Single-molecule force spectroscopy on histone H4 tail-cross-linked chromatin reveals fiber folding
The eukaryotic genome is highly compacted into a protein-DNA complex called chromatin. The cell controls access of transcriptional regulators to chromosomal DNA via several mechanisms that act on chromatin-associated proteins and provide a rich spectrum of epigenetic regulation. Elucidating the mech...
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sg-ntu-dr.10356-872332023-02-28T17:00:29Z Single-molecule force spectroscopy on histone H4 tail-cross-linked chromatin reveals fiber folding Kaczmarczyk, Artur Allahverdi, Abdollah Brouwer, Thomas B. Nordenskiöld, Lars Dekker, Nynke H. Van Noort, John School of Biological Sciences Chromatin Structure Chromatin Compaction The eukaryotic genome is highly compacted into a protein-DNA complex called chromatin. The cell controls access of transcriptional regulators to chromosomal DNA via several mechanisms that act on chromatin-associated proteins and provide a rich spectrum of epigenetic regulation. Elucidating the mechanisms that fold chromatin fibers into higher-order structures is therefore key to understanding the epigenetic regulation of DNA accessibility. Here, using histone H4-V21C and histone H2A-E64C mutations, we employed single-molecule force spectroscopy to measure the unfolding of individual chromatin fibers that are reversibly cross-linked through the histone H4 tail. Fibers with covalently linked nucleosomes featured the same folding characteristics as fibers containing wild-type histones but exhibited increased stability against stretching forces. By stabilizing the secondary structure of chromatin, we confirmed a nucleosome repeat length (NRL)-dependent folding. Consistent with previous crystallographic and cryo-EM studies, the obtained force-extension curves on arrays with 167-bp NRLs best supported an underlying structure consisting of zig-zag, two-start fibers. For arrays with 197-bp NRLs, we previously inferred solenoidal folding, which was further corroborated by force-extension curves of the cross-linked fibers. The different unfolding pathways exhibited by these two types of arrays and reported here extend our understanding of chromatin structure and its potential roles in gene regulation. Importantly, these findings imply that chromatin compaction by nucleosome stacking protects nucleosomal DNA from external forces up to 4 piconewtons. ASTAR (Agency for Sci., Tech. and Research, S’pore) MOE (Min. of Education, S’pore) Published version 2018-01-26T02:21:22Z 2019-12-06T16:37:47Z 2018-01-26T02:21:22Z 2019-12-06T16:37:47Z 2017 Journal Article Kaczmarczyk, A., Allahverdi, A., Brouwer, T. B., Nordenskiöld, L., Dekker, N. H., & Van Noort, J. (2017). Single-molecule force spectroscopy on histone H4 tail-cross-linked chromatin reveals fiber folding. Journal of Biological Chemistry, 292(42), 17506-17513. 0021-9258 https://hdl.handle.net/10356/87233 http://hdl.handle.net/10220/44349 10.1074/jbc.M117.791830 en Journal of Biological Chemistry © 2017 American Society for Biochemistry and Molecular Biology (ASBMB). This paper was published in Journal of Biological Chemistry and is made available as an electronic reprint (preprint) with permission of American Society for Biochemistry and Molecular Biology (ASBMB). The published version is available at: [http://dx.doi.org/10.1074/jbc.M117.791830]. One print or electronic copy may be made for personal use only. Systematic or multiple reproduction, distribution to multiple locations via electronic or other means, duplication of any material in this paper for a fee or for commercial purposes, or modification of the content of the paper is prohibited and is subject to penalties under law. 9 p. application/pdf |
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Chromatin Structure Chromatin Compaction Kaczmarczyk, Artur Allahverdi, Abdollah Brouwer, Thomas B. Nordenskiöld, Lars Dekker, Nynke H. Van Noort, John Single-molecule force spectroscopy on histone H4 tail-cross-linked chromatin reveals fiber folding |
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The eukaryotic genome is highly compacted into a protein-DNA complex called chromatin. The cell controls access of transcriptional regulators to chromosomal DNA via several mechanisms that act on chromatin-associated proteins and provide a rich spectrum of epigenetic regulation. Elucidating the mechanisms that fold chromatin fibers into higher-order structures is therefore key to understanding the epigenetic regulation of DNA accessibility. Here, using histone H4-V21C and histone H2A-E64C mutations, we employed single-molecule force spectroscopy to measure the unfolding of individual chromatin fibers that are reversibly cross-linked through the histone H4 tail. Fibers with covalently linked nucleosomes featured the same folding characteristics as fibers containing wild-type histones but exhibited increased stability against stretching forces. By stabilizing the secondary structure of chromatin, we confirmed a nucleosome repeat length (NRL)-dependent folding. Consistent with previous crystallographic and cryo-EM studies, the obtained force-extension curves on arrays with 167-bp NRLs best supported an underlying structure consisting of zig-zag, two-start fibers. For arrays with 197-bp NRLs, we previously inferred solenoidal folding, which was further corroborated by force-extension curves of the cross-linked fibers. The different unfolding pathways exhibited by these two types of arrays and reported here extend our understanding of chromatin structure and its potential roles in gene regulation. Importantly, these findings imply that chromatin compaction by nucleosome stacking protects nucleosomal DNA from external forces up to 4 piconewtons. |
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School of Biological Sciences |
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School of Biological Sciences Kaczmarczyk, Artur Allahverdi, Abdollah Brouwer, Thomas B. Nordenskiöld, Lars Dekker, Nynke H. Van Noort, John |
format |
Article |
author |
Kaczmarczyk, Artur Allahverdi, Abdollah Brouwer, Thomas B. Nordenskiöld, Lars Dekker, Nynke H. Van Noort, John |
author_sort |
Kaczmarczyk, Artur |
title |
Single-molecule force spectroscopy on histone H4 tail-cross-linked chromatin reveals fiber folding |
title_short |
Single-molecule force spectroscopy on histone H4 tail-cross-linked chromatin reveals fiber folding |
title_full |
Single-molecule force spectroscopy on histone H4 tail-cross-linked chromatin reveals fiber folding |
title_fullStr |
Single-molecule force spectroscopy on histone H4 tail-cross-linked chromatin reveals fiber folding |
title_full_unstemmed |
Single-molecule force spectroscopy on histone H4 tail-cross-linked chromatin reveals fiber folding |
title_sort |
single-molecule force spectroscopy on histone h4 tail-cross-linked chromatin reveals fiber folding |
publishDate |
2018 |
url |
https://hdl.handle.net/10356/87233 http://hdl.handle.net/10220/44349 |
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1759855350550364160 |