An encyclopedia of mouse DNA elements (Mouse ENCODE)

To complement the human Encyclopedia of DNA Elements (ENCODE) project and to enable a broad range of mouse genomics efforts, the Mouse ENCODE Consortium is applying the same experimental pipelines developed for human ENCODE to annotate the mouse genome.

The chromatin remodeling landscape of T helper cell differentiation (88.6)

T helper cell activation and differentiation occur in part through changes in gene expression. Dramatic changes in chromatin structure occur and are thought to play a role in regulation. Little is known about the remodeling enzymes responsible for these changes. Here, we asked how binding of the SWI/SNF remodeling subunit BRG1 changed genome-wide during T helper cell differentiation, using ChIP-seq. Globally, BRG1 binding was positively correlated with gene activity. We found BRG1 binding to promoter proximal regions but also found many distal BRG1 binding regions, including some known distal regulatory elements, suggesting a general role for BRG1 in long-distance gene regulation. BRG1 binding changed dramatically in response to both differentiation and activation. BRG1 binding was associated with DNase I Hypersensitivity and enhancer activity at newly identified regions. Moreover, many of these BRG1 binding regions are lineage or activation specific, a large number of them are greater than 10kb away from the nearest gene, and do not appear to be marked by a common histone code. Together, these findings suggest BRG1 integrates differentiation and activation signals to change chromatin structure. We speculate these events play a causal role in programming gene expression and cell fate. We also suggest that BRG1 binding may be a useful marker for identifying distal regulatory regions.