Type
PreprintAuthors
Khamis, Abdullah M.
Lioznova, Anna V.
Artemov, Artem V.
Ramensky, Vasily
Bajic, Vladimir B.

Medvedeva, Yulia A.
KAUST Department
Computational Bioscience Research Center (CBRC)Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Computer Science Program
Applied Mathematics and Computational Science Program
Date
2016-12-29Permanent link to this record
http://hdl.handle.net/10754/625213
Metadata
Show full item recordAbstract
DNA methylation is involved in regulation of gene expression. Although modern methods profile DNA methylation at single CpG sites, methylation levels are usually averaged over genomic regions in the downstream analyses. In this study we demonstrate that single CpG methylation can serve as a more accurate predictor of gene expression compared to average promoter / gene body methylation. CpG positions with significant correlation between methylation and expression of a gene nearby (named CpG traffic lights) are evolutionary conserved and enriched for exact TSS positions and active enhancers. Among all promoter types, CpG traffic lights are especially enriched in poised promoters. Genes that harbor CpG traffic lights are associated with development and signal transduction. Methylation levels of individual CpG traffic lights vary between cell types dramatically with the increased frequency of intermediate methylation levels, indicating cell population heterogeneity in CpG methylation levels. Being in line with the concept of the inherited stochastic epigenetic variation, methylation of such CpG positions might contribute to transcriptional regulation. Alternatively, one can hypothesize that traffic lights are markers of absent gene expression resulting from inactivation of their regulatory elements. The CpG traffic lights provide a promising insight into mechanisms of enhancer activity and gene regulation linking methylation of single CpG to expression.Citation
Khamis AM, Lioznova AV, Artemov AV, Ramensky V, Bajic VB, et al. (2016) CpG traffic lights are markers of regulatory regions in humans. Available: http://dx.doi.org/10.1101/095968.Sponsors
This work was supported by RFBR grant 14-04-00180 to YAM. VBB is supported by the base research fund of the King Abdullah University of Science and Technology (KAUST).Publisher
Cold Spring Harbor LaboratoryDOI
10.1101/095968Additional Links
http://www.biorxiv.org/content/early/2017/03/17/095968ae974a485f413a2113503eed53cd6c53
10.1101/095968
Scopus Count
Except where otherwise noted, this item's license is described as It is made available under a CC-BY-NC-ND 4.0 International license.