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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
...: each received a 2048-bp one-hot encoded DNA sequence as input and was trained to predict the chromatin accessibility signal at 4-bp resolution across the central 1024-bp region (Fig. 1). This resolution was chosen because transcription factor binding motifs typically span more than 4 bp (Stewart et al...
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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
..., including the lead variant rs17361251 and two proxies (LD r2 = 1), rs17276513 and rs17276527. The AAA haplotype is associated with higher chromatin accessibility and gene expression. Using 323 bp DNA elements containing the three-variant haplotypes (Supplemental Table 25), we observed significantly higher...
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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
...factors bind directly to the DNA to activate or repress transcription (Marr et al. 2021; Minnoye et al. 2021). Recent advances in sequencing technology have enabled the characterization of chromatin remodelers, nucleosome positioning, and chromatin accessibility using high-throughput assays like Ch...
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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
...-translational modifications, play a crucial role in regulating programs integral to a cell's identity, like gene expression and DNA replication. However, the transcriptional, chromatin, and replication timing profiles of adult stem cells in vivo remain poorly understood. Containing germline stem cells (GSCs) and somatic cyst...
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Method: Multicondition and multimodal temporal profile inference during mouse embryonic development
- Ran Zhang,
- Chengxiang Qiu,
- Galina N. Filippova,
- Gang Li,
- Jay Shendure,
- Jean-Philippe Vert,
- Xinxian Deng,
- William Stafford Noble,
- and Christine M. Disteche
Genome Res. October 2025 35: 2339-2351; Published in Advance August 14, 2025, doi:10.1101/gr.279997.124
...of a population of cells can profile changes in gene expression, chromatin accessibility and structure, and DNA methylation as the cells carry out essential biological functions, differentiate, traverse the cell cycle, degenerate, or undergo stages of disease progression.Although such measurements have proven...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
..., a particular gene of interest (GOI) remains a persistent experimental and conceptual challenge. This gene-centric question is complicated by the multilayered regulatory environment in which each gene resides, comprising 3D chromatin structure, enhancer–promoter looping, DNA accessibility, histone modifications...
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Research: Transcription and potential functions of a novel XIST isoform in male peripheral glia
- Kevin S. O'Leary,
- Meng-Yen Li,
- Kevyn Jackson,
- Lijie Shi,
- Elena Ezhkova,
- Bernice E. Morrow,
- and Deyou Zheng
Genome Res. February 2026 36: 257-274; Published in Advance December 12, 2025, doi:10.1101/gr.280832.125
...was independently described by a recent report from Gorin and Goodman (2025).Characterization of XIST transcript sequence and regulation in peripheral nervesNext, we sought to investigate how XIST achieves such specific expression by comparing chromatin accessibility data from assay for transposase-accessible...
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Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
- Qunlun Shen,
- Shuqin Zhang,
- and Shihua Zhang
Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
...to accept current annotation results.Single-cell technologies such as single-cell RNA sequencing (scRNA-seq) (Kharchenko 2021), single-cell spatial transcriptomics (scST) (Longo et al. 2021), and single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) (Fang et al. 2021) have...
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Method: Aggregation of recount3 RNA-seq data improves inference of consensus and tissue-specific gene coexpression networks
- Prashanthi Ravichandran,
- Princy Parsana,
- Rebecca Keener,
- Kasper D. Hansen,
- and Alexis Battle
Genome Res. September 2025 35: 2087-2103; Published in Advance July 17, 2025, doi:10.1101/gr.280808.125
...and 312 hubs which were specific to the cancer consensus network (Supplemental Table S11). Cancer-specific hub genes were enriched for pathways such as ncRNA metabolic processing (GO:0034660, P = 5.2 × 10−2) which is believed to play a role in metabolic reprogramming in cancer, DNA damage response (GO...
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Method: ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies
- Jordan H. Little,
- Guillermo Hoffmann Meyer,
- Aakash Grover,
- Alex Michael Francette,
- Raghavendran Partha,
- Karen M. Arndt,
- Martin Smith,
- Nathan Clark,
- and Maria Chikina
Genome Res. September 2025 35: 2041-2051; Published in Advance August 7, 2025, doi:10.1101/gr.280586.125
.... Histone chaperones interact with histones and modulate the disassembly and assembly of nucleosomes in an ATP-independent manner during DNA-templated processes (Hammond et al. 2017). In S. cerevisiae, Spt6p, Spn1p, and the FAcilitates Chromatin Transcription (FACT) complex, containing Spt16p and Pob3p...

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