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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
...(Fig. 6E). These findings track accessibility during the early establishment and late resolution of a regeneration-dependent transcriptome in RBC precursors. Chromatin accessibility and transcriptional landscapes can be used to define mechanisms of hematopoietic differentiation within distinct...
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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
....Transcriptional regulation in eukaryotes is profoundly influenced by chromatin status, integrating diverse cellular signals to control gene expression (Berger 2007). Chromatin dynamics are modulated by multiple mechanisms, including histone modifications, DNA methylation, and chromatin remodeling complexes (Shilatifard 2006...
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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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Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
- Shahmir Naseer,
- Thomas C Clark,
- Bertrand Collet,
- Pooran Dewari,
- Damir Baranasic,
- Daniel J Macqueen,
- Pierre Boudinot,
- and Samuel A.M. Martin
Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
...IP-seq data sets 293 To investigate the chromatin landscape underlying the antiviral immune response to poly I:C, 294 we applied ChromHMM modelling to the ATAC-seq, H3K27ac, and H3K27me3 datasets. 295 This integrative analysis identified five distinct chromatin states, annotated following the 296 framework...
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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
...characterize highly accessible chromatin regions (peak-focused evaluation) and their capacity to distinguish between accessible and inaccessible regions across the complete chromosomal landscape (-wide evaluation).Among the architectures employed in existing methods (CNNs, LSTMs, and dCNNs), dCNNs consistently...
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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
...KAS-ATAC reveals the -wide single-stranded accessible chromatin landscape of the human Samuel H. Kim1,6, Georgi K. Marinov2,6 and William J. Greenleaf2,3,4,5 1Cancer Biology Programs, School of Medicine, Stanford University, Stanford, California 94305, USA; 2Department of Genetics, School...
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Research: Landscape of microRNA and target expression variation and covariation in single mouse embryonic stem cells
- Marcel Tarbier,
- Sebastian D. Mackowiak,
- Vaishnovi Sekar,
- Franziska Bonath,
- Etka Yapar,
- Bastian Fromm,
- Omid R. Faridani,
- Inna Biryukova,
- and Marc R. Friedländer
Genome Res. February 2026 36: 291-302; Published in Advance January 12, 2026, doi:10.1101/gr.279914.124
...-miRNAs remain in the chromatin for some time after processing (Conrad et al. 2014), and also, pri-miRNAs have previously been reported in sequencing of single nuclei (Elias et al. 2023), where they are located. The paucity of full-length pri-miRNAs in the control cells further suggests that pri...
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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
...for Biotechnology, Huntsville, Alabama 35806, USA; 6Department of Medicine, Division of Endocrinology & Metabolism, University of California San Diego, La Jolla, California 92093, USA Corresponding author: agoren@ucsd.eduAbstractChromatin immunoprecipitation followed by sequencing (ChIP-seq) is widely used to study...
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Research: Transcriptomic landscape of transposable elements reveals LTR7-PLAAT4 as a potential oncogene and therapeutic target in pancreatic adenocarcinoma
- Meilong Shi,
- Chuanqi Teng,
- Shan Zhang,
- Xiaobo He,
- Lingyun Xu,
- Fengxian Han,
- Rongqi Wen,
- Ganjun Yu,
- Jingwen Liu,
- Yang Feng,
- Yanfeng Wu,
- Yan Ren,
- Gang Jin,
- and Jing Li
Genome Res. February 2026 36: 275-290; Published in Advance January 8, 2026, doi:10.1101/gr.280528.125
...), or other regulatory elements, and constitute a substantial portion of lincRNAs (Khorkova et al. 2015; Choudhary et al. 2023). Despite their potential importance, the transcriptomic landscape and clinical relevance of TE-derived elements in PAAD remain poorly characterized, partly due to limited sample...
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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
...Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells Jennifer A. Urban1, Daniel Ringwalt1, John M. Urban2,3, Wingel Xue1,5, Ryan Gleason1, Keji Zhao4 and Xin Chen1,2 1Department of Biology, The Johns Hopkins University...
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