Discovery and characterization of LNCSOX17 as an essential regulator in endoderm formation

Long noncoding RNAs (lncRNAs) have emerged as fundamental regulators in various biological processes, including embryonic development and cellular differentiation. Despite much progress over the past decade, the genome-wide annotation of lncRNAs remains incomplete and many known non-coding loci are poorly characterized. Here we report the discovery of a previously not annotated lncRNA that is transcribed 230 kb upstream of the SOX17 gene and located within the same topologically isolated domain. We therefore termed it LNCSOX17 and show that it is induced following SOX17 activation, but is more tightly restricted to early definitive endoderm than SOX17. Notably, loss of LNCSOX17 affects crucial functions independent of SOX17 and leads to an aberrant endodermal transcriptome, signaling pathway deregulation, and epithelial to mesenchymal transition defects. Consequently, cells lacking LNCSOX17 cannot further differentiate into more mature endodermal cell types. Our study identified LNCSOX17 and demonstrates its essential role as a new actor in early human endoderm, thereby further expanding the list of functionally important non-coding regulators. Overall design: cHi-C seq, 4C seq, RNAseq, ChIPseq and Oxford Nanopore cDNA seq were performed on hiPSCs/hESCs (day0), hiPSCs/hESCs derived endoderm (day5), intermediate differentiation stage (day3) or pancreatic progenitors (day9). Cells were grown as described in the methods section or in the protocol sections below. Libraries have been performed following manufacturer instructions and how described in the methods section or below.