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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: 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: LTRs activated by Epstein-Barr virus–induced transformation of B cells alter the transcriptome
- Amy Leung,
- Candi Trac,
- Hiroyuki Kato,
- Kevin R. Costello,
- Zhaoxia Chen,
- Rama Natarajan,
- and Dustin E. Schones
Genome Res. December 2018 28: 1791-1798; Published in Advance October 31, 2018, doi:10.1101/gr.233585.117
...as direct gene targets of Epstein-Barr virus (EBV) nuclear antigen 1 critical for EBV-infected B-lymphocyte survival. J Virol 90: 345–355. doi:10.1128/JVI.02318-15 ↵Thompson PJ, Macfarlan TS, Lorincz MC. 2016. Long terminal repeats: from parasitic elements to building blocks of the transcriptional...
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Research: The chromatin landscape of the histone-possessing Bacteriovorax bacteria
- Georgi K. Marinov,
- Benjamin Doughty,
- Anshul Kundaje,
- and William J. Greenleaf
Genome Res. January 2025 35: 109-123; Published in Advance November 21, 2024, doi:10.1101/gr.279418.124
...proposed to exhibit a range of divergent features compared with histones in archaea and eukaryotes. However, no functional genomic studies of the properties of Bdellovibrionota chromatin have been carried out. In this work, we map the landscape of chromatin accessibility, active transcription, and three...
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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 epigenetic studies. Nucleic Acids Res 47: e69. doi:10.1093/nar/gkz222 ↵Busby M, Xue C, Li C, Farjoun Y, Gienger E, Yofe I, Gladden A, Epstein CB, Cornett EM, Rothbart SB, et al. 2016. Systematic comparison of monoclonal versus polyclonal antibodies for mapping histone modifications by ChIP-seq. Epigenetics...
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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
...regulatory 113 elements across vertebrates. 114 Results 115 In this study we examine the modulation of gene expression, chromatin accessibility and 116 histone modifications in Atlantic salmon following stimulation using poly I:C, a mimic of 117 infection with an RNA virus. A major transcriptomic response...
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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
...,P). Collectively, these results indicate that Set2 and Ash1 play distinct roles in the transcriptional landscape of H3K36me3-marked genes in F. graminearum, with Set2 associated with actively transcribed genes and Ash1 enriched at loci with lower transcriptional activity.Ash1 activity modulates H3K27me3...
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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
...489: 57–74. doi:10.1038/nature11247 ↵The ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, et al. 2020. Expanded encyclopaedias of DNA elements in the human and mouse s. Nature 583: 699–710. doi:10.1038/s41586-020-2493-4 ↵Ernst J...
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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
...in understanding which architectural paradigms perform best for high-resolution chromatin accessibility prediction.In this work, we present a systematic evaluation of deep learning models for predicting ATAC-seq signals at 4-bp resolution from DNA sequence. We begin by extensively tuning three commonly used...
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Review: Navigating the landscape of epitranscriptomics and host immunity
- Elaine Huang,
- Clara Frydman,
- and Xinshu Xiao
Genome Res. April 2024 34: 515-529; Published in Advance May 3, 2024, doi:10.1101/gr.278412.123
...signature genes (Liu et al. 2019c). Alternatively, genetics-based approaches can be used to identify supporting evidence for dsRNA immunogenicity. Colocalization analysis between genetic variants associated with A-to-I editing (edQTLs) and risk loci for autoimmune and immune-mediated diseases facilitated...

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