Structural basis for the unique multifaceted interaction of DPPA3 with the UHRF1 PHD finger

Abstract

Ubiquitin-like with PHD and RING finger domain-containing protein 1 (UHRF1)-dependent DNA methylation is essential for maintaining cell fate during cell proliferation. Developmental pluripotency-associated 3 (DPPA3) is an intrinsically disordered protein that specifically interacts with UHRF1 and promotes DNA demethylation by inhibiting UHRF1 chromatin localization. However, the molecular basis of how DPPA3 interacts with and inhibits UHRF1 remains unclear. We aimed to determine the solution nuclear magnetic resonance structure of the mouse UHRF1 plant homeodomain (PHD) complexed with DPPA3. Induced α-helices in DPPA3 upon binding of UHRF1 PHD contribute to stable complex formation with multifaceted interactions, unlike canonical ligand proteins of the PHD domain. Mutations in the binding interface and unfolding of the DPPA3 helical structure inhibited binding to UHRF1 and its chromatin localization. Our results provide structural insights into the mechanism and specificity underlying the inhibition of UHRF1 by DPPA3.

CDCA7 is a hemimethylated DNA adaptor for the nucleosome remodeler HELLS

“…Alternatively, as it has been reported that UHRF1 and HELLS interact (25), this HELLS enrichment on ∆DNMT1 extract could be caused by chromatin enrichment of UHRF1, which directly binds hemimethylated DNA (30)(31)(32). To distinguish between these possibilities, we used recombinant mouse DPPA3 (mDPPA3), which binds to UHRF1 and inhibits its association with chromatin (51)(52)(53). In control egg extracts, DNMT1, UHRF1, HELLS and CDCA7e (a sole CDCA7 paralog present in Xenopus eggs) transiently associated with chromatin in S phase min after sperm nucleus addition to egg extracts) (Fig.…”