Epigenomic, genomic and transcriptomic profiling in CD14+ cells from MZ twins. (A) We analysed the following correlations at promoter regions: DNA methylation vs. gene expression, H2A.Z vs. gene expression and DNA methylation vs. H2A.Z. Gene expression levels are represented as log-transformed aligned average FPKM (fragments per kilobase of exon per million fragments mapped) from RNA-seq data. FPKM values were determined by TopHat and Cufflinks and assigned to TSSs. DNA methylation values were determined as β values using Illumina 450K array (see Materials and Methods) and are represented here as percentage of methylation bins. Probes on the Illumina 450K array were assigned to their closest TSS, discarding assignments >1 kb away. H2A.Z abundance is represented as normalised read counts from ChIP-seq data correlates positively with gene expression (Spearman's ρ = 0.50, P <10-3), DNA methylation is anti-correlated with H2A.Z (ρ = -0.59, P <10-3). Promoters were defined as TSS ± 1,000 bp. (B) Correlation coefficients of inter-individual DNA methylation differences. 31/32 and 21/22 plots correspond to MZ twin iiDMRs; 31/21, 31/11 and 11/22 correspond to iiDMRs found in unrelated individuals.
Gemma et al. Genome Biology 2013 14:R43 doi:10.1186/gb-2013-14-5-r43