GSE113386
Global distribution of DNA hydroxymethylation and DNA methylation in chronic lymphocytic leukemia
We studied global distribution of hydroxymethylation (5hmC) and DNA methylation (5mC) in during normal B-cell development and CLL maturation. To derive disease-specific epigenetic changes we have compared CLL subgroups to their corresponding cell of origin. Our data showed that naïve B-cells, compared to non-class switched and class switched memory B-cells, had higher levels of 5-hmC and 5-mC. By comparing with ChIP sequencing data of H3K27Ac and H3K4me1 modifications of CLL samples with 5hmC and 5mC levels, we observed an increase of 5-hmC at overall gene body regions, CpG island shores and regulatory elements. Comparing 5-hmC distribution with RNA sequencing we showed that genes with higher transcriptional activity had higher 5-hmC and vice versa. Thus, our study suggests that the global loss of 5-hmC levels, with significant increase at gene regulatory regions, constitute a novel hallmark of CLL pathogenesis. Overall design: Investigating the global distribution óf 5hmC and 5mC levels, Transcriptome analysis followed by  H3K27Ac, H3K4me1 histone mpodifications using hMeDIP seq, MeDIP seq, RNA seq and ChIP sequencing for same CLL pateint samples and normal B cells.