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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
...to that of a separate wild-type sample in terms of nucleosome and TF occupancy across all genes (R = 0.91 for nucleosome occupancy and R = 0.89 for TF occupancy), as well as their MNase fragment lengths and positions (Supplemental Fig. S2). By incorporating the full variability of MNase digestion and sequencing depth...
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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
...al. used LRS to confirm Lynch syndrome in a patient by detecting constitutional MLH1 promoter methylation in blood. Somatic loss of heterozygosity (LOH) in the patient's tumor led to the loss of the wild-type MLH1 allele, leaving only the methylated allele (O'Neill et al. 2024).Repeat expansion...
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Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
- Samuel H. Kim,
- Georgi K. Marinov,
- and William J. Greenleaf
Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
...of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet 46: 1311–1320. doi:10.1038/ng.3142 ↵Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, Davis S, Margulies EH, Chen Y, Bernat JA, Ginsburg D, et al. 2006. Genome-wide mapping of DNase...
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Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
- Jingwei Zhou,
- Yuhong Huang,
- Huan Ma,
- Yiqian Chen,
- Chuanye Chen,
- Fangpu Han,
- and Handong Su
Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
...), suggestive of breakage-induced end restructuring.View larger version: In this window In a new window Figure 2. Localized complex chromosomal structural variations at damaged centromeres in wheat ditelosomic lines. (A–C) Genomic-wide resequencing read depth analysis around centromere breakpoints...
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Method: A fast and adaptive detection framework for genome-wide chromatin loop mapping from Hi-C data
- Siyuan Chen,
- Jiuming Wang,
- Inkyung Jung,
- Zhaowen Qiu,
- Xin Gao,
- and Yu Li
Genome Res. August 2024 34: 1174-1184; Published in Advance August 13, 2024, doi:10.1101/gr.279274.124
...classifier for -wide detection. The limitation of the supervised classification framework primarily manifests in its detection speed and relatively small reception fields. Genome-wide detection with a binary classifier can be computationally inefficient as the small window causes scanning to be resource...
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Method: Genome-wide maps of CPD deamination in yeast reveal the impact of DNA sequence context and nucleosome architecture on cytosine deamination rates
- Marian F. Laughery,
- Bastian Stark,
- Benjamin Morledge-Hampton,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. January 2026 36: 183-196; Published in Advance December 9, 2025, doi:10.1101/gr.280384.124
...cytosine bases derived from UV-induced CPD lesions.Genome-wide map of CPD deamination in repair-deficient yeast cellsAlthough our aim was to analyze CPD deamination over a 48 h time course in nucleotide excision repair (NER)–deficient (i.e., rad14Δ) yeast cells, these cells are very sensitive to UV...
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Research: Genome-wide relaxation of selection and the evolution of the island syndrome in Orkney voles
- Xuejing Wang and
- Gerald Heckel
Genome Res. June 2024 34: 851-862; Published in Advance July 2, 2024, doi:10.1101/gr.278487.123
...window Figure 2. Genome-wide diversity and differentiation for common voles, M. arvalis, from the Orkney archipelago (brown) versus continental individuals (green). Density distributions (top) and Manhattan plots (bottom) for π, Tajima's D, and FST in 50 kb windows along the . Different chromosomes...
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Research: Genotype imputation from low-coverage data for medical and population genetic analyses
- Simone Andrea Biagini,
- Sara Becelaere,
- Mio Aerden,
- Tatjana Jatsenko,
- Laurens Hannes,
- Philip Van Damme,
- Jeroen Breckpot,
- Koenraad Devriendt,
- Bernard Thienpont,
- Joris Robert Vermeesch,
- Isabelle Cleynen,
- and Toomas Kivisild
Genome Res. September 2025 35: 1929-1941; Published in Advance July 22, 2025, doi:10.1101/gr.280175.124
...at the scale of tens of thousands to millions of individuals. With decreasing costs of sequencing, low-pass (at coverage <1×) whole- sequencing followed by imputation has become a cost-effective alternative for trait mapping and estimation of polygenic scores (PGSs) (Martin et al. 2021; Wasik et al. 2021...
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Research: Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection
- Shudi Zhao,
- Yuedong Li,
- Guanping Chen,
- Xingyang Wang,
- Nan Chen,
- and Xiaofeng Wu
Genome Res. November 2023 33: 1958-1974; Published in Advance October 23, 2023, doi:10.1101/gr.277931.123
...by making changes to both host and viral genetic regulatory network.MethodsCell culture, virus strain, and infectionBmN cells were cultured at 27°C in SF900 II SFM (Gibco) supplemented with 3% fetal bovine serum (FBS; Gibco). The T3 strain of BmNPV was maintained in our laboratory and used as the wild...
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Method: OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities
- Siavash Raeisi Dehkordi,
- Zhaoyang Jia,
- Joey Estabrook,
- Jen Hauenstein,
- Neil Miller,
- Naz Güleray-Lafci,
- Jürgen Neesen,
- Alex Hastie,
- Alka Chaubey,
- Andy Wing Chun Pang,
- Paul Dremsek,
- and Vineet Bafna
Genome Res. December 2025 35: 2671-2681; Published in Advance November 14, 2025, doi:10.1101/gr.280536.125
..., described in Supplemental Table S5. OMKar automates the interpretation as follows (see Supplemental Section S3.5): It aligns SVs in reconstructed chromosomes with their wild-type (WT) counterparts, identified by centromeric or segmental makeup. It uses the longest common subsequence algorithm to create...
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