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Morioka S, Oishi T, Hatazawa S, Kakuta T, Ogoshi T, Umeda K, Kodera N, Kurumizaka H, Shibata M. High-Speed Atomic Force Microscopy Reveals the Nucleosome Sliding and DNA Unwrapping/Wrapping Dynamics of Tail-less Nucleosomes. NANO LETTERS 2024; 24:5246-5254. [PMID: 38602428 DOI: 10.1021/acs.nanolett.4c00801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Each nucleosome contains four types of histone proteins, each with a histone tail. These tails are essential for the epigenetic regulation of gene expression through post-translational modifications (PTMs). However, their influence on nucleosome dynamics at the single-molecule level remains undetermined. Here, we employed high-speed atomic force microscopy to visualize nucleosome dynamics in the absence of the N-terminal tail of each histone or all of the N-terminal tails. Loss of all tails stripped 6.7 base pairs of the nucleosome from the histone core, and the DNA entry-exit angle expanded by 18° from that of wild-type nucleosomes. Tail-less nucleosomes, particularly those without H2B and H3 tails, showed a 10-fold increase in dynamics, such as nucleosome sliding and DNA unwrapping/wrapping, within 0.3 s, emphasizing their role in histone-DNA interactions. Our findings illustrate that N-terminal histone tails stabilize the nucleosome structure, suggesting that histone tail PTMs modulate nucleosome dynamics.
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Affiliation(s)
- Shin Morioka
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Takumi Oishi
- 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
| | - 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
| | - Takahiro Kakuta
- Graduate School of Natural Science and Technology, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Tomoki Ogoshi
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kenichi Umeda
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Noriyuki Kodera
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, 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
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Mikihiro Shibata
- WPI Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
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2
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Nikitina T, Guiblet WM, Cui F, Zhurkin VB. Histone N-tails modulate sequence-specific positioning of nucleosomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.30.569460. [PMID: 38076910 PMCID: PMC10705531 DOI: 10.1101/2023.11.30.569460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
The precise mechanisms governing sequence-dependent positioning of nucleosomes on DNA remain unknown in detail. Existing algorithms, taking into account the sequence-dependent deformability of DNA and its interactions with the histone globular domains, predict rotational setting of only 65% of human nucleosomes mapped in vivo. To uncover novel factors responsible for the nucleosome positioning, we analyzed potential involvement of the histone N-tails in this process. To this aim, we reconstituted the H2A/H4 N-tailless nucleosomes on human BRCA1 DNA (~100 kb) and compared their positions and sequences with those of the wild-type nucleosomes. In the case of H2A tailless nucleosomes, the AT content of DNA sequences is changed locally at superhelical location (SHL) ±4, while maintaining the same rotational setting as their wild-type counterparts. Conversely, the H4 tailless nucleosomes display widespread changes of the AT content near SHL ±1 and SHL ±2, where the H4 N-tails interact with DNA. Furthermore, a substantial number of H4 tailless nucleosomes exhibit rotational setting opposite to that of the wild-type nucleosomes. Thus, our findings strongly suggest that the histone N-tails are operative in selection of nucleosome positions, which may have wide-ranging implications for epigenetic modulation of chromatin states.
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Affiliation(s)
- Tatiana Nikitina
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, US
| | - Wilfried M. Guiblet
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, US
| | - Feng Cui
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, USA
| | - Victor B. Zhurkin
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, US
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3
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Kotlar RM, Jones ND, Senavirathne G, Gardner AM, Messer RK, Tan YY, Rabe AJ, Fishel R, Yoder KE. Retroviral prototype foamy virus intasome binding to a nucleosome target does not determine integration efficiency. J Biol Chem 2021; 296:100550. [PMID: 33744295 PMCID: PMC8050864 DOI: 10.1016/j.jbc.2021.100550] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 01/15/2023] Open
Abstract
Retroviral integrases must navigate host DNA packaged as chromatin during integration of the viral genome. Prototype foamy virus (PFV) integrase (IN) forms a tetramer bound to two viral DNA (vDNA) ends in a complex termed an intasome. PFV IN consists of four domains: the amino terminal extension domain (NED), amino terminal domain (NTD), catalytic core domain (CCD), and carboxyl terminal domain (CTD). The domains of the two inner IN protomers have been visualized, as well as the CCDs of the two outer IN protomers. However, the roles of the amino and carboxyl terminal domains of the PFV intasome outer subunits during integration to a nucleosome target substrate are not clear. We used the well-characterized 601 nucleosome to assay integration activity as well as intasome binding. PFV intasome integration to 601 nucleosomes occurs in clusters at four independent sites. We find that the outer protomer NED and NTD domains have no significant effects on integration efficiency, site selection, or binding. The CTDs of the outer PFV intasome subunits dramatically affect nucleosome binding but have little effect on total integration efficiency. The outer PFV IN CTDs did significantly alter the integration efficiency at one site. Histone tails also significantly affect intasome binding, but have little impact on PFV integration efficiency or site selection. These results indicate that binding to nucleosomes does not correlate with integration efficiency and suggests most intasome-binding events are unproductive.
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Affiliation(s)
- Randi M Kotlar
- Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, USA
| | - Nathan D Jones
- Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, USA; The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Gayan Senavirathne
- Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, USA; The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Anne M Gardner
- Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, USA; The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Ryan K Messer
- Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, USA; The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Yow Yong Tan
- Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, USA; The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Anthony J Rabe
- Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, USA; The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Richard Fishel
- Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, USA; The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Kristine E Yoder
- Cancer Biology and Genetics, The Ohio State University College of Medicine, Columbus, Ohio, USA; The Ohio State University Comprehensive Cancer Center, Columbus, Ohio, USA.
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4
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Kladova OA, Kuznetsov NA, Fedorova OS. Initial stages of DNA Base Excision Repair in Nucleosomes. Mol Biol 2021. [DOI: 10.1134/s0026893321020096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Caffrey PJ, Delaney S. Nucleosome Core Particles Lacking H2B or H3 Tails Are Altered Structurally and Have Differential Base Excision Repair Fingerprints. Biochemistry 2021; 60:210-218. [PMID: 33426868 DOI: 10.1021/acs.biochem.0c00877] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A recently discovered post-translational modification of histone proteins is the irreversible proteolytic clipping of the histone N-terminal tail domains. This modification is involved in the regulation of various biological processes, including the DNA damage response. In this work, we used chemical footprinting to characterize the structural alterations to nucleosome core particles (NCPs) that result from a lack of a histone H2B or H3 tail. We also examine the influence of these histone tails on excision of the mutagenic lesion 1,N6-ethenoadenine (εA) by the repair enzyme alkyladenine DNA glycosylase. We found that the absence of the H2B or H3 tail results in altered DNA periodicity relative to that of native NCPs. We correlated these structural alterations to εA excision by utilizing a global analysis of 21 εA sites in NCPs and unincorporated duplex DNA. In comparison to native NCPs, there is enhanced excision of εA in tailless H2B NCPs in regions that undergo DNA unwrapping. This enhanced excision is not observed for tailless H3 NCPs; rather, excision is inhibited in more static areas of the NCP not prone to unwrapping. Our results support in vivo observations of alkylation damage profiles and the potential role of tail clipping as a mechanism for overcoming physical obstructions caused by packaging in NCPs but also reveal the potential inhibition of repair by tail clipping in some locations. Taken together, these results further our understanding of how base excision repair can be facilitated or diminished by histone tail removal and contribute to our understanding of the underlying mechanism that leads to mutational hot spots.
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Affiliation(s)
- Paul J Caffrey
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
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Yao Z, Chen Y, Cao W, Shyh‐Chang N. Chromatin-modifying drugs and metabolites in cell fate control. Cell Prolif 2020; 53:e12898. [PMID: 32979011 PMCID: PMC7653270 DOI: 10.1111/cpr.12898] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 12/13/2022] Open
Abstract
For multicellular organisms, it is essential to produce a variety of specialized cells to perform a dazzling panoply of functions. Chromatin plays a vital role in determining cellular identities, and it dynamically regulates gene expression in response to changing nutrient metabolism and environmental conditions. Intermediates produced by cellular metabolic pathways are used as cofactors or substrates for chromatin modification. Drug analogues of metabolites that regulate chromatin-modifying enzyme reactions can also regulate cell fate by adjusting chromatin organization. In recent years, there have been many studies about how chromatin-modifying drug molecules or metabolites can interact with chromatin to regulate cell fate. In this review, we systematically discuss how DNA and histone-modifying molecules alter cell fate by regulating chromatin conformation and propose a mechanistic model that explains the process of cell fate transitions in a concise and qualitative manner.
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Affiliation(s)
- Ziyue Yao
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yu Chen
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Wenhua Cao
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ng Shyh‐Chang
- State Key Laboratory of Stem Cell and Reproductive BiologyInstitute of ZoologyChinese Academy of SciencesBeijingChina
- Institute for Stem Cell and RegenerationChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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7
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Stormberg T, Stumme-Diers M, Lyubchenko YL. Sequence-dependent nucleosome nanoscale structure characterized by atomic force microscopy. FASEB J 2019; 33:10916-10923. [PMID: 31284760 PMCID: PMC6766637 DOI: 10.1096/fj.201901094r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 06/04/2019] [Indexed: 01/14/2023]
Abstract
DNA sequence plays an important role in the assembly of nucleosomes, and DNA motifs with high specificity to nucleosomes have been identified. At the same time, important questions such as how the DNA sequence changes DNA wrapping and how the DNA sequence contributes to the interaction between the nucleosomes remain unclear. Here, we addressed these questions by comparing nanoscale properties of nucleosomes assembled on the highest nucleosome positioning sequence, the 601 motif, and essentially random DNA sequences. We used atomic force microscopy to measure the nucleosome positions and the DNA wrapping. The studies showed that nucleosomes assemble on the nonspecific sequence without any preference for position on DNA, but they wrap the same DNA length as DNA of the same length with the 601 sequence. Experiments with longer DNA containing the 601 motif along with nonspecific DNA, capable of forming dinucleosomes, revealed that dinucleosomes assembled on hybrid sequences show a preference for positioning near each other, with one always assembling on the 601 motif. These findings point to the interaction between the nucleosomes and suggest that internucleosomal interactions may play a large role in nucleosome positioning.-Stormberg, T., Stumme-Diers, M., Lyubchenko, Y. L. Sequence-dependent nucleosome nanoscale structure characterized by atomic force microscopy.
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Affiliation(s)
- Tommy Stormberg
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Micah Stumme-Diers
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, Omaha, Nebraska, USA
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8
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Rodriguez Y, Duan M, Wyrick JJ, Smerdon MJ. A cassette of basic amino acids in histone H2B regulates nucleosome dynamics and access to DNA damage. J Biol Chem 2018; 293:7376-7386. [PMID: 29588367 PMCID: PMC5949990 DOI: 10.1074/jbc.ra117.000358] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Revised: 03/12/2018] [Indexed: 12/25/2022] Open
Abstract
Nucleosome dynamics, such as spontaneous DNA unwrapping, are postulated to have a critical role in regulating the access of DNA repair machinery to DNA lesions within nucleosomes. However, the specific histone domains that regulate nucleosome dynamics and the impact of such changes in intrinsic nucleosome dynamics on DNA repair are not well understood. Previous studies identified a highly conserved region in the N-terminal tail of histone H2B known as the histone H2Brepression (or HBR) domain, which has a significant influence on gene expression, chromatin assembly, and DNA damage formation and repair. However, the molecular mechanism(s) that may account for these observations are limited. In this study, we characterized the stability and dynamics of ΔHBR mutant nucleosome core particles (NCPs) in vitro by restriction enzyme accessibility (REA), FRET, and temperature-induced sliding of histone octamers. Our results indicate that ΔHBR-NCPs are more dynamic, with a larger steady-state fraction of the NCP population occupying the unwrapped state than for WT-NCPs. Additionally, ΔHBR-histone octamers are more susceptible to temperature-induced sliding on DNA than WT histone octamers. Furthermore, we show that the activity of base excision repair enzymes at uracil lesions and single nucleotide gaps is enhanced in a site-specific manner in ΔHBR-NCPs. This enhanced activity correlates well with regions exhibiting increased DNA unwrapping. Finally, removal of the HBR domain is not sufficient to completely alleviate the structural constraints imposed by histone octamers on the activity of base excision repair enzymes.
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Affiliation(s)
- Yesenia Rodriguez
- From Biochemistry and Biophysics, School of Molecular Biosciences, Pullman, Washington 99164-7520
| | - Mingrui Duan
- From Biochemistry and Biophysics, School of Molecular Biosciences, Pullman, Washington 99164-7520
| | - John J Wyrick
- From Biochemistry and Biophysics, School of Molecular Biosciences, Pullman, Washington 99164-7520; Center for Reproductive Biology, Washington State University, Pullman, Washington 99164-7520
| | - Michael J Smerdon
- From Biochemistry and Biophysics, School of Molecular Biosciences, Pullman, Washington 99164-7520.
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9
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Shaytan AK, Armeev GA, Goncearenco A, Zhurkin VB, Landsman D, Panchenko AR. Coupling between Histone Conformations and DNA Geometry in Nucleosomes on a Microsecond Timescale: Atomistic Insights into Nucleosome Functions. J Mol Biol 2015; 428:221-237. [PMID: 26699921 DOI: 10.1016/j.jmb.2015.12.004] [Citation(s) in RCA: 101] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Revised: 12/04/2015] [Accepted: 12/07/2015] [Indexed: 12/16/2022]
Abstract
An octamer of histone proteins wraps about 200bp of DNA into two superhelical turns to form nucleosomes found in chromatin. Although the static structure of the nucleosomal core particle has been solved, details of the dynamic interactions between histones and DNA remain elusive. We performed extensively long unconstrained, all-atom microsecond molecular dynamics simulations of nucleosomes including linker DNA segments and full-length histones in explicit solvent. For the first time, we were able to identify and characterize the rearrangements in nucleosomes on a microsecond timescale including the coupling between the conformation of the histone tails and the DNA geometry. We found that certain histone tail conformations promoted DNA bulging near its entry/exit sites, resulting in the formation of twist defects within the DNA. This led to a reorganization of histone-DNA interactions, suggestive of the formation of initial nucleosome sliding intermediates. We characterized the dynamics of the histone tails upon their condensation on the core and linker DNA and showed that tails may adopt conformationally constrained positions due to the insertion of "anchoring" lysines and arginines into the DNA minor grooves. Potentially, these phenomena affect the accessibility of post-translationally modified histone residues that serve as important sites for epigenetic marks (e.g., at H3K9, H3K27, H4K16), suggesting that interactions of the histone tails with the core and linker DNA modulate the processes of histone tail modifications and binding of the effector proteins. We discuss the implications of the observed results on the nucleosome function and compare our results to different experimental studies.
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Affiliation(s)
- Alexey K Shaytan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Grigoriy A Armeev
- Faculty of Biology, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Alexander Goncearenco
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Victor B Zhurkin
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Landsman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA.
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10
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Rodriguez Y, Hinz JM, Smerdon MJ. Accessing DNA damage in chromatin: Preparing the chromatin landscape for base excision repair. DNA Repair (Amst) 2015; 32:113-119. [PMID: 25957487 PMCID: PMC4522338 DOI: 10.1016/j.dnarep.2015.04.021] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
DNA damage in chromatin comes in many forms, including single base lesions that induce base excision repair (BER). We and others have shown that the structural location of DNA lesions within nucleosomes greatly influences their accessibility to repair enzymes. Indeed, a difference in the location of uracil as small as one-half turn of the DNA backbone on the histone surface can result in a 10-fold difference in the time course of its removal in vitro. In addition, the cell has evolved several interdependent processes capable of enhancing the accessibility of excision repair enzymes to DNA lesions in nucleosomes, including post-translational modification of histones, ATP-dependent chromatin remodeling and interchange of histone variants in nucleosomes. In this review, we focus on different factors that affect accessibility of BER enzymes to nucleosomal DNA.
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Affiliation(s)
- Yesenia Rodriguez
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, United States
| | - John M Hinz
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, United States
| | - Michael J Smerdon
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, United States.
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11
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Bowman GD, Poirier MG. Post-translational modifications of histones that influence nucleosome dynamics. Chem Rev 2015; 115:2274-95. [PMID: 25424540 PMCID: PMC4375056 DOI: 10.1021/cr500350x] [Citation(s) in RCA: 319] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Gregory D. Bowman
- T.
C. Jenkins Department of Biophysics, Johns
Hopkins University, Baltimore, Maryland 21218, United States
| | - Michael G. Poirier
- Department of Physics, and Department of
Chemistry and Biochemistry, The Ohio State
University, Columbus, Ohio 43210, United
States
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12
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Singh M, Bag SK, Bhardwaj A, Ranjan A, Mantri S, Nigam D, Sharma YK, Sawant SV. Global nucleosome positioning regulates salicylic acid mediated transcription in Arabidopsis thaliana. BMC PLANT BIOLOGY 2015; 15:13. [PMID: 25604550 PMCID: PMC4318435 DOI: 10.1186/s12870-014-0404-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Accepted: 12/22/2014] [Indexed: 05/09/2023]
Abstract
BACKGROUND The nucleosome positioning regulates the gene expression and many other DNA-related processes in eukaryotes. Genome-wide mapping of nucleosome positions and correlation of genome-wide nucleosomal remodeling with the changes in the gene expression can help us understanding gene regulation on genome level. RESULTS In the present study, we correlate the gene expression and the genomic nucleosomal remodeling in response to salicylic acid (SA) treatment in A. thaliana. We have mapped genome-wide nucleosomes by performing tiling microarray using 146 bp mononucleosomal template DNA. The average nucleosomal coverage is approximately 346 bp per nucleosome both under the control and the SA-treated conditions. The nucleosomal coverage is more in the coding region than in the 5' regulatory regions. We observe approximately 50% nucleosomal remodeling on SA treatment where significant nucleosomal depletion and nucleosomal enrichment around the transcription start site (TSS) occur in SA induced genes and SA repressed genes respectively in response to SA treatment. Especially in the case of the SA-induced group, the nucleosomal remodeling over the minimal promoter in response to SA is especially significant in the Non-expresser of PR1 (NPR1)-dependent genes. A detailed investigation of npr1-1 mutant confirms a distinct role of NPR1 in the nucleosome remodeling over the core promoter. We have also identified several motifs for various hormonal responses; including ABRE elements in the remodeled nucleosomal regions around the promoter region in the SA regulated genes. We have further identified that the W-box and TGACG/C motif, reported to play an important role in SA-mediated induction, are enriched in nucleosome free regions (NFRs) of the promoter region of the SA induced genes. CONCLUSIONS This is the first study reporting genome-wide effects of SA treatment on the chromatin architecture of A. thaliana. It also reports significant role of NPR1 in genome-wide nucleosomal remodeling in response to SA.
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Affiliation(s)
- Mala Singh
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India.
| | - Sumit Kumar Bag
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India.
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001, India.
| | - Archana Bhardwaj
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India.
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001, India.
| | - Amol Ranjan
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India.
| | - Shrikant Mantri
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India.
| | - Deepti Nigam
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India.
| | | | - Samir Vishwanath Sawant
- CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow, 226001, India.
- Academy of Scientific and Innovative Research (AcSIR), Anusandhan Bhawan, 2 Rafi Marg, New Delhi, 110 001, India.
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13
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Lone IN, Shukla MS, Charles Richard JL, Peshev ZY, Dimitrov S, Angelov D. Binding of NF-κB to nucleosomes: effect of translational positioning, nucleosome remodeling and linker histone H1. PLoS Genet 2013; 9:e1003830. [PMID: 24086160 PMCID: PMC3784511 DOI: 10.1371/journal.pgen.1003830] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 08/12/2013] [Indexed: 01/29/2023] Open
Abstract
NF-κB is a key transcription factor regulating the expression of inflammatory responsive genes. How NF-κB binds to naked DNA templates is well documented, but how it interacts with chromatin is far from being clear. Here we used a combination of UV laser footprinting, hydroxyl footprinting and electrophoretic mobility shift assay to investigate the binding of NF-κB to nucleosomal templates. We show that NF-κB p50 homodimer is able to bind to its recognition sequence, when it is localized at the edge of the core particle, but not when the recognition sequence is at the interior of the nucleosome. Remodeling of the nucleosome by the chromatin remodeling machine RSC was not sufficient to allow binding of NF-κB to its recognition sequence located in the vicinity of the nucleosome dyad, but RSC-induced histone octamer sliding allowed clearly detectable binding of NF-κB with the slid particle. Importantly, nucleosome dilution-driven removal of H2A–H2B dimer led to complete accessibility of the site located close to the dyad to NF-κB. Finally, we found that NF-κB was able to displace histone H1 and prevent its binding to nucleosome. These data provide important insight on the role of chromatin structure in the regulation of transcription of NF-κB dependent genes. In eukaryotes DNA is hierarchically packaged into chromatin by histones. The fundamental subunit of chromatin is the nucleosome. The packaging of DNA into nucleosomes not only restricts DNA accessibility for regulatory proteins but also provides opportunities to regulate DNA based processes. Accessibility of transcription factor NF-κB to their recognition sequences embedded in nucleosomes is highly controversial. On one hand in vivo studies have suggested that packaging of DNA into chromatin plays an important role in regulating the expression of NF-κB dependent genes, and on the other hand some in vitro studies reported that NF-κB can bind by itself to its recognition sequences embedded in the nucleosome. In this study, we show that NF-κB can specifically bind to its recognition sequences placed at the end of the nucleosome but not when placed inside the nucleosome core. We then demonstrate that disruption of nucleosome is necessary for the productive binding of NF-κB. Finally, we show that the presence of histone H1 does not affect the specific binding of NF-κB to its cognate sequence, when its binding region overlaps with the binding site of NF-κB. We propose that histone eviction is needed for NF-κB to bind specifically to its recognition sequence embedded in the nucleosome.
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Affiliation(s)
- Imtiaz Nisar Lone
- Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, CNRS-UMR 5239, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Manu Shubhdarshan Shukla
- Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, CNRS-UMR 5239, Ecole Normale Supérieure de Lyon, Lyon, France
- Université Joseph Fourier - Grenoble 1, INSERM Institut Albert Bonniot, U823, Site Santé-BP 170, Grenoble, France
| | - John Lalith Charles Richard
- Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, CNRS-UMR 5239, Ecole Normale Supérieure de Lyon, Lyon, France
- Université Joseph Fourier - Grenoble 1, INSERM Institut Albert Bonniot, U823, Site Santé-BP 170, Grenoble, France
| | - Zahary Yordanov Peshev
- Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, CNRS-UMR 5239, Ecole Normale Supérieure de Lyon, Lyon, France
- Institute of Electronics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Stefan Dimitrov
- Université Joseph Fourier - Grenoble 1, INSERM Institut Albert Bonniot, U823, Site Santé-BP 170, Grenoble, France
- * E-mail: (SD); (DA)
| | - Dimitar Angelov
- Université de Lyon, Laboratoire de Biologie Moléculaire de la Cellule, CNRS-UMR 5239, Ecole Normale Supérieure de Lyon, Lyon, France
- * E-mail: (SD); (DA)
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14
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Iwasaki W, Miya Y, Horikoshi N, Osakabe A, Taguchi H, Tachiwana H, Shibata T, Kagawa W, Kurumizaka H. Contribution of histone N-terminal tails to the structure and stability of nucleosomes. FEBS Open Bio 2013; 3:363-9. [PMID: 24251097 PMCID: PMC3821030 DOI: 10.1016/j.fob.2013.08.007] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Revised: 08/15/2013] [Accepted: 08/15/2013] [Indexed: 12/17/2022] Open
Abstract
Histones are the protein components of the nucleosome, which forms the basic architecture of eukaryotic chromatin. Histones H2A, H2B, H3, and H4 are composed of two common regions, the "histone fold" and the "histone tail". Many efforts have been focused on the mechanisms by which the post-translational modifications of histone tails regulate the higher-order chromatin architecture. On the other hand, previous biochemical studies have suggested that histone tails also affect the structure and stability of the nucleosome core particle itself. However, the precise contributions of each histone tail are unclear. In the present study, we determined the crystal structures of four mutant nucleosomes, in which one of the four histones, H2A, H2B, H3, or H4, lacked the N-terminal tail. We found that the deletion of the H2B or H3 N-terminal tail affected histone-DNA interactions and substantially decreased nucleosome stability. These findings provide important information for understanding the complex roles of histone tails in regulating chromatin structure.
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Affiliation(s)
- Wakana Iwasaki
- Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan ; RIKEN, 2-1 Hirosawa, Wako-shi, Saitama 351-0198, Japan
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15
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16
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Davis WB, Bjorklund CC, Deline M. Probing the effects of DNA-protein interactions on DNA hole transport: the N-terminal histone tails modulate the distribution of oxidative damage and chemical lesions in the nucleosome core particle. Biochemistry 2012; 51:3129-42. [PMID: 22409399 DOI: 10.1021/bi201734c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The ability of DNA to transport positive charges, or holes, over long distances is well-established, but the mechanistic details of how this process is influenced by packaging into DNA-protein complexes have not been fully delineated. In eukaryotes, genomic DNA is packaged into chromatin through its association with the core histone octamer to form the nucleosome core particle (NCP), a complex whose structure can be modulated through changes in the local environment and the histone proteins. Because (i) varying the salt concentration and removing the histone tails influence the structure of the NCP in known ways and (ii) previous studies have shown that DNA hole transport (HT) occurs in the nucleosome, we have used our previously described 601 sequence NCPs to test the hypothesis that DNA HT dynamics can be modulated by structural changes in a DNA-protein complex. We show that at low salt concentrations there is a sharp increase in long-range DNA HT efficiency in the NCP as compared to naked DNA. This enhancement of HT can be negated by either removal of the histone tails at low salt concentrations or disruption of the interaction of the packaged DNA and the histone tails by increasing the buffer's ionic strength. Association of the histone tails with 601 DNA at low salt concentrations shifts the guanine damage spectrum to favor lesions like 8-oxoguanine in the NCP, most likely through modulation of the rate of the reaction of the guanine radical cation with oxygen. These experimental results indicate that for most genomic DNA, the influence of DNA-protein interactions on DNA HT will depend strongly on the level of protection of the DNA nucleobases from oxygen. Further, these results suggest that the oxidative damage arising from DNA HT may vary in different genomic regions depending on the presence of either euchromatin or heterochromatin.
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Affiliation(s)
- William B Davis
- School of Molecular Biosciences, Biotechnology/Life Sciences 135, Washington State University, Pullman, Washington 99164-7520, USA.
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17
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Liu N, Hayes JJ. Preparation of nucleosomes containing a specific H2A-H2A cross-link forming a DNA-constraining loop structure. Methods Mol Biol 2012; 833:351-71. [PMID: 22183604 DOI: 10.1007/978-1-61779-477-3_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
ATP-dependent chromatin-remodeling complexes use the energy of ATP hydrolysis to alter nucleosome structure, increase the accessibility of trans-acting factors, and induce nucleosome movement on the nucleosomal DNA. Recent studies suggest that bulge propagation is a major component of the mechanism for SWI/SNF remodeling. We describe in detail a method to prepare a mononucleosomal substrate in which the two H2A N-terminal tails are cross-linked in an intranucleosomal fashion, forming a closed loop around the two superhelical winds of DNA. This substrate is useful for researchers who wish to test processes in which the DNA is transiently or permanently lifted off the histone surface, such as in the bulge propagation model. Our method allows assessment of the extent of cross-linking within the population of nucleosomes used in small-scale experiments, such as assays to test SWI/SNF-remodeling activities.
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Affiliation(s)
- Ning Liu
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, NY, USA
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18
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Yang Z, Hayes JJ. The divalent cations Ca2+ and Mg2+ play specific roles in stabilizing histone-DNA interactions within nucleosomes that are partially redundant with the core histone tail domains. Biochemistry 2011; 50:9973-81. [PMID: 22007636 DOI: 10.1021/bi201377x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We previously reported that reconstituted nucleosomes undergo sequence-dependent translational repositioning upon removal of the core histone tail domains under physiological conditions, indicating that the tails influence the choice of position. We report here that removal of the core histone tail domains increases the exposure of the DNA backbone in nucleosomes to hydroxyl radicals, a nonbiased chemical cleavage reagent, indicative of an increase in the motility of the DNA on the histone surface. Moreover, we demonstrate that the divalent cations Mg(2+) and Ca(2+) can replace the role of the tail domains with regard to stabilization of histone-DNA interactions within the nucleosome core and restrict repositioning of nucleosomes upon tail removal. However, when nucleosomes were incubated with Mg(2+) after tail removal, the original distribution of translational positions was not re-established, indicating that divalent cations increase the energy barrier between translational positions rather than altering the free energy differences between positions. Interestingly, other divalent cations such as Zn(2+), Fe(2+), Co(2+), and Mn(2+) had little or no effect on the stability of histone-DNA interactions within tailless nucleosomes. These results support the idea that specific binding sites for Mg(2+) and Ca(2+) ions exist within the nucleosome and play a critical role in nucleosome stability that is partially redundant with the core histone tail domains.
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Affiliation(s)
- Zungyoon Yang
- Department of Biochemistry and Biophysics, University of Rochester Medical Center, Rochester, New York 14642, USA
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19
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SWI/SNF- and RSC-catalyzed nucleosome mobilization requires internal DNA loop translocation within nucleosomes. Mol Cell Biol 2011; 31:4165-75. [PMID: 21859889 DOI: 10.1128/mcb.05605-11] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The multisubunit SWI/SNF and RSC complexes utilize energy derived from ATP hydrolysis to mobilize nucleosomes and render the DNA accessible for various nuclear processes. Here we test the idea that remodeling involves intermediates with mobile DNA bulges or loops within the nucleosome by cross-linking the H2A N- or C-terminal tails together to generate protein "loops" that constrict separation of the DNA from the histone surface. Analyses indicate that this intranucleosomal cross-linking causes little or no change in remodeling-dependent exposure of DNA sequences within the nucleosome to restriction enzymes. However, cross-linking inhibits nucleosome mobilization and blocks complete movement of nucleosomes to extreme end positions on the DNA fragments. These results are consistent with evidence that nucleosome remodeling involves intermediates with DNA loops on the nucleosome surface but indicate that such loops do not freely diffuse about the surface of the histone octamer. We propose a threading model for movement of DNA loops around the perimeter of the nucleosome core.
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20
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Abstract
The DNA of eukaryotic cells is spooled around large histone protein complexes, forming nucleosomes that make up the basis for a high-order packaging structure called chromatin. Compared to naked DNA, nucleosomal DNA is less accessible to regulatory proteins and regulatory processes. The exact positions of nucleosomes therefore influence several cellular processes, including gene expression, chromosome segregation, recombination, replication, and DNA repair. Here, we review recent technological advances enabling the genome-wide mapping of nucleosome positions in the model eukaryote Saccharomyces cerevisiae. We discuss the various parameters that determine nucleosome positioning in vivo, including cis factors like AT content, variable tandem repeats, and poly(dA:dT) tracts that function as chromatin barriers and trans factors such as chromatin remodeling complexes, transcription factors, histone-modifying enzymes, and RNA polymerases. In the last section, we review the biological role of chromatin in gene transcription, the evolution of gene regulation, and epigenetic phenomena.
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Jagannathan I, Pepenella S, Hayes JJ. Activity of FEN1 endonuclease on nucleosome substrates is dependent upon DNA sequence but not flap orientation. J Biol Chem 2011; 286:17521-9. [PMID: 21454907 DOI: 10.1074/jbc.m111.229658] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
We demonstrated previously that human FEN1 endonuclease, an enzyme involved in excising single-stranded DNA flaps that arise during Okazaki fragment processing and base excision repair, cleaves model flap substrates assembled into nucleosomes. Here we explore the effect of flap orientation with respect to the surface of the histone octamer on nucleosome structure and FEN1 activity in vitro. We find that orienting the flap substrate toward the histone octamer does not significantly alter the rotational orientation of two different nucleosome positioning sequences on the surface of the histone octamer but does cause minor perturbation of nucleosome structure. Surprisingly, flaps oriented toward the nucleosome surface are accessible to FEN1 cleavage in nucleosomes containing the Xenopus 5S positioning sequence. In contrast, neither flaps oriented toward nor away from the nucleosome surface are cleaved by the enzyme in nucleosomes containing the high-affinity 601 nucleosome positioning sequence. The data are consistent with a model in which sequence-dependent motility of DNA on the nucleosome is a major determinant of FEN1 activity. The implications of these findings for the activity of FEN1 in vivo are discussed.
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Affiliation(s)
- Indu Jagannathan
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642, USA
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22
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Infante JJ, Law GL, Wang IT, Chang HWE, Young ET. Activator-independent transcription of Snf1-dependent genes in mutants lacking histone tails. Mol Microbiol 2011; 80:407-22. [PMID: 21338416 DOI: 10.1111/j.1365-2958.2011.07583.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Transcriptional regulation of Snf1-dependent genes occurs in part by histone-acetylation-dependent binding of the transcription factor Adr1. Analysis of previously published microarray data indicated unscheduled transcription of a large number of Snf1- and Adr1-dependent genes when either the histone H3 or H4 tail was deleted. Quantitative real-time PCR confirmed that the tails were important to preserve stringent transcriptional repression of Snf1-dependent genes when glucose was present. The absence of the tails allowed Adr1 and RNA Polymerase II to bind promoters in normally inhibitory conditions. The promoters escaped glucose repression to a limited extent and the weak constitutive ADH2 transcription induced by deletion of the histone tails was transcription factor- and Snf1-independent. These effects were apparently due to a permissive chromatin structure that allowed transcription in the absence of repression mediated by the histone tails. Deleting REG1, and thus activating Snf1 in the H3 tail mutant enhanced transcription in repressing conditions, indicating that Snf1 and the H3 tail influence transcription independently. Deleting REG1 in the histone H4 tail mutant appeared to be lethal, even in the absence of Snf1, suggesting that Reg1 and the H4 tail have redundant functions that are important for cell viability.
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Affiliation(s)
- Juan J Infante
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
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Abstract
Epigenetics, broadly defined as the inheritance of non-Mendelian phenotypic traits, can be more narrowly defined as heritable alterations in states of gene expression ("on" versus "off") that are not linked to changes in DNA sequence. Moreover, these alterations can persist in the absence of the signals that initiate them, thus suggesting some kind of "memory" to epigenetic forms of regulation. How, for example, during early female mammalian development, is one X chromosome selected to be kept in an active state, while the genetically identical sister X chromosome is "marked" to be inactive, even though they reside in the same nucleus, exposed to the same collection of shared trans-factors? Once X inactivation occurs, how are these contrasting chromatin states maintained and inherited faithfully through subsequent cell divisions? Chromatin states, whether active (euchromatic) or silent (heterochromatic) are established, maintained, and propagated with remarkable precision during normal development and differentiation. However, mistakes made in establishing and maintaining these chromatin states, often executed by a variety of chromatin-remodeling activities, can lead to mis-expression or mis-silencing of critical downstream gene targets with far-reaching implications for human biology and disease, notably cancer. Though chromatin biologists have identified many of the "inputs" that are important for controlling chromatin states, the detailed mechanisms by which these processes work remain largely opaque, in part due to the staggering complexity of the chromatin polymer, the physiologically relevant form of our genome. The primary objective of this article is to serve as a "call to arms" for chemists to contribute to the development of the precision tools needed to answer pressing molecular problems in this rapidly moving field.
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Affiliation(s)
- C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA.
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24
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Nag R, Kyriss M, Smerdon JW, Wyrick JJ, Smerdon MJ. A cassette of N-terminal amino acids of histone H2B are required for efficient cell survival, DNA repair and Swi/Snf binding in UV irradiated yeast. Nucleic Acids Res 2009; 38:1450-60. [PMID: 20007597 PMCID: PMC2836547 DOI: 10.1093/nar/gkp1074] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The highly charged histone N-terminal domains are engaged in inter- and intra-nucleosomal interactions, and contain a host of sites used for posttranslational modification. We have studied the effect of deleting residues 30–37 from the N-terminal domain of histone H2B in yeast cells, on nucleotide excision repair (NER) following UV irradiation, as these cells are quite sensitive to UV. We find that H2B Δ30–37 cells exhibit reduced NER efficiency at three specific chromatin loci: the transcriptionally active, RPB2 locus; the transcriptionally silenced, nucleosome-loaded HML locus; and the transcriptionally repressed, non-silenced, GAL10 locus. Nuclease digestion studies indicate that H2B Δ30–37 chromatin has increased nucleosome accessibility and/or nucleosome mobility. In addition, H2B Δ30–37 mutants acquire more DNA damage, compared to wt cells, following the same dose of UV radiation. Reducing the level of damage in H2B Δ30–37 cells to match that of wt cells restores the NER rate to wt levels in the RPB2 and GAL10 loci, but NER efficiency remains low in the silenced HML locus. Interestingly, recruitment of Snf5 to the HML locus is reduced in H2B Δ30–37 cells and more transient following UV irradiation. This may reflect a lower binding affinity of the SWI/SNF complex to H2B Δ30–37 nucleosomes.
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Affiliation(s)
- Ronita Nag
- Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA
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25
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Le NT, Ho TB, Tran DH. Characterizing nucleosome dynamics from genomic and epigenetic information using rule induction learning. BMC Genomics 2009; 10 Suppl 3:S27. [PMID: 19958491 PMCID: PMC2788380 DOI: 10.1186/1471-2164-10-s3-s27] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Eukaryotic genomes are packaged into chromatin, a compact structure containing fundamental repeating units, the nucleosomes. The mobility of nucleosomes plays important roles in many DNA-related processes by regulating the accessibility of regulatory elements to biological machineries. Although it has been known that various factors, such as DNA sequences, histone modifications, and chromatin remodelling complexes, could affect nucleosome stability, the mechanisms of how they regulate this stability are still unclear. RESULTS In this paper, we propose a novel computational method based on rule induction learning to characterize nucleosome dynamics using both genomic and histone modification information. When applied on S. cerevisiae data, our method produced totally 98 rules characterizing nucleosome dynamics on chromosome III and promoter regions. Analyzing these rules we discovered that, some DNA motifs and post-translational modifications of histone proteins play significant roles in regulating nucleosome stability. Notably, these DNA motifs are strong determinants for nucleosome forming and inhibiting potential; and these histone modifications have strong relation with transcriptional activities, i.e. activation and repression. We also found some new patterns which may reflect the cooperation between these two factors in regulating the stability of nucleosomes. CONCLUSION DNA motifs and histone modifications can individually and, in some cases, cooperatively regulate nucleosome stability. This suggests additional insights into mechanisms by which cells control important biological processes, such as transcription, replication, and DNA repair.
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Affiliation(s)
- Ngoc Tu Le
- School of Knowledge Science, Japan Advanced Institute of Science and Technology, 1-1 Asahidai, Nomi, Ishikawa 923-1292, Japan.
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26
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Cole HA, Tabor-Godwin JM, Hayes JJ. Uracil DNA glycosylase activity on nucleosomal DNA depends on rotational orientation of targets. J Biol Chem 2009; 285:2876-85. [PMID: 19933279 DOI: 10.1074/jbc.m109.073544] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The activity of uracil DNA glycosylases (UDGs), which recognize and excise uracil bases from DNA, has been well characterized on naked DNA substrates but less is known about activity in chromatin. We therefore prepared a set of model nucleosome substrates in which single thymidine residues were replaced with uracil at specific locations and a second set of nucleosomes in which uracils were randomly substituted for all thymidines. We found that UDG efficiently removes uracil from internal locations in the nucleosome where the DNA backbone is oriented away from the surface of the histone octamer, without significant disruption of histone-DNA interactions. However, uracils at sites oriented toward the histone octamer surface were excised at much slower rates, consistent with a mechanism requiring spontaneous DNA unwrapping from the nucleosome. In contrast to the nucleosome core, UDG activity on DNA outside the core DNA region was similar to that of naked DNA. Association of linker histone reduced activity of UDG at selected sites near where the globular domain of H1 is proposed to bind to the nucleosome as well as within the extra-core DNA. Our results indicate that some sites within the nucleosome core and the extra-core (linker) DNA regions represent hot spots for repair that could influence critical biological processes.
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Affiliation(s)
- Hope A Cole
- Department of Biochemistry and Biophysics, University of Rochester, Rochester, New York 14642, USA
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27
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Cichewicz RH. Epigenome manipulation as a pathway to new natural product scaffolds and their congeners. Nat Prod Rep 2009; 27:11-22. [PMID: 20024091 DOI: 10.1039/b920860g] [Citation(s) in RCA: 196] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The covalent modification of chromatin is an important control mechanism used by fungi to modulate the transcription of genes involved in secondary metabolite production. To date, both molecular-based and chemical approaches targeting histone and DNA posttranslational processes have shown great potential for rationally directing the activation and/or suppression of natural-product-encoding gene clusters. In this Highlight, the organization of the fungal epigenome is summarized and strategies for manipulating chromatin-related targets are presented. Applications of these techniques are illustrated using several recently published accounts in which chemical-epigenetic methods and mutant studies were successfully employed for the de novo or enhanced production of structurally diverse fungal natural products (e.g., anthraquinones, cladochromes, lunalides, mycotoxins, and nygerones).
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Affiliation(s)
- Robert H Cichewicz
- Natural Products Discovery Group and Graduate Program in Ecology and Evolutionary Biology, Department of Chemistry and Biochemistry, 620 Parrington Oval, Room 208, University of Oklahoma, Norman, OK 73019, USA.
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28
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Segal E, Widom J. What controls nucleosome positions? Trends Genet 2009; 25:335-43. [PMID: 19596482 PMCID: PMC2810357 DOI: 10.1016/j.tig.2009.06.002] [Citation(s) in RCA: 282] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2009] [Revised: 06/02/2009] [Accepted: 06/02/2009] [Indexed: 10/20/2022]
Abstract
The DNA of eukaryotic genomes is wrapped in nucleosomes, which strongly distort and occlude the DNA from access to most DNA-binding proteins. An understanding of the mechanisms that control nucleosome positioning along the DNA is thus essential to understanding the binding and action of proteins that carry out essential genetic functions. New genome-wide data on in vivo and in vitro nucleosome positioning greatly advance our understanding of several factors that can influence nucleosome positioning, including DNA sequence preferences, DNA methylation, histone variants and post-translational modifications, higher order chromatin structure, and the actions of transcription factors, chromatin remodelers and other DNA-binding proteins. We discuss how these factors function and ways in which they might be integrated into a unified framework that accounts for both the preservation of nucleosome positioning and the dynamic nucleosome repositioning that occur across biological conditions, cell types, developmental processes and disease.
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Affiliation(s)
- Eran Segal
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel.
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Bertin A, Durand D, Renouard M, Livolant F, Mangenot S. H2A and H2B tails are essential to properly reconstitute nucleosome core particles. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:1083-94. [PMID: 17882413 DOI: 10.1007/s00249-007-0212-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Revised: 06/25/2007] [Accepted: 07/24/2007] [Indexed: 02/05/2023]
Abstract
The conformation of recombinant Nucleosome Core Particles (NCPs) lacking H2A and H2B histone tails (gH2AgH2B) are studied. The migration of these particles in acrylamide native gels is slowed down compared to intact reconstituted NCPs. gH2AgH2B NCPs are also much more sensitive to nuclease digestion than intact NCPs. Small angle X-ray scattering (SAXS) experiments point out that the absence of H2A and H2B tails produces small but significant conformational changes of the octamers conformation (without wrapped DNA), whereas gH2AgH2B NCP conformations are significantly altered. A separation of about 25-30 bp from the core could account for the experimental curves, but other types of DNA superhelix deformation cannot be excluded. The distorted gH2AgH2B octamer may not allow the correct winding of DNA around the core. The absence of the H2A and H2B tails would further prevent the secondary sliding of the DNA around the core and therefore impedes the stabilisation of the particle. Cryo-electron microscopy on the same particles also shows a detachment of DNA portions from the particle core. The effect is even stronger because the vitrification of the samples worsens the instability of gH2AgH2B NCPs.
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Affiliation(s)
- Aurélie Bertin
- Laboratoire de Physique des Solides, CNRS UMR 8502, Université Paris-Sud, 91405, Orsay Cedex, France.
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30
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Parra MA, Wyrick JJ. Regulation of gene transcription by the histone H2A N-terminal domain. Mol Cell Biol 2007; 27:7641-8. [PMID: 17724083 PMCID: PMC2169066 DOI: 10.1128/mcb.00742-07] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Histone N-terminal domains play critical roles in regulating chromatin structure and gene transcription. Relatively little is known, however, about the role of the histone H2A N-terminal domain in transcription regulation. We have used DNA microarrays to characterize the changes in genome-wide expression caused by mutations in the N-terminal domain of histone H2A. Our results indicate that the N-terminal domain of histone H2A functions primarily to repress the transcription of a large subset of the Saccharomyces cerevisiae genome and that most of the H2A-repressed genes are also repressed by the histone H2B N-terminal domain. Using the histone H2A microarray data, we selected three reporter genes (BNA1, BNA2, and GCY1), which we subsequently used to map regions in the H2A N-terminal domain responsible for this transcriptional repression. These studies revealed that a small subdomain in the H2A N-terminal tail, comprised of residues 16 to 20, is required for the transcriptional repression of these reporter genes. Deletion of either the entire histone H2A N-terminal domain or just this small subdomain imparts sensitivity to UV irradiation. Finally, we show that two residues in this H2A subdomain, serine-17 and arginine-18, are specifically required for the transcriptional repression of the BNA2 reporter gene.
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Affiliation(s)
- Michael A Parra
- School of Molecular Biosciences, Washington State University, Fulmer Hall 675, Pullman, WA 99164-4660, USA
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