Sall4 regulates distinct transcription circuitries in different blastocyst-derived stem cell lineages

Stem cells self-renew or differentiate under the governance of a stem cell-specific transcriptional program with each transcription factor orchestrating the activities of a particular set of genes. Here we demonstrate that a single transcription factor is able to regulate distinct core circuitries in two different blastocyst-derived stem cell lines, embryonic stem (ES) and extra-embryonic endoderm (XEN) cells. The transcription factor, Sall4, is required for early embryonic development and for ES cell pluripotency. Sall4 is also expressed in XEN cells and depletion of Sall4 disrupts self-renewal and induces differentiation. Genome-wide analysis reveals Sall4 is regulating different gene sets in ES and XEN cells, and depletion of Sall4 targets in the respective cell types induces differentiation. With Oct4, Sox2 and Nanog, Sall4 forms a crucial interconnected auto-regulatory network in ES cells. In XEN cells, Sall4 regulates key XEN lineageassociated genes, Gata4, Gata6, Sox7 and Sox17. Our findings demonstrate how Sall4 functions as an essential stemness factor for two different stem cell lines. Keywords: ES/XEN comparison, ES Sall4 KD/control KD comparison, and XEN Sall4 KD/control KD comparison In this study, we delineated the core circuitries that are regulated by Sall4 in governing the distinctive blastocyst-derived stem cell lines. We dissected crucial components of the Sall4-driven circuitries through loss-of-function analyses, and showed that these are required for maintaining the stem cell states. Six gene expression experiments have been performed: ES wildtype, ES Sall4 KD, ES control KD, XEN wildtype, XEN Sall4 KD and XEN Sall4 control KD. Each experiment has 3 replicates (see Samples GSM313602..GSM313619). Data were normalized with cross-correlation method; differential expression was based on the mean of the log2 fold changes (see supplementary files below). ChIP-chip experiments have also been performed (see Samples GSM319610..GSM320264).