Distinct functions of genome-wide chromatin remodeling in the differentiation of T helper Type 1 and 2 cells

T helper type 1 and 2 (Th1 and Th2) cells play critical roles in infectious, autoimmune and allergic diseases. Here we mapped genome-wide distribution of DNase I hypersensitive (DHS) sites in Th1, Th2 and their precursors naïve CD4 T cells. DHS sites were found unevenly distributed in the genomes with highest densities within 2kb of the transcription start sites (TSS). At the whole genome level, the DHS values, representing chromatin openness, but not the numbers of DHS sites showed strong positive correlation with gene expression. Th1 and Th2 differentiations were accompanied by changes of genome-wide distribution of DHS sites. The differentiated cells assumed more open chromatin structures than their precursors. During Th1 differentiation changes of DHS values could be statistically positively or negatively associated with changes of gene expression depending on the locations of the DHS sites, whereas only positive association was found during Th2 differentiation.