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Method: Size-based expectation maximization for characterizing nucleosome positions and subtypes
- Jianyu Yang,
- Kuangyu Yen,
- and Shaun Mahony
Genome Res. September 2024 34: 1334-1343; Published in Advance June 17, 2024, doi:10.1101/gr.279138.124
...; Papp and Müller 2006; Wang et al. 2008). Histone variants, such as H2A.Z and H3.3, have also been reported to play roles in many important biological events, such as DNA replication and enhancer activity (Chen et al. 2013b; Zentner and Henikoff 2013).The most common technique for studying nucleosome...
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Research: Ultraviolet damage and repair maps in Drosophila reveal the impact of domain-specific changes in nucleosome repeat length on repair efficiency
- Benjamin Morledge-Hampton,
- Kathiresan Selvam,
- Manish Chauhan,
- Alan G. Goodman,
- and John J. Wyrick
Genome Res. February 2025 35: 257-267; Published in Advance January 6, 2025, doi:10.1101/gr.279605.124
...and two H2A–H2B dimers) to form a nucleosome, and groups of nucleosomes are further folded into higher-order chromatin structures (Luger et al. 1997; McGinty and Tan 2015). Although chromatin packaging can protect the DNA from damage (Takata et al. 2013), it also inhibits the accessibility of DNA repair...
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Method: Genome-wide prediction of DNA mutation effect on nucleosome positions for yeast synthetic genomics
- Etienne Routhier,
- Edgard Pierre,
- Ghazaleh Khodabandelou,
- and Julien Mozziconacci
Genome Res. February 2021 31: 317-326; Published in Advance December 18, 2020, doi:10.1101/gr.264416.120
...to other genomic tracks and other species. Whereas we have validated here the high potential of this approach by studying how the DNA sequence drives nucleosome positioning in yeast, we anticipate that it will be a very valuable tool to study nucleosome positioning rules in more complex organisms...
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Research: Parent-of-origin-dependent nucleosome organization correlates with genomic imprinting in maize
- Xiaomei Dong,
- Jian Chen,
- Tong Li,
- En Li,
- Xiangbo Zhang,
- Mei Zhang,
- Weibin Song,
- Haiming Zhao,
- and Jinsheng Lai
Genome Res. July 2018 28: 1020-1028; Published in Advance June 14, 2018, doi:10.1101/gr.230201.117
...G, Jones PA. 2012. Gene reactivation by 5-Aza-2′-deoxycytidine–induced demethylation requires SRCAP–mediated H2A.Z insertion to establish nucleosome depleted regions. PLoS Genet 8: e1002604. ↵Zhang M, Zhao H, Xie S, Chen J, Xu Y, Wang K, Zhao H, Guan H, Hu X, Jiao Y, et al. 2011. Extensive...
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Research: GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency in Paramecium
- Stefano Gnan,
- Mélody Matelot,
- Marion Weiman,
- Olivier Arnaiz,
- Frédéric Guérin,
- Linda Sperling,
- Mireille Bétermier,
- Claude Thermes,
- Chun-Long Chen,
- and Sandra Duharcourt
Genome Res. April 2022 32: 699-709; Published in Advance March 9, 2022, doi:10.1101/gr.276125.121
...core histones (H2A, H2B, H3, and H4) and 146–147 bp of DNA wrapped around it (Luger et al. 1997; Parmar and Padinhateeri 2020). Nucleosomes are not randomly located along the but are positioned with respect to DNA sequence. The affinity of DNA for histone octamers and the energy needed to bend...
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Method: Absolute nucleosome occupancy map for the Saccharomyces cerevisiae genome
- Elisa Oberbeckmann,
- Michael Wolff,
- Nils Krietenstein,
- Mark Heron,
- Jessica L. Ellins,
- Andrea Schmid,
- Stefan Krebs,
- Helmut Blum,
- Ulrich Gerland,
- and Philipp Korber
Genome Res. December 2019 29: 1996-2009; Published in Advance November 6, 2019, doi:10.1101/gr.253419.119
..., United Kingdom; 7Laboratory of Functional Genome Analysis (LAFUGA), Gene Center, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, 81377 Munich, Germany ↵8 These authors contributed equally to the work. Corresponding author: pkorber@lmu.deAbstractMapping of nucleosomes, the basic...
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Method: Defining TP53 pioneering capabilities with competitive nucleosome binding assays
- Xinyang Yu and
- Michael J. Buck
Genome Res. January 2019 29: 107-115; Published in Advance November 8, 2018, doi:10.1101/gr.234104.117
...amplified via PCR and column-purified (Qiagen) and quantified. In vitro nucleosomes were generated from H2A/H2B dimer and H3.1/H4 tetramer (NEB). All 16 nucleosome sequences were mixed at equal molar amounts. Mixed DNAs were then added to histones at octamer/DNA molar ratios of 1.5:1 in 2 M Na...
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Method: Mapping nucleosome positions using DNase-seq
- Jianling Zhong,
- Kaixuan Luo,
- Peter S. Winter,
- Gregory E. Crawford,
- Edwin S. Iversen,
- and Alexander J. Hartemink
Genome Res. March 2016 26: 351-364; Published in Advance January 15, 2016, doi:10.1101/gr.195602.115
...along the genome. Compared to methods that require genetically modified histones, our DNase-based approach is easily applied in any organism, which we demonstrate by producing maps in yeast and human. Compared to micrococcal nuclease (MNase)-based methods that map nucleosomes based on cuts in linker...
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Research: Canonical nucleosome organization at promoters forms during genome activation
- Yong Zhang,
- Nadine L. Vastenhouw,
- Jianxing Feng,
- Kai Fu,
- Chenfei Wang,
- Ying Ge,
- Andrea Pauli,
- Paul van Hummelen,
- Alexander F. Schier,
- and X. Shirley Liu
Genome Res. February 2014 24: 260-266; Published in Advance November 27, 2013, doi:10.1101/gr.157750.113
.... Nucleosome organization in the Drosophila . Nature 453: 358–362. Nekrasov M, Amrichova J, Parker BJ, Soboleva TA, Jack C, Williams R, Huttley GA, Tremethick DJ. 2012. Histone H2A.Z inheritance during the cell cycle and its impact on promoter organization and dynamics. Nat Struct Mol Biol 19: 1076–1083. Pauli...
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Research: Local nucleosome dynamics and eviction following a double-strand break are reversible by NHEJ-mediated repair in the absence of DNA replication
- Vinay Tripuraneni,
- Gonen Memisoglu,
- Heather K. MacAlpine,
- Trung Q. Tran,
- Wei Zhu,
- Alexander J. Hartemink,
- James E. Haber,
- and David M. MacAlpine
Genome Res. May 2021 31: 775-788; Published in Advance April 2, 2021, doi:10.1101/gr.271155.120
...is thought to be MRX-dependent, the RSC complex may interact with the broken DNA to create space for recognition and repair factors by sliding nucleosomes away from the DSB and also prevent histone octamers from sliding towards the free ends and off the DNA. The displacement of the H2A/H2B dimer immediately...

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