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Method: Automated chromatin profiling with spa-ChIP-seq uncovers the impacts of condition variations
- Yuwei Cao,
- Lauren Patel,
- Lauren Alcoser,
- Eric Mendenhall,
- Christopher Benner,
- Sven Heinz,
- and Alon Goren
Genome Res. January 2026 36: 129-141; Published in Advance December 12, 2025, doi:10.1101/gr.281320.125
...localization signals are sensitive to changing the antibody–to–cell-number ratio, whereas the stronger signals remain unaffected. This finding underscores the importance of maintaining consistent antibody–to–cell-number ratio for comparative studies, such as treatment responses or chromatin-QTL mapping...
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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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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
...associated with the shutdown of transcription upon quiescence entry (e.g., Snt2, recruiting factor for Rpd3) (Baker et al. 2013; McKnight et al. 2015) or the remodeling of chromatin/maintenance of the NFR (e.g., Rsc3, Rsc30) (Badis et al. 2008).Some of the TFBSs we found are puzzling, like those recognized...
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Research: Regeneration alters open chromatin and cis-regulatory landscape of erythroid precursors
- Yichao Zhou,
- Venkatasai Rahul Dogiparthi,
- Hannah L. Harris,
- Suhita Ray,
- Avik Choudhuri,
- Song Yang,
- Yi Zhou,
- Leonard I. Zon,
- M. Jordan Rowley,
- and Kyle J. Hewitt
Genome Res. July 2025 35: 1518-1529; Published in Advance June 2, 2025, doi:10.1101/gr.279949.124
...progenitors and precursors temporarily rewire their transcriptome, up- and downregulating hundreds of genes to accelerate the production of mature RBCs. Effective regeneration requires communication between critical cytokine signals (e.g., BMP4) and cis-regulatory elements on chromatin which coordinate...
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Research: Synergistic regulation by H3K36 and H3K27 methylation defines the chromatin landscape to control virulence and secondary metabolism in a fungal pathogen
- Xingmin Han,
- Chenghui Xu,
- Yiyi Ren,
- Meiling Guo,
- Jiayue Yan,
- Xuan Wang,
- Chao Liu,
- Qin Gu,
- Xing-Xing Shen,
- Zhonghua Ma,
- and Yun Chen
Genome Res. November 2025 35: 2472-2487; Published in Advance October 14, 2025, doi:10.1101/gr.280560.125
...2012; Zhao et al. 2019). Beyond histone lysine methylation, some SET domain proteins possess additional domains, such as tudor and chromo domains, facilitating recruitment to specific chromatin regions for gene regulation (Schotta et al. 2002; Zhu et al. 2013; Jurkowska et al. 2017; Chandrasekaran et...
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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
...fate determinants plays a critical role in specifying these identities. Epigenetic mechanisms, such as histones and their post-translational modifications, regulate chromatin compaction, transcription, and DNA replication timing to influence cell fate decisions. In stem cells, epigenetic regulation...
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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
..., these observations underscore the concept that transcriptional activity is associated with chromatin state, suggesting that the recruitment of TFs and reorganization of nucleosomes are required to facilitate the progression of transcriptional machinery.Differential TF binding activity can be identified by analyzing...
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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
...and Rowley (2022). Within the nucleus, chromatin organizes into a functional 3D landscape critical for development and differentiation (Rowley and Corces 2018; Zheng and Xie 2019; Harris and Rowley 2024). Whole- methodologies such as chromatin immunoprecipitation sequencing (ChIP-seq), assay for transposase...
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Method: Statistically rigorous and computationally efficient chromatin stripe detection with Quagga
- Fan Feng,
- Sean Moran,
- Anders S. Hansen,
- Xiaotian Zhang,
- and Jie Liu
Genome Res. January 2026 36: 159-168; Published in Advance November 12, 2025, doi:10.1101/gr.280132.124
..., Houston, Texas 77030, USA; 6Department of Computer Science and Engineering, University of Michigan, Ann Arbor, Michigan 48103, USA ↵7 These authors contributed equally to this work. Corresponding authors: Xiaotian.Zhang@uth.tmc.edu, drjieliu@umich.eduAbstractChromatin stripes are architectural chromatin...
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Method: Resolving the chromatin impact of mosaic variants with targeted Fiber-seq
- Stephanie C. Bohaczuk,
- Zachary J. Amador,
- Chang Li,
- Benjamin J. Mallory,
- Elliott G. Swanson,
- Jane Ranchalis,
- Mitchell R. Vollger,
- Katherine M. Munson,
- Tom Walsh,
- Morgan O. Hamm,
- Yizi Mao,
- Andre Lieber,
- and Andrew B. Stergachis
Genome Res. December 2024 34: 2269-2278; Published in Advance December 9, 2024, doi:10.1101/gr.279747.124
...∼60 CTG repeats. This suggests that the observed chromatin phenotype of DM1 requires a critical number of CTG repeats, which may be reached either by age-related somatic expansion in adult-onset DM1 or congenitally present in individuals born with large germline CTG repeats.Next, we sought to apply...

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