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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
...the observation is not confounded by TF binding. Nucleosome fragility is not associated with a specific epigenetic state Through comparisonwith previously generated data sets, we asked whether any histone post-translationalmodifications, histone variants, or chromatin states were positively associated...
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Research: Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation
- Marina Veil,
- Lev Y. Yampolsky,
- Björn Grüning,
- and Daria Onichtchouk
Genome Res. March 2019 29: 383-395; Published in Advance January 23, 2019, doi:10.1101/gr.240572.118
...DNA properties of HNAR promote both high nucleosome occupancy and differential binding of TFs. In the first step, already before ZGA, Pou5f3 and Nanog destabilize nucleosomes at HNAR centers -wide. In the second step, post-ZGA, Nanog, Pou5f3, and SoxB1 maintain open chromatin state on the subset...
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Research: Spatiotemporal kinetics of CAF-1-dependent chromatin maturation ensures transcription fidelity during S-phase
- Boning Chen,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. December 2023 33: 2108-2118; Published in Advance December 11, 2023, doi:10.1101/gr.278273.123
.... (D) Nucleosome occupancy at all time points for the 41,663 high-confidence nucleosomes, defined as nucleosomes with occupancy greater than the 25th percentile in both WT and cac1Δ cells following the 40-min chase period.NCOP of WT cells revealed that EdU-labeled nascent chromatin at the fork...
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Research: Widespread association of the Argonaute protein AGO2 with meiotic chromatin suggests a distinct nuclear function in mammalian male reproduction
- Kimberly N. Griffin,
- Benjamin William Walters,
- Haixin Li,
- Huafeng Wang,
- Giulia Biancon,
- Toma Tebaldi,
- Carolyn B. Kaya,
- Jean Kanyo,
- TuKiet T. Lam,
- Andy L. Cox,
- Stephanie Halene,
- Jean-Ju Chung,
- and Bluma J. Lesch
Genome Res. September 2022 32: 1655-1668; Published in Advance September 15, 2022, doi:10.1101/gr.276578.122
...reproduction.Cells control gene expression through multiple mechanisms, including regulation of chromatin state and transcription in the nucleus, mRNA export to the cytoplasm, and translation to protein. Argonaute (AGO) proteins play a major role in fine-tuning gene expression through post...
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Method: DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing
- Kaifu Chen,
- Yuanxin Xi,
- Xuewen Pan,
- Zhaoyu Li,
- Klaus Kaestner,
- Jessica Tyler,
- Sharon Dent,
- Xiangwei He,
- and Wei Li
Genome Res. February 2013 23: 341-351; Published in Advance November 28, 2012, doi:10.1101/gr.142067.112
...that DANPOS is also robust in defining functional dynamic nucleosomes, not only in promoters, but also in distal regulatory regions in the mammalian . [Supplemental material is available for this article.] Nucleosomes are fundamental building blocks of primary chromatin structure. Each nucleosome is composed...
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Research: Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8–Tup1 corepressor
- Kaifu Chen,
- Marenda A. Wilson,
- Calley Hirsch,
- Anjanette Watson,
- Shoudan Liang,
- Yue Lu,
- Wei Li,
- and Sharon Y.R. Dent
Genome Res. February 2013 23: 312-322; Published in Advance November 2, 2012, doi:10.1101/gr.141952.112
...structure have been limited to a few target genes. These studies revealed a variety of effects of the corepressor on chromatin architectures. In some instances, Cyc8–Tup1 influences nucleosome locations only in the promoter region, as is the case at RNR2 and RNR3 (Li and Reese 2001; Davie et al. 2002...
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Research: Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence
- Manuela Baquero Pérez,
- Gertjan Laenen,
- Isabelle Loïodice,
- Mickaël Garnier,
- Ugo Szachnowski,
- Antonin Morillon,
- Myriam Ruault,
- and Angela Taddei
Genome Res. October 2025 35: 2226-2239; Published in Advance August 12, 2025, doi:10.1101/gr.279874.124
...relocate from the nuclear periphery to the center of the nucleus into a hypercluster; chromatin is found in a compacted, hypoacetylated state; and transcription is globally shutdown. Yet, Q cells can restart transcription within minutes of refeeding. Here, we follow the global decrease of transcription...
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Method: A modular dCas9-SunTag DNMT3A epigenome editing system overcomes pervasive off-target activity of direct fusion dCas9-DNMT3A constructs
- Christian Pflueger,
- Dennis Tan,
- Tessa Swain,
- Trung Nguyen,
- Jahnvi Pflueger,
- Christian Nefzger,
- Jose M. Polo,
- Ethan Ford,
- and Ryan Lister
Genome Res. August 2018 28: 1193-1206; Published in Advance June 15, 2018, doi:10.1101/gr.233049.117
...to colored circles), suggesting that CTCF occupancy is reduced by >30% for all three CTCF target sites (SHB, MIR152, and CCDC85C) due to mCG deposition. The remaining chromatin-bound CTCF was found to have mCG in its core binding, indicating a possible transition state where CTCF is either poised to leave...
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Perspective: Epigenomics and the structure of the living genome
- Nir Friedman and
- Oliver J. Rando
Genome Res. October 2015 25: 1482-1490; doi:10.1101/gr.190165.115
...of “fragile” nucleosomes is obtained only after relatively light MNase digestion of chromatin (Weiner et al. 2010; Xi et al. 2011). Moreover, while nucleosomes are by far the most widespread DNA-binding factors that interfere with MNase digestion, many other DNA-binding proteins provide some level...
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Research: RSC-dependent constructive and destructive interference between opposing arrays of phased nucleosomes in yeast
- Dwaipayan Ganguli,
- Răzvan V. Chereji,
- James R. Iben,
- Hope A. Cole,
- and David J. Clark
Genome Res. October 2014 24: 1637-1649; Published in Advance July 11, 2014, doi:10.1101/gr.177014.114
...of the four core histones, H2A, H2B, H3, and H4, forming a histone octamer, around which is wrapped ;147 bp of DNA (Luger et al. 1997). Early nuclease digestion studies of chromatin in nuclei revealed a characteristic ladder of DNA bands in a gel, indicating that nucleosomes are regularly spaced along the DNA...

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