KIAA1522 isoform switching regulates LTR-RTs activity in distinct pluripotency states of hESCs.

Human embryonic stem cells (hESCs) can be classified as having naïve and primed pluripotency states. While several studies have reported different gene expression networks between these two pluripotency states, the role of alternative splicing (AS) in regulating these differences has not been well characterized. In this study, we performed RNA sequencing and identified differential AS events in 784 genes between naïve and primed hESCs. Among these, KIAA1522, whose function has not been well studied, has state-specific isoforms regulated by alternative first exon (AFE). This splicing event resulted in isoforms with distinct N-terminal domains and subcellular localization. Notably, the sequences and alternative isoform patterns of KIAA1522 were conserved between humans and mice. Further investigation using cleavage under targets and tagmentation (CUT&Tag) experiments in cells with specific-isoform overexpression or knockdown revealed the opposite activity of long terminal repeat retrotransposons (LTR-RTs) and motif enrichment profiles. The naïve-specific (N-P) isoform upregulated naïve marker gene expression and preferentially activated LTR-RTs by binding to the motifs enriched for POU and FOX family transcription factor binding sites. Conversely, the primed-specific (P-P) isoform promoted primed marker gene expression and suppressed LTR-RTs activity by binding to the motifs enriched for zinc finger protein binding sites. Collectively, KIAA1522 regulates the balance between naïve and primed pluripotency states through isoform-specific regulation of LTR-RTs activity and collaboration with distinct transcriptional regulators. In summary, our results characterize the splicing atlas of hESCs in naïve and primed states and reveal the regulatory function and mechanism of AFE usage by KIAA1522.