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Method: Unsupervised contrastive peak caller for ATAC-seq
- Ha T.H. Vu,
- Yudi Zhang,
- Geetu Tuteja,
- and Karin S. Dorman
Genome Res. July 2023 33: 1133-1144; Published in Advance May 22, 2023, doi:10.1101/gr.277677.123
..., Ames, Iowa 50011, USA ↵4 These authors contributed equally to this work. Corresponding author: kdorman@iastate.eduAbstractThe assay for transposase-accessible chromatin with sequencing (ATAC-seq) is a common assay to identify chromatin accessible regions by using a Tn5 transposase that can access, cut...
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Resource: An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants
- Can Yuan,
- Lijing Tang,
- Thomas Lopdell,
- Vyacheslav A. Petrov,
- Claire Oget-Ebrad,
- Gabriel Costa Monteiro Moreira,
- José Luis Gualdrón Duarte,
- Arnaud Sartelet,
- Zhangrui Cheng,
- Mazdak Salavati,
- D. Claire Wathes,
- Mark A. Crowe,
- GplusE Consortium,
- Wouter Coppieters,
- Mathew Littlejohn,
- Carole Charlier,
- Tom Druet,
- Michel Georges,
- and Haruko Takeda
Genome Res. October 2023 33: 1848-1864; Published in Advance September 26, 2023, doi:10.1101/gr.277947.123
...on gene expression (G = Q allele = higher PLAG1/CHCHD7 expression = more accessible; A = q allele = lower PLAG1/CHCHD7 expression = less accessible). Moreover, the rs209821678 variant lies in a trough revealed in the ATAC-seq mode profile, suggesting that the corresponding segments mediated binding...
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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
...outperformed others in both peak-focused and -wide settings (Fig. 2A, Supplemental Fig. S2). However, upon incorporating ConvNeXt V2 blocks in the stem of these architectures, all models demonstrated similar high correlations with the experimental ATAC-seq values in the accessible regions as well as on whole...
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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
...the spatial and temporal dynamics of enhancer–promoter interactions. Understanding how enhancers interact with promoters will deepen our understanding of the regulation of gene expression and the molecular underpinnings of transcriptional control.Gene expression programs are encoded by cis-regulatory elements...
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Research: Genetic effects on chromatin accessibility uncover mechanisms of liver gene regulation and quantitative traits
- Kevin W. Currin,
- Hannah J. Perrin,
- Gautam K. Pandey,
- Abdalla A. Alkhawaja,
- Swarooparani Vadlamudi,
- Annie E. Musser,
- Amy S. Etheridge,
- K. Alaine Broadaway,
- Jonathan D. Rosen,
- Arushi Varshney,
- Amarjit S. Chaudhry,
- Paul J. Gallins,
- Fred A. Wright,
- Yi-hui Zhou,
- Stephen C.J. Parker,
- Laura M. Raffield,
- Erin G. Schuetz,
- Federico Innocenti,
- and Karen L. Mohlke
Genome Res. July 2025 35: 1485-1502; Published in Advance May 20, 2025, doi:10.1101/gr.279741.124
....ResultsGenetic effects on liver chromatin accessibilityWe profiled chromatin accessibility using ATAC-seq (Buenrostro et al. 2013; Corces et al. 2017) in liver tissue samples from 138 human individuals, consisting of 89 males and 49 females (Fig. 1A; Supplemental Table 1). The ages of donors ranged from 2 to 81 years...
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Method: Unified integration of spatial transcriptomics across platforms with LLOKI
- Ellie Haber,
- Ajinkya Deshpande,
- Jian Ma,
- and Spencer Krieger
Genome Res. December 2025 35: 2722-2733; Published in Advance November 13, 2025, doi:10.1101/gr.280803.125
...GENE (CZI Cell Science Program et al. 2025), and the Human Cell Atlas (Regev et al. 2017). Similarly, integrating spatial transcriptomics (ST) data sets, which contain both spatial coordinates and gene expression, enables comparative analysis across samples, technologies, and conditions, revealing cellular...
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Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
- Sarah M. Leichter,
- Kami Ahmad,
- and Steven Henikoff
Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
...and derepression of enhancer activity under stress-associated conditions. These results point to chromatin-level changes that may prime these cells for altered transcriptional programs with age.Polycomb repression of barrier membrane genes in aging enterocytesA major defect of the aging Drosophila gut is breakdown...
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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. April 2026 36: 849-864; Published in Advance March 4, 2026, doi:10.1101/gr.281113.125
...-upregulated, with the dopaminergic synapse pathway in the former and the PD pathway in the latter (Supplemental Fig. S7).Age-associated differential chromatin accessibility in subclassesTo investigate epigenomic changes in the substantia nigra with aging, we visualized scATAC-seq data using UMAP at a 500-base pair (bp) resolution...
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Research: Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development
- Song Zhang,
- Chao Wang,
- Shenghua Qin,
- Choulin Chen,
- Yongzhou Bao,
- Yuanyuan Zhang,
- Lingna Xu,
- Qingyou Liu,
- Yunxiang Zhao,
- Kui Li,
- Zhonglin Tang,
- and Yuwen Liu
Genome Res. December 2024 34: 2190-2202; Published in Advance October 21, 2024, doi:10.1101/gr.278344.123
...myofiber formation and hypertrophy stages. By developing an innovative approach integrating SE temporal patterns, eRNA annotation, -wide association study (GWAS) signals, and self-transcribing active regulatory region sequencing (STARR-seq) experiments, Our study not only reveals the critical enhancer...
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Method: methyl-ATAC-seq measures DNA methylation at accessible chromatin
- Roman Spektor,
- Nathaniel D. Tippens,
- Claudia A. Mimoso,
- and Paul D. Soloway
Genome Res. June 2019 29: 969-977; Published in Advance June 3, 2019, doi:10.1101/gr.245399.118
...methylation analyses to accessible regulatory regions of the .ResultsFigure 1 shows the workflow and sample results for mATAC-seq. It includes two primary modifications during the transposition step of the Omni-ATAC-seq protocol: (1) Methylated oligonucleotides are loaded onto Tn5 to generate the transposome...

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