Global molecular features in transcription and chromatin accessibility in human extended pluripotent stem cells

Human extended pluripotent stem (hEPS) cell is a newly established human embryonic stem cell (hESC) line with the capacity of chimerizing both embryonic and extraembryonic tissues compared with primed hESCs which are inefficient to contribute to the inner cell mass (ICM). The molecular mechanism underlying the pluripotency of hEPS cells is still not clear. We conducted RNA-seq and ATAC-seq analysis to investigate the differential expression profiling and genomic chromatin accessibility features. According to our data, more than 2000 genes were specially up-regulated in hEPS cells. Furthermore, the open chromatin regions in these two human embryonic stem cell lines were quite different. In hEPS cells, transcriptional factors binding motifs associated with pluripotency maintenance were enriched in chromatin accessible regions. Integrating the results from ATAC-seq and RNA-seq, we identified new regulatory features which were important for pluripotency maintenance and cell development in hEPS cells. Together, these results provided a new perspective on the understanding of molecular features of hESCs in different pluripotent states and a novel resource for further studies on regenerative medicine by using hEPS cells.