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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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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
.... High sensitivity mapping of methylated cytosines. Nucleic Acids Res 22: 2990–2997. doi:10.1093/nar/22.15.2990 ↵Cokus SJ, Feng S, Zhang X, Chen Z, Merriman B, Haudenschild CD, Pradhan S, Nelson SF, Pellegrini M, Jacobsen SE. 2008. Shotgun bisulphite sequencing of the Arabidopsis reveals DNA methylation...
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Research: Ultraviolet damage and repair maps in Drosophila reveal the impact of domain-specific changes in nucleosome repeat length on repair efficiency
- Benjamin Morledge-Hampton,
- Kathiresan Selvam,
- Manish Chauhan,
- Alan G. Goodman,
- and John J. Wyrick
Genome Res. February 2025 35: 257-267; Published in Advance January 6, 2025, doi:10.1101/gr.279605.124
..., analysis of repair activity at the 30 min time point indicated elevated CPD repair in linker DNA compared with nucleosomal DNA (Fig. 3B). These results are consistent with previous -wide studies in yeast cells showing that repair of CPDs is more efficient in linker DNA (Mao et al. 2016). Notably...
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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
.... Genome-wide mapping of nucleosome positioning and DNA methylation within individual DNA molecules. Genome Res 22: 2497–2506. doi:10.1101/gr.143008.112 ↵Kouzine F, Gupta A, Baranello L, Wojtowicz D, Ben-Aissa K, Liu J, Przytycka TM, Levens D. 2013. Transcription-dependent dynamic supercoiling is a short...
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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
...-positive genes during diapause of Asian corn borer larvae. (E) Heatmaps showing the dynamics of H3K27me3 (left) and DNA methylation (right) on H3K27me3-positive genes during diapause of Asian corn borer larvae. (F–H) Genome-wide correlation plots depicting the association between H3K9me3 and DNA...
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Method: Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine
- Bo Yan,
- Duan Wang,
- and Laurence Ettwiller
Genome Res. June 2024 34: 904-913; Published in Advance June 10, 2024, doi:10.1101/gr.278294.123
...- or targeted- sequencing show the same germline variation calling accuracy and sensitivity compared with standard DNA-seq. Additionally, regional methylation levels provide an accurate map of the human methylome.Cytosine methylation is the main epigenetic DNA modification found in higher Eukaryotes. In humans...
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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
...been extensively assessed, their impact on epigenetics has been poorly studied and limited to specific genomic regions. Here, we investigated the hypothesis that some STRs act as independent regulators of local DNA methylation in the human and modify risk of common human traits. To address...
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Method: Genome-wide prediction of DNA mutation effect on nucleosome positions for yeast synthetic genomics
- Etienne Routhier,
- Edgard Pierre,
- Ghazaleh Khodabandelou,
- and Julien Mozziconacci
Genome Res. February 2021 31: 317-326; Published in Advance December 18, 2020, doi:10.1101/gr.264416.120
...Hub (https://github.com/etirouthier/NucleosomeDensity/blob/master/Results_nucleosome/mutasome_scerevisiae.bw) and can be used freely by others, when designing genetically modified yeast, to anticipate the effect of induced mutations on nucleosome positioning. We also use this track to analyze the DNA motifs...
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Research: Genome-wide maps of alkylation damage, repair, and mutagenesis in yeast reveal mechanisms of mutational heterogeneity
- Peng Mao,
- Alexander J. Brown,
- Ewa P. Malc,
- Piotr A. Mieczkowski,
- Michael J. Smerdon,
- Steven A. Roberts,
- and John J. Wyrick
Genome Res. October 2017 27: 1674-1684; Published in Advance September 14, 2017, doi:10.1101/gr.225771.117
.... Only well-positioned nucleosomes (NCP score≥ 1) are depicted. Genome-wide maps of DNA repair and mutagenesis Genome Research 1675 www..org associated with 3meA lesions (relative to T-associated reads) was more apparent when yeast cells were treated with a higher dose of MMS (0.4% for 10 min...
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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
...-cell data.The chromatin loop serves as a crucial structural variant that bridges promoters with regulatory regions, playing a pivotal role in DNA replication and gene transcription. It is closely related to DNA replication and gene transcription. Moreover, it serves as a vital regulator, enabling...
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