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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
..., identify segmentally duplicated genes, and enable the phasing of reads (Logsdon et al. 2020). The phasing specifically allows for the assignment of haplotypes to pathogenic variants, enhancing diagnostic utility. LRS advancements enable the simultaneous measurement of DNAm profiles alongside genetic data...
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Research: A genome-wide survey reveals a diverse array of enhancers coordinates the Drosophila innate immune response
- Lianne B Cohen,
- Tamara Hadzic,
- Caitlin Sauer,
- Julia R Gibbs,
- and Zeba Wunderlich
Genome Res. April 15, 2026 gr.281432.125; Published in Advance April 15, 2026, doi:10.1101/gr.281432.125
...Methods 547 Genome-wide reporter library construction 548 To generate a -wide reporter library, genomic DNA was isolated from both male and 549 female iso-1 flies, fragmented via sonication, and size selected (500-750 bps). To prepare and 550 clone these fragments into the the pSTARR-seq fly plasmid (AddGene...
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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
...interplay of nucleosomes and TFs together in the context of transcriptional regulation is crucial for better understanding gene regulation within an organism.Although numerous efforts to construct gene regulatory networks (GRNs) have used -wide expression profiling under various genetic and environmental...
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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
...sequences, both in UV-irradiated yeast cells and in human skin cancers. CPD deamination is suppressed near the transcription start and end sites of yeast genes, which may in part by mediated by DNA-bound transcription factors. Finally, we show that the wrapping of DNA in nucleosomes modulates CPD...
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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
...predicted bias profile from the observed ATAC/KAS-ATAC insertion profile.Data accessAll raw and processed sequencing data generated in this study have been submitted to the NCBI Gene Expression Omnibus (GEO; https://www.ncbi.nlm.nih.gov/geo/) under accession number GSE264534. Except where explicitly...
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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
...performed on the g:Profiler web server (Raudvere et al. 2019) with a P-value threshold at 0.01 for the genes falling at least 50% in the regions. We also looked for potential regulatory elements that overlapped >50% with outliers detected by DBSCAN by lifting regulatory regions of M. musculus (release 102...
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Resource: Genome-wide identification of tandem repeats associated with splicing variation across 49 tissues in humans
- Kohei Hamanaka,
- Daisuke Yamauchi,
- Eriko Koshimizu,
- Kei Watase,
- Kaoru Mogushi,
- Kinya Ishikawa,
- Hidehiro Mizusawa,
- Naomi Tsuchida,
- Yuri Uchiyama,
- Atsushi Fujita,
- Kazuharu Misawa,
- Takeshi Mizuguchi,
- Satoko Miyatake,
- and Naomichi Matsumoto
Genome Res. March 2023 33: 435-447; Published in Advance March 27, 2023, doi:10.1101/gr.277335.122
...is associated with gene regulation. Although previous studies reported several tandem repeats regulating gene splicing in cis (spl-TRs), no large-scale study has been conducted. In this study, we established a -wide catalog of 9537 spl-TRs with a total of 58,290 significant TR–splicing associations across 49...
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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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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
...activation of several antiviral genes. (A–H) Normalized ATAC-seq, H3K27ac ChIP-seq, RNA-seq profiles, and Hi-C contacts showing the regulatory network of enhancers at eight antiviral gene—KWMTBOMO04623 (A), KWMTBOMO05356 (B), KWMTBOMO05588 (C), KWMTBOMO13292 (D), KWMTBOMO15542 (E), KWMTBOMO16000 (F...

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