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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
...—allowing us to interrogate methylation associated with specific alleles. It can even be phased to group with specific somatic mutations, allowing us to observe genomic and epigenomic interactions.We lack robust statistical or analytical tools that identify loci with different methylation between germline...
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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
...-axis, and fragment length is plotted on the y-axis, indicating nucleosome or TF-sized DNA. (C) Genome-wide map of chromatin changes in response to genetic perturbations. Loci with significant chromatin changes in response to a deletion are highlighted in purple (those reflecting the mutant deletion itself...
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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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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
...Cas9 and Cas9 specificity using ssDNA mapping. Genome Biol 24: 85. doi:10.1186/s13059-023-02930-z ↵Marinov GK, Shipony Z, Kundaje A, Greenleaf WJ. 2023b. Genome-wide mapping of active regulatory elements using ATAC-seq. Methods Mol Biol 2611: 3–19. doi:10.1007/978-1-0716-2899-7_1 ↵McGhee JD, Wood WI...
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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
...@cse.cuhk.edu.hk, xin.gao@kaust.edu.saAbstractChromatin loop identification plays an important role in molecular biology and 3D genomics research, as it constitutes a fundamental process in transcription and gene regulation. Such precise chromatin structures can be identified across -wide interaction matrices via Hi...
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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: Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)
- Pengfei Lv,
- Xingzhuo Yang,
- Xianguo Zhao,
- Zhangwu Zhao,
- and Juan Du
Genome Res. May 2024 34: 725-739; Published in Advance June 12, 2024, doi:10.1101/gr.278661.123
...of H3K9me3 and H3K27me3 in the nondiapause (C), prediapause (D), and diapause (E) stages. (F–H) Venn diagram shows the number of genes with H3K9me3 peaks, H3K27me3 peaks, or both at the nondiapause (F), prediapause (G), and diapause (H) stages. (I–K) Genome-wide correlation plots showing correlation...
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Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
- Sheila Lutz,
- Megan Lawler,
- Samuel Amidon,
- and Frank W Albert
Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
...dissect this region and identify two 28 causal variants in two genes, MKT1 and SAL1. Engineering these variants alone and in 29 combination reveals gene-by-environment interactions at both genes, as well as epistatic 30 interactions between them that were dependent on the environment. CRI-SPA-Map...
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Research: Genome-wide evaluation of the effect of short tandem repeat variation on local DNA methylation
- Alejandro Martin-Trujillo,
- Paras Garg,
- Nihir Patel,
- Bharati Jadhav,
- and Andrew J. Sharp
Genome Res. February 2023 33: 184-196; Published in Advance December 28, 2022, doi:10.1101/gr.277057.122
...regulatory roles in DNA methylation (Fig. 1), we first performed a -wide QTL analysis between STR genotypes and DNA methylation levels of nearby CpGs in a discovery cohort of 245 samples collected by the Pediatric Cardiac Genomics Consortium (PCGC). This analysis identified a total of 19,129 pairwise...
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Method: Scalable cell-specific coexpression networks for granular regulatory pattern discovery with NeighbourNet
- Yidi Deng,
- Jiadong Mao,
- Jarny Choi,
- and Kim-Anh Lê Cao
Genome Res. April 2026 36: 785-801; Published in Advance March 5, 2026, doi:10.1101/gr.281171.125
...In parallel, we incorporate prior knowledge by mapping observed coexpression edges to curated regulatory and signaling interaction databases. This step produces context-specific gene regulatory networks (GRNs) with regulatory directories and allows for the inference of upstream signaling pathways (USPs...
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