Distinct Roles for SETa and SETß in Early Cell Fate Decisions [RNA-Seq]

SET, the nuclear proto-oncogene, is primarily expressed as SETa in embryonic stem cells. Upon pluripotency exit, a transcriptional switch driven by alternative promoters causes SETß to largely replace SETa expression. Functional distinctions between the two isoforms have been difficult to ascertain, partly due to the redundancy between SETa and SETß in their protein structure and activity. In this study, we use embryonic stem cells (ESCs) with inducible SET isoform-specific expression to investigate the differences between both SET isoforms. Time-course RNA-seq analyses in SET-KO backgrounds as well as isoform-specific ChIP-seq experiments reveal regulatory functions for SETa and SETß. Despite sharing many binding sites and binding partners, SETa has a stronger activation function on its target genes, while SETß downregulates FGF4. As KLF5 specifically regulates SETa, this implicates SET isoform switching at the KLF5/FGF signalling axis during primitive endoderm specification. Together, we propose a model of how distinct roles of SETa and SETß may regulate cell identity in the early blastocyst. Overall design: RNA-seq of WT and SETa or SETb isoform specific KO of R1 ESCs. In addition, RNA-seq of SET isoform specific addback/overexpression experiments and in KH2 ESCs.