, USA
| | - Jim Persinger
- The University of Texas MD Anderson Cancer Center, Department of Epigenetics & Molecular Carcinogenesis, Science Park, Smithville, TX, 78957, USA
- Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, USA
| | - Blaine Bartholomew
- The University of Texas MD Anderson Cancer Center, Department of Epigenetics & Molecular Carcinogenesis, Science Park, Smithville, TX, 78957, USA.
- Center for Cancer Epigenetics, MD Anderson Cancer Center, Houston, USA.
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Speranzini V, Pilotto S, Sixma TK, Mattevi A. Touch, act and go: landing and operating on nucleosomes. EMBO J 2016; 35:376-88. [PMID: 26787641 DOI: 10.15252/embj.201593377] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/10/2015] [Indexed: 12/16/2022] Open
Abstract
Chromatin-associated enzymes are responsible for the installation, removal and reading of precise post-translation modifications on DNA and histone proteins. They are specifically recruited to the target gene by associated factors, and as a result of their activity, they contribute in modulating cell identity and differentiation. Structural and biophysical approaches are broadening our knowledge on these processes, demonstrating that DNA, histone tails and histone surfaces can each function as distinct yet functionally interconnected anchoring points promoting nucleosome binding and modification. The mechanisms underlying nucleosome recognition have been described for many histone modifiers and related readers. Here, we review the recent literature on the structural organization of these nucleosome-associated proteins, the binding properties that drive nucleosome modification and the methodological advances in their analysis. The overarching conclusion is that besides acting on the same substrate (the nucleosome), each system functions through characteristic modes of action, which bring about specific biological functions in gene expression regulation.
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Affiliation(s)
| | - Simona Pilotto
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Titia K Sixma
- Division of Biochemistry and Cancer Genomics Center, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Andrea Mattevi
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
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Liu Y, Zheng W, Zhang W, Chen N, Liu Y, Chen L, Zhou X, Chen X, Zheng H, Li X. Photoaffinity labeling of transcription factors by DNA-templated crosslinking. Chem Sci 2015; 6:745-751. [PMID: 28706637 PMCID: PMC5494549 DOI: 10.1039/c4sc01953a] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Accepted: 09/30/2014] [Indexed: 12/24/2022] Open
Abstract
Characterization of transcription factor-DNA interaction is of high importance in elucidating the molecular mechanisms of gene transcriptions. DNA-based affinity probes were developed to capture and identify transcription factors by covalent crosslinking; however, the requirement of a crosslinker on the affinity probe remains a disadvantage, as the crosslinker itself often interferes with the protein-DNA interactions. We report a dual-probe method able to capture DNA-binding transcription factors with unmodified protein-binding sites in scenarios where conventional probes have failed. We have also shown the method's converse application in selecting specific transcription factor-binding DNA sequences from a probe library and its extension to studying proteins recognizing epigenetic marks. This study may provide a new tool for exploring DNA-binding proteins in biology.
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Affiliation(s)
- Ying Liu
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Wenlu Zheng
- Key Laboratory of Chemical Genomics , School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , China 518055
| | - Wan Zhang
- Key Laboratory of Chemical Genomics , School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , China 518055
| | - Nan Chen
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Yang Liu
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Li Chen
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Xiaozhou Zhou
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Xingshuo Chen
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Haifeng Zheng
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
| | - Xiaoyu Li
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education , Beijing National Laboratory of Molecular Sciences , College of Chemistry and Molecular Engineering , Peking University , Beijing , China 100871 .
- Key Laboratory of Chemical Genomics , School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , China 518055
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Abstract
In the eukaryotic nucleus, processes of DNA metabolism such as transcription, DNA replication, and repair occur in the context of DNA packaged into nucleosomes and higher order chromatin structures. In order to overcome the barrier presented by chromatin structures to the protein machinery carrying out these processes, the cell relies on a class of enzymes called chromatin remodeling complexes which catalyze ATP-dependent restructuring and repositioning of nucleosomes. Chromatin remodelers are large multi-subunit complexes which all share a common SF2 helicase ATPase domain in their catalytic subunit, and are classified into four different families-SWI/SNF, ISWI, CHD, INO80-based on the arrangement of other domains in their catalytic subunit as well as their non-catalytic subunit composition. A large body of structural, biochemical, and biophysical evidence suggests chromatin remodelers operate as histone octamer-anchored directional DNA translocases in order to disrupt DNA-histone interactions and catalyze nucleosome sliding. Remodeling mechanisms are family-specific and depend on factors such as how the enzyme engages with nucleosomal and linker DNA, features of DNA loop intermediates, specificity for mono- or oligonucleosomal substrates, and ability to remove histones and exchange histone variants. Ultimately, the biological function of chromatin remodelers and their genomic targeting in vivo is regulated by each complex's subunit composition, association with chromatin modifiers and histone chaperones, and affinity for chromatin signals such as histone posttranslational modifications.
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Abstract
Epigenetic mechanisms regulate expression of the genome to generate various cell types during development or orchestrate cellular responses to external stimuli. Recent studies highlight that bacteria can affect the chromatin structure and transcriptional program of host cells by influencing diverse epigenetic factors (i.e., histone modifications, DNA methylation, chromatin-associated complexes, noncoding RNAs, and RNA splicing factors). In this article, we first review the molecular bases of the epigenetic language and then describe the current state of research regarding how bacteria can alter epigenetic marks and machineries. Bacterial-induced epigenetic deregulations may affect host cell function either to promote host defense or to allow pathogen persistence. Thus, pathogenic bacteria can be considered as potential epimutagens able to reshape the epigenome. Their effects might generate specific, long-lasting imprints on host cells, leading to a memory of infection that influences immunity and might be at the origin of unexplained diseases.
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Affiliation(s)
- Hélène Bierne
- Institut Pasteur, Unité des Interactions Bactéries-Cellules, Paris F-75015, France.
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