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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
...regions of a few kilobases, rich in dinucleotides CpG, for which it has been functionally demonstrated that they control, in cis, the monoallelic expression of all imprinted genes within a cluster (Arnaud 2010; Kelsey and Feil 2013). Although most of them overlap CpG islands (regions >200 bp with GC...
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Mini-Review: The chromatin tapestry as a framework for neurodevelopment
- Ben Nolan,
- Timothy E. Reznicek,
- Christopher T. Cummings,
- and M. Jordan Rowley
Genome Res. October 2024 34: 1477-1486; doi:10.1101/gr.278408.123
..., here we highlight work showing impacts on additional features of the chromatin tapestry.A study examining chromatin dynamics in fibroblasts from patients with CdLS to that of control fibroblasts noted that NIPBL binding is strongly associated with regions of high GC content, including CpG islands...
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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
...to CpG methylation when MboI is not (Belaghzal et al. 2017).The difference in called stripe length and the number of stripes called is supported in the aggregate epigenomics pileup, in which we performed an epigenomic pileup of averaged transcription factor signal for CTCF-stripes or EP...
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Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
- Laura Blanco-Berdugo,
- Alexis Garretson,
- and Beth L. Dumont
Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
...Fig. 6A) and arise in regions of similar GC content (two-tailed Wilcoxon rank-sum test, P = 0.215) (Supplemental Fig. 6B). Likewise, we detect no significant enrichment or depletion of ART-associated dnSNVs in CpG islands (Fisher's exact test, P = 0.686) (Supplemental Fig. 6C). The majority of dn...
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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
...al. 2019; Barešić et al. 2020), often enhancers (Davidson et al. 2011; Edwards et al. 2012; Corradin and Scacheri 2014). Initial studies portioning the heritability of both childhood and adult onset disorders into regions of open chromatin and their associated cell types implicate the period...
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Research: Revisiting chromatin packaging in mouse sperm
- Qiangzong Yin,
- Chih-Hsiang Yang,
- Olga S. Strelkova,
- Jingyi Wu,
- Yu Sun,
- Sneha Gopalan,
- Liyan Yang,
- Job Dekker,
- Thomas G. Fazzio,
- Xin Zhiguo Li,
- Johan Gibcus,
- and Oliver J. Rando
Genome Res. December 2023 33: 2079-2093; Published in Advance December 21, 2023, doi:10.1101/gr.277845.123
...-Toneu and Peters 2023). A number of studies have mapped the locations of retained nucleosomes, with the majority of reports in humans and mice finding nucleosomes enriched at CpG island regulatory elements associated with key developmental genes (Arpanahi et al. 2009; Hammoud et al. 2009; Brykczynska et al. 2010...
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Method: Resolving the chromatin impact of mosaic variants with targeted Fiber-seq
- Stephanie C. Bohaczuk,
- Zachary J. Amador,
- Chang Li,
- Benjamin J. Mallory,
- Elliott G. Swanson,
- Jane Ranchalis,
- Mitchell R. Vollger,
- Katherine M. Munson,
- Tom Walsh,
- Morgan O. Hamm,
- Yizi Mao,
- Andre Lieber,
- and Andrew B. Stergachis
Genome Res. December 2024 34: 2269-2278; Published in Advance December 9, 2024, doi:10.1101/gr.279747.124
...within the 160 kb targeted region, thereby identifying whether it arose from chromatin fibers containing the normal or pathogenic repeat expansion (Fig. 2C; Supplemental Fig. S2; Methods). Pathogenic DMPK CTG repeat expansions have previously been associated with increased CpG methylation upstream...
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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
...regulators in GSC-like cells. To characterize chromatin landscapes, we develop a cell-type-specific chromatin profiling assay to map H3K4me3-, H3K27me3-, and H3K9me3-enriched regions, corresponding to the euchromatic, facultative heterochromatic, and constitutive heterochromatic domains, respectively...
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Research: Deciphering D4Z4 CpG methylation gradients in fascioscapulohumeral muscular dystrophy using nanopore sequencing
- Russell J. Butterfield,
- Diane M. Dunn,
- Brett Duval,
- Sarah Moldt,
- and Robert B. Weiss
Genome Res. September 2023 33: 1439-1454; Published in Advance October 5, 2023, doi:10.1101/gr.277871.123
...RD complexes through their methyl-CpG-binding protein domain 2 (MBD2) subunits to specific methyl-CpGs. Recent studies indicate that MBD2 has high affinity for large and densely methylated CpG islands, allowing recruitment of NuRD to facilitate nucleosome positioning, histone deacetylation, and chromatin...
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Research: MHC in newts illuminates the evolutionary dynamics of complex regions in giant genomes
- Wiesław Babik,
- Katarzyna Dudek,
- Gemma Palomar,
- Marzena Marszałek,
- Grzegorz Dubin,
- Maximina H. Yun,
- and Magdalena Migalska
Genome Res. February 2026 36: 303-317; Published in Advance January 12, 2026, doi:10.1101/gr.281127.125
...MHC in newts illuminates the evolutionary dynamics of complex regions in giant s Wiesław Babik1, Katarzyna Dudek1, Gemma Palomar1,2, Marzena Marszałek1,3, Grzegorz Dubin4, Maximina H. Yun5,6 and Magdalena Migalska1 1Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University...

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