LncRNA DEANR1 facilitates human endoderm differentiation by activating FOXA2 expression

Long non-coding RNAs (lncRNAs) regulate diverse biological processes including cell lineage specification. Here we report transcriptome profiling of human endoderm and pancreatic cell lineages using purified cell populations. Analysis of the data sets allowed the identification of hundreds of lncRNAs exhibiting differentiation stage-specific expression patterns. As a first step in characterizing these lncRNAs, we focus on an endoderm-specific lncRNA DEANR1 (Definitive Endoderm Associated long Non-coding RNA1) and demonstrate that it plays an important role in human endoderm differentiation. DEANR1 contributes to endoderm differentiation by positively regulating endoderm factor FOXA2 expression. Importantly, overexpression of FOXA2 is able to rescue endoderm differentiation defects caused by DEANR1 depletion. Mechanistically, DEANR1 facilitates FOXA2 activation by helping SMAD2/3 recruitment to the FOXA2 promoter. Thus, our study not only reveals a large set of differentiation stage-specific lncRNAs, but also characterizes a novel lncRNA important for endoderm differentiation. Here we perform RNA-seq based transcriptome profiling using undifferentiated human ESCs (one sample), definitive endoderm (two replicates), pancreatic progenitors(three replicates) as well as sorted human primary alpha cells (two replicates), beta cells (two replicates) and exocrine cells (one sample). Moreover, we perform RNA-seq based transcriptome profiling for WT, FOXA2 knockdown, and DEANR1 knockdown of differentiated definitive endoderm samples (two replicates for each).