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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
...quantitative nucleotide resolution of methylation. It converts unmethylated cytosine to uracil by chemical deamination, while methylated DNA remains unconverted (Fig. 1B). After polymerase chain reaction (PCR), the methylated and unmethylated bases are distinguished as cytosine (C) to thymine (T) single...
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Method: Methyl-SNP-seq reveals dual readouts of methylome and variome at molecule resolution while enabling target enrichment
- Bo Yan,
- Duan Wang,
- Romualdas Vaisvila,
- Zhiyi Sun,
- and Laurence Ettwiller
Genome Res. November/December 2022 32: 2079-2091; Published in Advance November 4, 2022, doi:10.1101/gr.277080.122
...-specific methylation analysis in humans to identification of methyltransferase specificity in complex bacterial communities.The covalent modification of cytosine by a methyl group leads to the formation of 5-methylcytosine (5mC), a key epigenetic modification of genomic DNA that occurs in a large number of organisms...
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Method: Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution
- Zhiyi Sun,
- Romualdas Vaisvila,
- Laura-Madison Hussong,
- Bo Yan,
- Chloé Baum,
- Lana Saleh,
- Mala Samaranayake,
- Shengxi Guan,
- Nan Dai,
- Ivan R. Corrêa, Jr.,
- Sriharsa Pradhan,
- Theodore B. Davis,
- Thomas C. Evans, Jr.,
- and Laurence M. Ettwiller
Genome Res. February 2021 31: 291-300; Published in Advance January 19, 2021, doi:10.1101/gr.265306.120
...genomic DNA spiked with unmethylated lambda, cytosine methylated XP12, and hydroxymethylated T4gt phage genomic DNAs. Lambda and XP12 control DNAs were used to measure the deamination rates of APOBEC3A on C and 5mC, respectively, and T4gt DNA was used to monitor 5hmC protection by BGT. By using...
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Research: Epigenetic modification and inheritance in sexual reversal of fish
- Changwei Shao,
- Qiye Li,
- Songlin Chen,
- Pei Zhang,
- Jinmin Lian,
- Qiaomu Hu,
- Bing Sun,
- Lijun Jin,
- Shanshan Liu,
- Zongji Wang,
- Hongmei Zhao,
- Zonghui Jin,
- Zhuo Liang,
- Yangzhen Li,
- Qiumei Zheng,
- Yong Zhang,
- Jun Wang,
- and Guojie Zhang
Genome Res. April 2014 24: 604-615; Published in Advance February 2, 2014, doi:10.1101/gr.162172.113
...were produced, which yielded an average depth of 223 per strand for each sample (Supplemental Table S2) with ;90% of genomic cytosines (Cs) being covered by at least two unique reads (Supplemental Table S3). We identified an average of 14.5 million methylated cytosines (mCs) in each sample (see Methods...
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Research: Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer
- Gary C. Hon,
- R. David Hawkins,
- Otavia L. Caballero,
- Christine Lo,
- Ryan Lister,
- Mattia Pelizzola,
- Armand Valsesia,
- Zhen Ye,
- Samantha Kuan,
- Lee E. Edsall,
- Anamaria Aranha Camargo,
- Brian J. Stevenson,
- Joseph R. Ecker,
- Vineet Bafna,
- Robert L. Strausberg,
- Andrew J. Simpson,
- and Bing Ren
Genome Res. February 2012 22: 246-258; Published in Advance December 7, 2011, doi:10.1101/gr.125872.111
...3 was not mapped in HMEC, we cannot assess this phenomenon directly in these cells. However, to identify potential H3K9me3 domains, we searched for regions depleted of DNA methylation that are simultaneously depleted of H3K27me3. These large domains, putatively similar to the H3K9me3 enriched...
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Research: Global profiling of DNA methylation erasure in mouse primordial germ cells
- Sylvain Guibert,
- Thierry Forné,
- and Michael Weber
Genome Res. April 2012 22: 633-641; Published in Advance February 22, 2012, doi:10.1101/gr.130997.111
...mammalian development in primordial germ cells (PGCs), yet the targets and kinetics of this process are poorly characterized. Here we provide a map of cytosine methylation on a large portion of the genome in developing male and female PGCs isolated from mouse embryos. We show that DNA methylation erasure...
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Methods: High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing
- Emily Hodges,
- Andrew D. Smith,
- Jude Kendall,
- Zhenyu Xuan,
- Kandasamy Ravi,
- Michelle Rooks,
- Michael Q. Zhang,
- Kenny Ye,
- Arindam Bhattacharjee,
- Leonardo Brizuela,
- W. Richard McCombie,
- Michael Wigler,
- Gregory J. Hannon,
- and James B. Hicks
Genome Res. September 2009 19: 1593-1605; Published in Advance July 6, 2009, doi:10.1101/gr.095190.109
...distinguish methylation states in a semi-quantitative, allele-specific manner at individual CpGs within a defined region. Established protocols that positively identify 5-methylcytosine residues in single strands of genomic DNA exploit the sodium bisulfite-induced deamination of cytosine to uracil. Under...
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Method: Multiplex mapping of chromatin accessibility and DNA methylation within targeted single molecules identifies epigenetic heterogeneity in neural stem cells and glioblastoma
- Nancy H. Nabilsi,
- Loic P. Deleyrolle,
- Russell P. Darst,
- Alberto Riva,
- Brent A. Reynolds,
- and Michael P. Kladde
Genome Res. February 2014 24: 329-339; Published in Advance October 8, 2013, doi:10.1101/gr.161737.113
...-patch, a multiplexed, targeted method for simultaneous mapping of chromatin accessibility and DNA methylation on single molecules To obtain combinedDNAmethylation and chromatin accessibility data on individual DNA strands or molecules, nuclei are probed with M.CviPI, which methylates cytosine in accessible GC...
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Method: methyl-ATAC-seq measures DNA methylation at accessible chromatin
- Roman Spektor,
- Nathaniel D. Tippens,
- Claudia A. Mimoso,
- and Paul D. Soloway
Genome Res. June 2019 29: 969-977; Published in Advance June 3, 2019, doi:10.1101/gr.245399.118
..., and is generally associated with transcriptionally inactive regions. Bisulfite sequencing (BS-seq) uses selective chemical deamination of unmodified cytosines to uracil, leaving 5mC unchanged. The extent of methylation at a given CpG in a sample is detected after amplification, sequencing, aligning reads...
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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
...bp) have a methylated cytosine (C) at the center, whereas negative samples are nonmethylated, as confirmed by SMRT sequencing. All input DNA sequences are processed into 41 bp fixed-length samples. Sequences <41 bp are symmetrically padded with N's. Longer sequences are segmented into consecutive...
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