Cellular Heterogeneity-Adjusted cLonal Methylation (CHALM) improves prediction of gene expression.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 33452255.
- Also identified by DOI 10.1038/s41467-020-20492-7 and PMC identifier 7811027.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
Promoter DNA methylation is a well-established mechanism of transcription repression, though its global correlation with gene expression is weak. This weak correlation can be attributed to the failure of current methylation quantification methods to consider the heterogeneity among sequenced bulk cells. Here, we introduce Cell Heterogeneity-Adjusted cLonal Methylation (CHALM) as a methylation quantification method. CHALM improves understanding of the functional consequences of DNA methylation, including its correlations with gene expression and H3K4me3. When applied to different methylation datasets, the CHALM method enables detection of differentially methylated genes that exhibit distinct biological functions supporting underlying mechanisms.
Medical subject headings
- DNA Methylation
- Epigenesis, Genetic
- Epigenomics
- Promoter Regions, Genetic