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Chromatin module inference on cellular trajectories identifies key transition points and poised epigenetic states in diverse developmental processes

ABSTRACT: During cell fate transitions the chromatin organization of the precursor cell changes from that of the endpoint cell. Current computational approaches to analyze chromatin modifications across multiple cell types do not model how the cell types are related on a lineage or over time. To overcome this limitation, we have developed a method called CMINT (Chromatin Module INference on Trees), a probabilistic clustering approach to systematically capture chromatin state dynamics across multiple cell types. Using the output from CMINT we gained novel insights into chromatin state dynamics of reprogramming to induced pluripotent stem cells (iPSCs.) We found that chromatin changes could occur without large gene expression changes; different combinations of activating marks were associated with specific reprogramming factors; in partially reprogrammed cells there was an order of acquisition of chromatin marks at pluripotency loci; and multivalent states, comprising previously undetermined combinations of activating and repressive histone modifications, were enriched for an architectural protein.

ORGANISM(S): Mus musculus

PROVIDER: GSE97222 | GEO | 2017/03/31

SECONDARY ACCESSION(S): PRJNA381013

REPOSITORIES: GEO

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