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Resource: Epigenomics of embryogenesis in turbot
- Oscar Aramburu,
- Belen G Pardo,
- Ada Jimenez-Gonzalez,
- Andrés Blanco-Hortas,
- Daniel Macqueen,
- Carmen Bouza,
- and Paulino Martinez
Genome Res. November 4, 2025 gr.280355.124; Published in Advance November 4, 2025, doi:10.1101/gr.280355.124
...to the hypergeometric test. This suggests that 630 most promoters were already accessible without major alterations in global 631 chromatin accessibility between consecutive stages, pointing to the key 632 regulatory role of enhancers on gene expression. This asynchronism between 633 chromatin accessibility of CREs...
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Mini-Review: Revisiting models of enhancer–promoter communication in gene regulation
- Gilad Barshad and
- Charles G. Danko
Genome Res. June 2025 35: 1277-1286; doi:10.1101/gr.278389.123
...bidirectionally, transcribes 20–60 bp, and enters a paused state, known as the promoter proximal pause (Fig. 1; Buckley et al. 2014; Jonkers et al. 2014; Henriques et al. 2018). At enhancers, these short and typically bidirectional transcription units encode enhancer-templated RNAs (eRNAs), which are terminated...
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Method: k-mer cross-species profiling reveals taxon-specific TE expansions accompanied by KZFP co-option and functional impacts in ruminants
- Pengju Zhao,
- Jiayi He,
- Chen Peng,
- Yuelang Zhang,
- Chong Wang,
- Dongyou Yu,
- Lingzhao Fang,
- and Zhengguang Wang
Genome Res. March 23, 2026 gr.281289.125; Published in Advance March 23, 2026, doi:10.1101/gr.281289.125
...methodology but also facilitates the examination of 395 KZFP-TE coevolutionary processes. To gain deeper insights into ruminant TE relationships, 396 we employed global de novo assembly utilizing LongRepMarker for TE consensus sequence 397 detection, as opposed to utilizing conventional conserved TE sequences...
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Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
- Wenhai Zhang,
- Yuansheng Liu,
- Guangyi Li,
- Jialu Xu,
- Enlian Chen,
- Alexander Schönhuth,
- and Xiao Luo
Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
...for multiple species provides a detailed view of strain diversity and abundance across different species, enhancing our understanding of microbial dynamics. Additionally, strain-level profiling for a single species allows for in-depth analysis of strain variation within that species. To comprehensively...
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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
...amounts of antibodies had minimal impact on the global ChIP-seq signal, and the overall trend is that higher amounts of antibodies may lead to only slightly higher ChIP enrichment (Supplemental Fig. S4). However, when we equally divided the ChIP-seq peaks into four quartiles based on the normalized read...
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Resource: A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq
- Sophia C. Gaynor-Gillett,
- Lijun Cheng,
- Manman Shi,
- Jason Liu,
- Gaoyuan Wang,
- Megan Spector,
- Qiuyu Guo,
- Le Qi,
- Mary Flaherty,
- Martha Wall,
- Ahyeon Hwang,
- Mengting Gu,
- Zhanlin Chen,
- Yuhang Chen,
- PsychENCODE Consortium,
- Jennifer R. Moran,
- Jing Zhang,
- Donghoon Lee,
- Mark Gerstein,
- Daniel Geschwind,
- and Kevin P. White
Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124
...the reads fell within our initial target regions. Over 89% of our sequencing reads qualified as “on-target” (Supplemental Table S3).View this table: In this window In a new window Table 1. Quality assessment of CapSTARR-seq data setIdentification of CapSTARR-seq active enhancer regionsWe called peaks from...
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Mini-Review: Evolution of genome-wide methylation profiling technologies
- Carolina Montano and
- Winston Timp
Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
...with global developmental delay. They also identified other genetic variations (insertions, SNVs, SVs, duplications, deletions) occurring in cis with proximal regulatory element hypermethylation and predicted to disrupt regulatory element activity.X-Chromosome inactivationAllele-specific methylation...
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Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
- Yao Wang,
- Dong Yu,
- Yue Mei,
- ZhiDa Fu,
- Jian Lin,
- Di Wu,
- Yuan Yang,
- and Hongli Yan
Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
...). Hepatocellular carcinoma (HCC) is the most common PLC, accounting for >80% of cases (Llovet et al. 2021). China is among the areas associated with the highest risk of developing HCC, accounting for 42.5% of the global incidence of liver cancer (Bray et al. 2024; Miao et al. 2024). Notably, ∼90% of HCC cases...
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Research: Integrating genetic variation with deep learning provides context for variants impacting transcription factor binding during embryogenesis
- Olga M. Sigalova,
- Mattia Forneris,
- Frosina Stojanovska,
- Bingqing Zhao,
- Rebecca R. Viales,
- Adam Rabinowitz,
- Fayrouz Hammal,
- Benoît Ballester,
- Judith B. Zaugg,
- and Eileen E.M. Furlong
Genome Res. May 2025 35: 1138-1153; Published in Advance April 15, 2025, doi:10.1101/gr.279652.124
...that are essential for mesoderm specification to differentiated muscle and are cobound to many developmental enhancers (Sandmann et al. 2006, 2007; Jakobsen et al. 2007; Zinzen et al. 2009), allowing us to assess the impact of genetic variation on potential cooperative binding. Second, the fourth factor, CTCF...
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Resource: Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson's disease
- Kangli Wang,
- Weikun Xia,
- Yingli Gu,
- Songpeng Zu,
- Qian Yang,
- Maria Luisa Amaral,
- Yaozhi Wang,
- Allen Wang,
- Xiang-Dong Fu,
- William C. Mobley,
- and Bing Ren
Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...Single-nucleus multiomic profiling of the aging mouse substantia nigra reveals conserved gene alterations linked to Parkinson’s disease Kangli Wang,1 Weikun Xia,1 Yingli Gu,1 Songpeng Zu,1 Qian Yang,2 Maria Luisa Amaral,1 Yaozhi Wang,1 Allen Wang,2 Xiang-Dong Fu,3 William C. Mobley,4 and Bing Ren1...
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