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Research: Revisiting chromatin packaging in mouse sperm
- Qiangzong Yin,
- Chih-Hsiang Yang,
- Olga S. Strelkova,
- Jingyi Wu,
- Yu Sun,
- Sneha Gopalan,
- Liyan Yang,
- Job Dekker,
- Thomas G. Fazzio,
- Xin Zhiguo Li,
- Johan Gibcus,
- and Oliver J. Rando
Genome Res. December 2023 33: 2079-2093; Published in Advance December 21, 2023, doi:10.1101/gr.277845.123
...permeabilizing the sperm head. Analysis of library insert sizes revealed a dominant peak of ∼75-bp inserts (Fig. 1B), corresponding to short accessible loci, but no notable signature of nucleosome-sized footprints. This reflects a relatively flat landscape of Tn5 insertions across the primarily protamine-packaged...
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Research: Nucleosome repositioning in chronic lymphocytic leukemia
- Kristan V. Piroeva,
- Charlotte McDonald,
- Charalampos Xanthopoulos,
- Chelsea Fox,
- Christopher T. Clarkson,
- Jan-Philipp Mallm,
- Yevhen Vainshtein,
- Luminita Ruje,
- Lara C. Klett,
- Stephan Stilgenbauer,
- Daniel Mertens,
- Efterpi Kostareli,
- Karsten Rippe,
- and Vladimir B. Teif
Genome Res. October 2023 33: 1649-1661; Published in Advance September 12, 2023, doi:10.1101/gr.277298.122
...and its implications in primary cancer cells is scarce. Here, we conducted a -wide comparison of high-resolution nucleosome maps in peripheral blood B cells from patients with chronic lymphocytic leukemia (CLL) and healthy individuals at single-base-pair resolution. Our investigation uncovered significant...
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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: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
- Samuel H. Kim,
- Georgi K. Marinov,
- and William J. Greenleaf
Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
.... Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res 22: 2497–2506. doi:10.1101/gr.143008.112 ↵Kouzine F, Gupta A, Baranello L, Wojtowicz D, Ben-Aissa K, Liu J, Przytycka TM, Levens D. 2013. Transcription-dependent dynamic supercoiling is a short...
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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
...-validating approaches to measure absolute nucleosome occupancy across the Saccharomyces cerevisiae via restriction enzymes and DNA methyltransferases. The resulting high-resolution (9-bp) map shows uniform absolute occupancies. Most nucleosome positions are occupied in most cells: 97% of all nucleosomes called...
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Research: Nucleosome remodeling at origins of global genome–nucleotide excision repair occurs at the boundaries of higher-order chromatin structure
- Patrick van Eijk,
- Shuvro Prokash Nandi,
- Shirong Yu,
- Mark Bennett,
- Matthew Leadbitter,
- Yumin Teng,
- and Simon H. Reed
Genome Res. January 2019 29: 74-84; Published in Advance December 14, 2018, doi:10.1101/gr.237198.118
...structure throughout the entire , revealing that chromatin is remodeled at only a subset of nucleosomes, via discrete local changes. Since UV-induced lesions are essentially distributed uniformly throughout the , our observations suggest that repair of damage may be initiated through nucleosome remodeling...
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Research: Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans
- Tess E. Jeffers and
- Jason D. Lieb
Genome Res. January 2017 27: 75-86; Published in Advance November 14, 2016, doi:10.1101/gr.208173.116
...Tess E. Jeffers and Jason D. Lieb Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey 08544, USA Nucleosomes have structural and regulatory functions in all eukaryotic DNA-templated processes. The position of nucleosomes on DNA and the stability...
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Research: A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depends on histone recycling in transcribed chromatin
- J. Peter Svensson,
- Manu Shukla,
- Victoria Menendez-Benito,
- Ulrika Norman-Axelsson,
- Pauline Audergon,
- Indranil Sinha,
- Jason C. Tanny,
- Robin C. Allshire,
- and Karl Ekwall
Genome Res. June 2015 25: 872-883; Published in Advance March 16, 2015, doi:10.1101/gr.188870.114
...(Fig. 2F). Stratifying the turnover scores based on transcription levels revealed that transcription played a role in nucleosome conservation (Fig. 2G). We Figure 2. Transcription-dependent nucleosome turnover is related to the position of nucleosomes within genes. (A,B) ChIP was used to measure...
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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
..., Regev A, Liu X, Rinn J, Schier AF. 2010. Chromatin signature of embryonic pluripotency is established during activation. Nature 464: 922–926. Weiner A, Hughes A, Yassour M, Rando O, Friedman N. 2010. Highresolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res 20: 90...
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Research: Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation
- Yuanxin Xi,
- Jianhui Yao,
- Rui Chen,
- Wei Li,
- and Xiangwei He
Genome Res. May 2011 21: 718-724; Published in Advance March 1, 2011, doi:10.1101/gr.117101.110
.... Genome Res 18: 1084–1091. Weiner A, Hughes A, Yassour M, Rando OJ, Friedman N. 2010. Highresolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res 20: 90–100. Workman JL, Kingston RE. 1998. Alteration of nucleosome structure as amechanismof transcriptional regulation...

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