Deciphering chromatin status across an entire genome must seem like trying to navigate through an Amazon rain forest without a guide. Luckily, new work just published begins the process of creating chromatin state roadmaps to help point epigenetics researchers down the right path.
To make that journey a little smoother, a research group from MIT and Harvard’s Broad Institute took on the project of mapping chromatin states in nine human cell types. In each cell-line they tracked nine different chromatin marks via ChIP-seq, which they then analyzed to look for regulatory elements, functional roles and cell-type specificities.
After gathering up the data, the team took a closer look at cell-type related patterns, especially those in promoter and enhancer regions. What they came up with were profiles for:
- Chromatin state
- Gene Expression
- Regulatory motif enrichment
- Regulator expression
Correlations between all of these profiles could then be used to tease out things like cell specific activators and repressors, or tag enhancers to putative target genes. The Broad-ies also noticed that disease linked single nucleotide polymorphisms (SNPs) were often found in enhancers specific to that cell-type, and in some cases pointed to a mechanism that connected them.
Of course with only nine cell types studied so far, there is still a ways to go before a complete human chromatin state map is finished. But the scientists feel that the utility of their work for analyzing genome wide association studies (GWAS) and for unraveling cis-regulatory networks has already been proven.
Find your way to the rest of the details over at Nature, March 2011.