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Research: A DNA methylation haplotype block landscape in human tissues and preimplantation embryos reveals regulatory elements defined by comethylation patterns
- Yan Feng,
- Zhiqiang Zhang,
- Yuyang Hong,
- Yi Ding,
- Leiqin Liu,
- Siqi Gao,
- Hai Fang,
- and Jiantao Shi
Genome Res. December 2023 33: 2041-2052; Published in Advance November 8, 2023, doi:10.1101/gr.278146.123
...A). For example, if two CpG sites covered by 18 sequencing reads are either both methylated (n = 11) or both unmethylated (n = 7), they are considered significantly comethylated (R2 = 1, P = 0.0008) (Fig. 1A, left panel). These comethylated CpG regions are called DNA methylation haplotype blocks...
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Research: New guidelines for DNA methylome studies regarding 5-hydroxymethylcytosine for understanding transcriptional regulation
- Le Li,
- Yuwei Gao,
- Qiong Wu,
- Alfred S.L. Cheng,
- and Kevin Y. Yip
Genome Res. April 2019 29: 543-553; Published in Advance February 19, 2019, doi:10.1101/gr.240036.118
...C signals in WGBS data, with at least 25%–40% of the differentially methylated regions (DMRs) identified from 5mC signals not detected from WGBS data. Our results also confirm a previous finding that methylation signals at transcript bodies are more indicative of gene expression levels than promoter...

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