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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
...patterns, acting as molecular fingerprints that reveal their cellular origins. Scientists have developed highly specific “liquid biopsies,” noninvasive biomarkers that identify the DNA's tissue or cell-type source by analyzing cfDNA methylation patterns (Yu et al. 2023a). This has led to applications...
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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
...revealed a roughly periodic pattern of CPD deamination, particularly at distal positions (i.e., −73 to −20 and +20 to +73) in the nucleosome DNA (Supplemental Fig. S9, top). In general, normalized dCPD levels were lower at minor-out rotational settings (Supplemental Fig. S9, dashed lines) and higher...
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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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Research: Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations
- Xiu Fan,
- Qili Qian,
- Wenran Li,
- Tianzi Liu,
- Changqing Zeng,
- Peilin Jia,
- Huandong Lin,
- Xin Gao,
- Li Jin,
- Mingfeng Xia,
- Sijia Wang,
- and Fan Liu
Genome Res. October 2025 35: 2173-2188; Published in Advance August 1, 2025, doi:10.1101/gr.280155.124
...and stochastic accumulation of epigenetic changes, such as DNA methylation variability, with advancing age. Although increasingly recognized for its potential role in aging biology, its extent, biological significance, and population specificity remain insufficiently characterized. Here, we present the first...
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Research: Distinct classes of lamina-associated domains are defined by differential patterns of repressive histone methylation
- Caden J. Martin,
- Elizabeth A. Oser,
- Prabakaran Nagarajan,
- Liudmila V. Popova,
- Benjamin D. Sunkel,
- Benjamin Z. Stanton,
- and Mark R. Parthun
Genome Res. September 2025 35: 1959-1974; Published in Advance August 5, 2025, doi:10.1101/gr.280380.124
...that the different patterns of PTM enrichment between the three LAD clusters could affect their three-dimensional organization within the nucleus. We performed 3D DNA FISH to test whether the association with the nuclear lamina varies between clusters, using Lamin A/C staining to visualize the nuclear periphery (Fig...
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Research: Transposable elements contribute to the evolution of host shift–related genes in cactophilic Drosophila species
- Daniel Siqueira de Oliveira,
- Anaïs Larue,
- William Vilas Boas Nunes,
- Francois Sabot,
- Alejandra Bodelón,
- María Pilar García Guerreiro,
- Cristina Vieira,
- and Claudia Marcia Aparecida Carareto
Genome Res. March 2026 36: 487-505; Published in Advance February 10, 2026, doi:10.1101/gr.280463.125
...a transposase domain derived from an Hsmar1 insertion conserved in primates, providing functional DNA-binding to target methylation (Cordaux et al. 2006). Such exaptation and domestication events can often be identified by the occurrence of chimeric transcripts, which are mRNAs with both gene- and TE...
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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
...expansion of the CGG repeat in the 5′ UTR of FMR1 [MIM: 309550] becomes methylated and results in transcriptional silencing (Sutcliffe et al. 1992). A second possible mechanism could be that STR variation modulates the binding of transcription factors (TFs) to specific DNA motifs by creating or disrupting...
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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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Research: Confounding factors in assessing the enriched expression of somatic mutant allele in bulk tumor samples
- Kohei Hagiwara,
- Andrew Thrasher,
- Nadezhda V Terekhanova,
- and Jinghui Zhang
Genome Res. March 4, 2026 gr.281003.125; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
...can be caused by cis-activation of the 26 mutant allele or silencing of the wild-type allele and has been investigated by examining the 27 enrichment of mutant allele in RNA relative to DNA. Here we show that this mutation-based 28 approach can be confounded by gene expression differences in tumor...
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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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