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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
...CL. 1992. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci 89: 1827–1831. doi:10.1073/pnas.89.5.1827 ↵Fu Y, Aganezov S, Mahmoud M, Beaulaurier J, Juul S, Treangen TJ, Sedlazeck FJ. 2024. MethPhaser: methylation...
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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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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 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
...these questions, we first analyzed two independent data sets comprising PCR-free whole- sequencing (WGS) and -wide DNA methylation levels derived from whole-blood samples in 245 (discovery cohort) and 484 individuals (replication cohort). Using genotypes for 131,635 polymorphic STRs derived from WGS using Hip...
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Research: Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy
- Hadi Rahmaninejad,
- Yao Xiao,
- Maxime M.C. Tortora,
- and Geoffrey Fudenberg
Genome Res. August 2025 35: 1745-1757; Published in Advance July 8, 2025, doi:10.1101/gr.280108.124
...with shorter 2- to 11-min lifetimes (Nakahashi et al. 2013; Hansen et al. 2017, 2020; Kieffer-Kwon et al. 2017; Oomen et al. 2019; Soochit et al. 2021; Narducci and Hansen 2025). SPT for CTCF indicated a slightly more rapid 1-min lifetime (Hansen et al. 2017). Tracking DNA, often via integrated arrays...
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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
....The regulatory activity of enhancers and the correspondence with certain promoters are closely related to the chromatin accessibility, histone modification, and DNA interaction frequency (The ENCODE Project Consortium 2012; Shibata et al. 2012; Whalen et al. 2016). In eukaryotic cells, the is dynamic...
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Research: Genomic origin, fragmentomics, and transcriptional properties of long cell-free DNA molecules in human plasma
- Huiwen Che,
- Peiyong Jiang,
- L.Y. Lois Choy,
- Suk Hang Cheng,
- Wenlei Peng,
- Rebecca W.Y. Chan,
- Jing Liu,
- Qing Zhou,
- W.K. Jacky Lam,
- Stephanie C.Y. Yu,
- So Ling Lau,
- Tak Y. Leung,
- John Wong,
- Vincent Wai-Sun Wong,
- Grace L.H. Wong,
- Stephen L. Chan,
- K.C. Allen Chan,
- and Y.M. Dennis Lo
Genome Res. February 2024 34: 189-200; Published in Advance February 26, 2024, doi:10.1101/gr.278556.123
..., the cfDNA cleavage was relatively enriched at the cytosine of methylated CpGs (position 0), followed by a rapid decrease at the nucleotide 1 position immediately preceding methylated CpGs. We found that the cleavage of long molecules did not show such a pattern at methylated cytosines but showed...
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Research: KDM1A maintains genome-wide homeostasis of transcriptional enhancers
- Saurabh Agarwal,
- Katherine M. Bonefas,
- Patricia M. Garay,
- Emily Brookes,
- Yumie Murata-Nakamura,
- Robert S. Porter,
- Todd S. Macfarlan,
- Bing Ren,
- and Shigeki Iwase
Genome Res. February 2021 31: 186-197; Published in Advance January 7, 2021, doi:10.1101/gr.234559.118
...of histone H3 lysine 4 (H3K4me1) can distinguish enhancers from promoters (Heintzman et al. 2007, 2009). In response to various environmental and developmental cues, TFs bind to specific DNA elements (Zaret and Carroll 2011; Spitz and Furlong 2012), and subsequent recruitment of methyltransferases KMT2C...
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Research: Nucleosome binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites
- Patrick D. Wilson,
- Xinyang Yu,
- Christopher R. Handelmann,
- and Michael J. Buck
Genome Res. March 2025 35: 404-416; Published in Advance February 10, 2025, doi:10.1101/gr.279541.124
...affinity to its DNA-binding sites at all possible positions within the nucleosome core particle. Using Pioneer-seq, we analyzed the binding affinities of TP53, TP63, and TP73 to 10 TP53 family binding sites across the nucleosome core particle. We find that the affinities of TP53, TP63, and TP73...
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Method: EnDeep4mC predicts DNA N⁴-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
- Shuyu Zhang,
- Quan Zou,
- Mengting Niu,
- Zhibin Lv,
- Antony Stalin,
- and Ximei Luo
Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
...types and methylated base positions from bacteria using nanopore sequencing with multi-scale neural network. Bioinformatics 41: btaf397. doi:10.1093/bioinformatics/btaf397 ↵Cheng X. 1995. DNA modification by methyltransferases. Curr Opin Struct Biol 5: 4–10. doi:10.1016/0959-440x(95)80003-j ↵Deaton AM...
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