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Research: Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation
- Kevin Moyung,
- Yulong Li,
- Heather K. MacAlpine,
- Alexander J. Hartemink,
- and David M. MacAlpine
Genome Res. January 2026 36: 115-128; Published in Advance December 9, 2025, doi:10.1101/gr.279637.124
...interplay of nucleosomes and TFs together in the context of transcriptional regulation is crucial for better understanding gene regulation within an organism.Although numerous efforts to construct gene regulatory networks (GRNs) have used -wide expression profiling under various genetic and environmental...
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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...-in orientations in vitro (Song et al. 2011, 2014). However, to what extent nucleosomes modulate CPD deamination in other sequence contexts and across the of intact cells remains unclear.Genome-wide sequencing methods have emerged as powerful tools to understand how different genomic and chromatin contexts impact...
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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
...510515, China Corresponding authors: kuangyuyen@ihcams.ac.cn, mahony@psu.eduAbstractGenome-wide nucleosome profiles are predominantly characterized using MNase-seq, which involves extensive MNase digestion and size selection to enrich for mononucleosome-sized fragments. Most available MNase-seq analysis...
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Research: Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites
- Patrick D. Wilson,
- Xinyang Yu,
- Christopher R. Handelmann,
- and Michael J. Buck
Genome Res. March 2025 35: 404-416; Published in Advance February 10, 2025, doi:10.1101/gr.279541.124
...to these 20 bp binding sites (hereafter termed “TP53 family binding sites”) as a tetramer, specifically a dimer of dimers that are each bound to an RRRCWWGYYY repeat (Brandt et al. 2009).Eukaryotic DNA is organized into chromatin, which is made up of nucleosomes (Cooper 2000). A nucleosome comprises...
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Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
- Christine R. Keenan,
- Hannah D. Coughlan,
- Nadia Iannarella,
- Andres Tapia del Fierro,
- Andrew Keniry,
- Timothy M. Johanson,
- Wing Fuk Chan,
- Alexandra L. Garnham,
- Lachlan W. Whitehead,
- Marnie E. Blewitt,
- Gordon K. Smyth,
- and Rhys S. Allan
Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
...gene expression and differential interactivity of that gene, suggesting either that gene expression per se is highly correlated to the interactivity of that gene with other genomic elements such as enhancers or other gene promoters or that the mechanism causing gene expression to alter similarly...
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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
...; Hu et al. 2017). However, to what extent variations in chromatin organization cause regional differences in UV damage formation is controversial (García-Nieto et al. 2017; Roberts et al. 2019).In eukaryotic cells, 147 bp of genomic DNA wrap around a histone octamer (consisting of an H3–H4 tetramer...
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Resource: CGC1, a new reference genome for Caenorhabditis elegans
- Kazuki Ichikawa,
- Massa J. Shoura,
- Karen L. Artiles,
- Dae-Eun Jeong,
- Chie Owa,
- Haruka Kobayashi,
- Yoshihiko Suzuki,
- Manami Kanamori,
- Yu Toyoshima,
- Yuichi Iino,
- Ann E. Rougvie,
- Lamia Wahba,
- Andrew Z. Fire,
- Erich M. Schwarz,
- and Shinichi Morishita
Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
...organization, and the functions of highly repetitive genomic loci. Genetic polymorphism in wild isolates of C. elegans should be more reliably assigned to SNVs and genomic islands of elevated diversity in the CGC1 assembly than in N2 (Crombie et al. 2019; Lee et al. 2021). Even for putatively identical wild...
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Research: Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy
- Hadi Rahmaninejad,
- Yao Xiao,
- Maxime M.C. Tortora,
- and Geoffrey Fudenberg
Genome Res. August 2025 35: 1745-1757; Published in Advance July 8, 2025, doi:10.1101/gr.280108.124
...and static snapshots obtained from genomic data (Fudenberg et al. 2017; van Ruiten and Rowland 2021).Observations in living cells, however, argue strongly for a dynamic view of organization (Hansen 2020). Protein dynamics of CTCF and cohesin have been quantified with fluorescent recovery after photobleaching...
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Research: Transcription factor activity and nucleosome organization in mitosis
- Nicola Festuccia,
- Nick Owens,
- Thaleia Papadopoulou,
- Inma Gonzalez,
- Alexandra Tachtsidi,
- Sandrine Vandoermel-Pournin,
- Elena Gallego,
- Nancy Gutierrez,
- Agnès Dubois,
- Michel Cohen-Tannoudji,
- and Pablo Navarro
Genome Res. February 2019 29: 250-260; Published in Advance January 17, 2019, doi:10.1101/gr.243048.118
...on summits of interphase EP300 ChIP-seq peaks excluding promoters. Note that in E, MNase-seq signal is from 128 U digestions. Full data sets can be found in Supplemental Figure S8B.Chromatin accessibility and nucleosome organization as a function of ESRRB bookmarkingWe then focused on the analysis...
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Research: The impact of SWI/SNF and NuRD inactivation on gene expression is tightly coupled with levels of RNA polymerase II occupancy at promoters
- Sachin Pundhir,
- Jinyu Su,
- Marta Tapia,
- Anne Meldgaard Hansen,
- James Seymour Haile,
- Klaus Hansen,
- and Bo Torben Porse
Genome Res. March 2023 33: 332-345; Published in Advance March 16, 2023, doi:10.1101/gr.277089.122
....Z and H3.3 histone variants in NuRD- and SWI/SNF-mediated changes in Pol II release kinetics at target promotersSWI/SNF and NuRD predominantly target nucleosomes flanking the TSS at gene promoters (de Dieuleveult et al. 2016), and canonical H3 and H2A components of these nucleosomes are frequently...
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