DIGIT regulates endoderm differentiation of human embryonic stem cells

Endoderm differentiation is a critical step leading to development of the gastrointestinal system. We found that DIGIT is a lncRNA that is required for endoderm differentiation. We used directional RNA sequencing (RNA-seq) to globally evaluate the effects of loss of DIGIT expression during endoderm differentiation and chromatin immunoprecipitation and sequencing (ChIP-seq) to define the sites occupied by SMAD3 during endoderm diferentiation. Analysis of genome-wide coding and noncoding gene expression using RNA-seq in human embryonic stem cells (hESCs) and DIGiT-deficient (DIGIT KO) hESCs under hESC culture conditions and after four days of endoderm differentiation. SMAD3 Chip-seq was performed to define enhancers activated during endoderm differentiation.