Epigenetic landscapes explain partially reprogrammed cells and identify key reprogramming genes.

ABSTRACT: A common metaphor for describing development is a rugged "epigenetic landscape" where cell fates are represented as attracting valleys resulting from a complex regulatory network. Here, we introduce a framework for explicitly constructing epigenetic landscapes that combines genomic data with techniques from spin-glass physics. Each cell fate is a dynamic attractor, yet cells can change fate in response to external signals. Our model suggests that partially reprogrammed cells are a natural consequence of high-dimensional landscapes, and predicts that partially reprogrammed cells should be hybrids that co-express genes from multiple cell fates. We verify this prediction by reanalyzing existing datasets. Our model reproduces known reprogramming protocols and identifies candidate transcription

SUBMITTER: Lang AH 

PROVIDER: S-EPMC4133049 | biostudies-literature | 2014 Aug

REPOSITORIES: biostudies-literature