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Review: The superpowers of imprinting control regions
- Bertille Montibus,
- Franck Court,
- and Philippe Arnaud
Genome Res. January 2026 36: 1-19; Published in Advance December 10, 2025, doi:10.1101/gr.281215.125
...allele-specific gene expression across large imprinted domains. In this review, we highlight the features that define ICRs as a distinct class of cis-regulatory regions, from their ability to maintain germline-inherited DNA methylation to their multifunctional roles in transcriptional control. For each...
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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
...with the up- and downregulation of genes and use these signatures to reveal regulatory mechanisms previously unexplored in expression-based studies. Finally, we demonstrate that chromatin features are predictive of transcriptional activity, and we leverage these features to reconstruct chromatin...
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Research: Epigenetic and evolutionary features of ape subterminal heterochromatin
- DongAhn Yoo,
- Katherine M. Munson,
- and Evan E. Eichler
Genome Res. January 2026 36: 38-49; Published in Advance October 22, 2025, doi:10.1101/gr.280987.125
...12% (10/82) of haplotype comparisons show >99% sequence identity with >50% alignment coverage. Most haplotype comparisons show >10% sequence divergence (Supplemental Figs. S10–S13). A comparison with other genomic regions, including centromere, acrocentric, and remaining regions, reveals...
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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
...features in which a singular loop anchor interacts with a contiguous region of DNA so, at the bulk sequencing level, it appears as a long stripe on chromatin contact matrices. Stripes are thought to play an important role in gene regulation and have been implicated in regulating a cell's lineage...
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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: 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...
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Resource: Allele-specific transcription factor binding across human brain regions offers mechanistic insight into eQTLs
- Ashlyn G. Anderson,
- Belle A. Moyers,
- Jacob M. Loupe,
- Ivan Rodriguez-Nunez,
- Stephanie A. Felker,
- James M.J. Lawlor,
- William E. Bunney,
- Blynn G. Bunney,
- Preston M. Cartagena,
- Adolfo Sequeira,
- Stanley J. Watson,
- Huda Akil,
- Eric M. Mendenhall,
- Gregory M. Cooper,
- and Richard M. Myers
Genome Res. August 2024 34: 1224-1234; Published in Advance August 16, 2024, doi:10.1101/gr.278601.123
...D). Consequently, this variant likely impacts the expression of BEGAIN through changes in 3D chromatin structure resulting from altered cohesin binding.View larger version: In this window In a new window Figure 5. ASB analysis assists with fine-mapping eQTLs. (A) Genomic tracks for the 100 kb region...
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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
...epigenomic 121 changes in chromatin state following this stimulation and shed light on regulatory elements 122 and TFBSs influencing antiviral transcriptional responses in a complex teleost . 123 Genomic sequencing data and sample metadata 124 Thirty-eight datasets were generated, comprising ATAC-seq (12...
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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
...first approach the question of what regulates your GOI transcriptionally, you should start by compiling available information on chromatin landscape (especially regulatory region hallmarks) and TF binding from browsers (e.g., UCSC Genome Browser) and user-friendly databases (e.g., Harmonizome). For most...
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Research: Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice
- Leandros Boukas,
- Teresa Romeo Luperchio,
- Afrooz Razi,
- Kasper D. Hansen,
- and Hans T. Bjornsson
Genome Res. May 2024 34: 696-710; Published in Advance May 3, 2024, doi:10.1101/gr.278416.123
...in KS1 and KS2 = 60.01 and 1508.9, respectively.Aging-related regions show preferentially disrupted chromatin accessibility in KS1 and KS2 neurons but not in B or T cellsOur findings yield insights into (1) the genomic distribution of the chromatin defects in KS1 and KS2 and (2) the cell type...

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