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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
...factors bind directly to the DNA to activate or repress transcription (Marr et al. 2021; Minnoye et al. 2021). Recent advances in sequencing technology have enabled the characterization of chromatin remodelers, nucleosome positioning, and chromatin accessibility using high-throughput assays like Ch...
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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
...enriched with BRG1 (Fig. 2I). The regions that gained nucleosomes in both M-CLL and U-CLL versus NBCs had a more than threefold enrichment of BRG1 in comparison with neighboring regions (Fig. 2J). (2) The loci bound by another chromatin remodeler, CHD1, in lymphoblastoid B cells (The ENCODE Project...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...-translational modifications, play a crucial role in regulating programs integral to a cell's identity, like gene expression and DNA replication. However, the transcriptional, chromatin, and replication timing profiles of adult stem cells in vivo remain poorly understood. Containing germline stem cells (GSCs) and somatic cyst...
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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
...by the TP53 (MA0106.3) or TP63 (MA0525.2) motif occurring within each ChIP-seq peak. Locations with multiple motifs were excluded from the analysis. Appropriate MNase-seq data were not available for TP73. To capture nucleosome positioning before TP53 or TP63 binding and any resultant chromatin remodeling...
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Method: Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase
- Maria Grazia Mendoza-Ferri,
- Gwendoline Lozachmeur,
- Maximilien Duvina,
- Laetitia Perret,
- Didier Merciris,
- Anne Gigout,
- and Marco Antonio Mendoza-Parra
Genome Res. July 2025 35: 1633-1645; Published in Advance May 13, 2025, doi:10.1101/gr.280305.124
...a bivalent chromatin-state configuration at the tail of the embryo and a coenrichment signature of the histone modifications H3K4me3 and H3K27ac at the medial level of the spinal cord (Fig. 4m), in agreement with gene expression revealed by in situ hybridization (Allen Developing Mouse Brain Atlas) (Fig. 4n...
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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
...nucleosomes (Cannistraro and Taylor 2010; Song et al. 2011, 2014). Nucleosomes are the fundamental packaging unit of eukaryotic chromatin and are composed of an octamer of histone proteins and ∼147 bp of DNA (Luger et al. 1997). As the nucleosomal DNA wraps around the histone octamer, the minor groove...
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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
..., 8092 Zurich, Switzerland; 4Institut Cochin, Inserm U1016, CNRS UMR 8104, Université Paris Cité, 75014 Paris, France Corresponding authors: ekaterina.krymova@sdsc.ethz.ch, valentina.boeva@inf.ethz.chAbstractFine-grained prediction of chromatin accessibility from DNA sequence is a foundational step...
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Resource: Haplotype-resolved 3D chromatin architecture of the hybrid pig
- Yu Lin,
- Jing Li,
- Yiren Gu,
- Long Jin,
- Jingyi Bai,
- Jiaman Zhang,
- Yujie Wang,
- Pengliang Liu,
- Keren Long,
- Mengnan He,
- Diyan Li,
- Can Liu,
- Ziyin Han,
- Yu Zhang,
- Xiaokai Li,
- Bo Zeng,
- Lu Lu,
- Fanli Kong,
- Ying Sun,
- Yongliang Fan,
- Xun Wang,
- Tao Wang,
- An'an Jiang,
- Jideng Ma,
- Linyuan Shen,
- Li Zhu,
- Yanzhi Jiang,
- Guoqing Tang,
- Xiaolan Fan,
- Qingyou Liu,
- Hua Li,
- Jinyong Wang,
- Li Chen,
- Liangpeng Ge,
- Xuewei Li,
- Qianzi Tang,
- and Mingzhou Li
Genome Res. February 2024 34: 310-325; Published in Advance March 13, 2024, doi:10.1101/gr.278101.123
..., skeletal muscle, and brain) from hybrid pigs generated by reciprocal crosses of phenotypically and physiologically divergent Berkshire and Tibetan pigs, we uncover extensive chromatin reorganization between homologous chromosomes across multiple scales. Haplotype-based interrogation of multi-omic data...
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Mini-Review: The chromatin tapestry as a framework for neurodevelopment
- Ben Nolan,
- Timothy E. Reznicek,
- Christopher T. Cummings,
- and M. Jordan Rowley
Genome Res. October 2024 34: 1477-1486; doi:10.1101/gr.278408.123
...landscape in addition to loops. For example, the cohesin loader can activate chromatin remodelers to reposition and evict nucleosomes indicating that the loading of cohesin is not only important for creating chromatin loops, but can also change the local nucleosome landscape (Lopez-Serra et al. 2014; Muñoz...
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Research: Regulation of nucleosome positioning by a CHD Type III chromatin remodeler and its relationship to developmental gene expression in Dictyostelium
- James L. Platt,
- Nicholas A. Kent,
- Alan R. Kimmel,
- and Adrian J. Harwood
Genome Res. April 2017 27: 591-600; Published in Advance March 22, 2017, doi:10.1101/gr.216309.116
...the first in vivo study for action of a CHD Type III protein on chromatin remodeling. In vitro studies had previously shown that ISWI and CHD proteins exhibit an ATP-dependent nucleosome sliding activity on artificial DNA templates (Hamiche et al. 1999; Langst et al. 1999; Stockdale et al. 2006; Bouazoune...
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