Tfcp2l1 recruits Thrap3 to sustain ESC self-renewal via Jmjd1c exon-5 splicing and DNA repair choice

How embryonic stem cells (ESCs) maintain genomic integrity while sustaining self-renewal remains poorly understood. We find that transcription factor CP2-like 1 (Tfcp2l1) recruits Thrap3 in mouse ESCs, where this complex maintains RNA polymerase II activity and promotes transcription of Tfcp2l1 target genes. In addition, Thrap3 supports mESC self-renewal. Interestingly, knockdown of either Tfcp2l1 or Thrap3 induces highly overlapping alternative-splicing changes, including reduced inclusion of exon-5 in Jmjd1c. Further studies reveal that skipping of Jmjd1c exon-5 weakens the association between Jmjd1c and Mdc1, accompanied by elevated Mdc1-associated dimethylation, leading to reduced Mdc1 and Rnf8 interaction and diminished K63-linked ubiquitin signalling. These alterations impair chromatin recruitment of the Rap80 and Brca1 repair complex and increase Rad51 foci formation, indicative of a shift in DNA repair pathway preference. Accordingly, loss of Tfcp2l1 or Thrap3 results in accumulated DNA damage, hypersensitivity to genotoxic stress, compromised ESC self-renewal and enhanced apoptosis. Similar phenotypes can be recapitulated in human ESCs. Together, our findings provide new insights into how ESCs coordinate genome maintenance with self-renewal.