Characterization of CpG sites that escape methylation on the inactive human X-chromosome

Epigenetics. 2015;10(9):810-8. doi: 10.1080/15592294.2015.1069461. Epub 2015 Jul 15.


In many whole genome studies of gene expression or modified cytosines, data from probes localized to the X-chromosome are removed from analyses due to gender bias. Previously, we observed population differences in cytosine modifications between Caucasian and African lymphoblastoid cell lines (LCLs) on the autosomes using whole genome arrays to measure modified cytosines. DNA methylation plays a critical role in establishment and maintenance of X-chromosome inactivation in females. Therefore, we reasoned that by investigating cytosine modification patterns specifically on the X-chromosome, we could obtain valuable information about a chromosome that is often disregarded in genome-wide analyses. We investigated population differences in cytosine modification patterns along the X-chromosome between Caucasian and African LCLs and identified novel sites that escape methylation on the inactive X-chromosome (Xi) in females. We characterized the chromatin state of these loci by incorporating the extensive histone modification ChIP-seq data generated by ENCODE. To explore the relationship between DNA and histone modifications further, we hypothesized that BRD4, a protein that binds acetylated histones, could be preventing some sites from becoming de novo methylated. To test this, we treated 4 female LCLs with JQ1, a small molecule inhibitor of BRD4, but found that JQ1 treatment induced minor changes in cytosine modification levels, and the majority of sites escaping methylation on the Xi remained unmethylated. This suggests that other epigenetic mechanisms or transcription factors are likely playing a larger role in protecting these sites from de novo methylation on the Xi.

Keywords: DNA methylation; Illumina 450K array; JQ1; X-chromosome; lymphoblastoid cell lines.

Publication types

  • Comparative Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Azepines / pharmacology
  • Black People / genetics*
  • Cell Cycle Proteins
  • Cell Line
  • Chromatin / metabolism
  • Chromosomes, Human, X / drug effects
  • Chromosomes, Human, X / metabolism*
  • CpG Islands* / drug effects
  • Cytosine / metabolism
  • DNA Methylation* / drug effects
  • Female
  • Humans
  • Male
  • Nuclear Proteins / antagonists & inhibitors
  • Nuclear Proteins / metabolism
  • Transcription Factors / antagonists & inhibitors
  • Transcription Factors / metabolism
  • Triazoles / pharmacology
  • White People / genetics*
  • X Chromosome Inactivation* / drug effects


  • (+)-JQ1 compound
  • Azepines
  • BRD4 protein, human
  • Cell Cycle Proteins
  • Chromatin
  • Nuclear Proteins
  • Transcription Factors
  • Triazoles
  • Cytosine

Associated data

  • GEO/GSE62111