title: Guanine quadruplex DNA structure restricts methylation of CpG dinucleotides genome-wide.
abstract: Cytosine methylation in mammals is important for epigenetic control of the transcriptome. Although altered methylation is frequently encountered in disease situations, particularly cancer, the relationship between genome-wide methylation and DNA structure is poorly understood. It is now evident that alternative DNA forms are functionally relevant in replication, recombination and transcription. Herein, we researched the role of alternative DNA structure in cytosine methylation using quadruplex DNA as a case study. Our findings from analysis of 2.1 million CpGs in humans, across 12 tissues from the Human Epigenome Project (HEP), revealed a striking correlation within each tissue: CpGs with low methylation were enriched (P = 5.24E(-20)) whereas CpGs with high methylation were relatively depleted (P = 9.28E(-15)), within quadruplex-forming regions. This was further substantiated on considering 1.07E(8) methylcytosines from genome-wide sequencing within embryonic stem cells and differentiated fibroblasts. To further test the predictions we experimentally determined methylation in >600,000 CpGs across 18 individuals using bisulfite mapping and found significantly low methylation of CpGs within quadruplex-forming regions (P = 1.36E(-08)). Together, these suggest the role of guanine-quadruplexes in CpG methylation and directly impact our understanding of the inter-relationship between DNA conformation and global cytosine methylation.
authors.affiliation: G.N.R. Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India.
authors.forename: Rashi
authors.initials: R
authors.lastname: Halder
authors.forename: Kangkan
authors.initials: K
authors.lastname: Halder
authors.forename: Priyanka
authors.initials: P
authors.lastname: Sharma
authors.forename: Gaurav
authors.initials: G
authors.lastname: Garg
authors.forename: Shantanu
authors.initials: S
authors.lastname: Sengupta
authors.forename: Shantanu
authors.initials: S
authors.lastname: Chowdhury
mesh_terms: D001483:Base Sequence; D019175:DNA Methylation / Q000235:genetics*; D021901:DNA, Intergenic / Q000235:genetics; D015226:Dinucleoside Phosphates / Q000235:genetics*; D053595:Embryonic Stem Cells / Q000378:metabolism; D005091:Exons / Q000235:genetics; D054856:G-Quadruplexes; D015894:Genome, Human / Q000235:genetics*; D006801:Humans; D007438:Introns / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D015203:Reproducibility of Results
chemical_list: D021901:DNA, Intergenic; D015226:Dinucleoside Phosphates; C015772:CpG dinucleotide