The RNA-binding proteins DND1 and NANOS3 collaborate to form a heterodimeric complex that recognizes a specific AUGAAUU heptanucleotide sequence (N3-DRE) in mRNA 3'-UTRs through a continuous binding surface, achieving 85-fold higher affinity than individual proteins and creating a high-specificity recognition motif distinct from their individual preferences. This collaborative recognition mechanism functions as a two-factor authorization system that suppresses N3-DRE-containing transcripts encoding cell cycle and epigenetic regulators, thereby coordinating primordial germ cell survival and developmental reprogramming in mammalian embryos.

The RNA-binding proteins DND1 and NANOS3 are essential for primordial germ cell survival. Their co-immunoprecipitation and overlapping loss-of-function phenotypes suggest joint function, yet how they co-regulate target mRNAs remains unclear. Here, we developed Tandem PAR-CLIP and identified a DND1–NANOS3 ribonucleoprotein that specifically recognizes an AUGAAUU heptanucleotide on target mRNAs, termed the NANOS3-dependent DND1 Recognition Element (N3-DRE). mRNAs containing 3′-UTR N3-DREs are aberrantly upregulated in DND1- or NANOS3-deficient germ cells and encode key cell-cycle and epigenome regulators, such as CDK1. Genome editing showed that the N3-DRE is essential for Cdk1 repression in mouse PGCs in vivo. A 1.7-Å crystal structure of the ternary complex of DND1, NANOS3, and CDK1- N3-DRE RNA revealed a continuous RNA-binding surface that confers high-affinity, sequence- specific recognition. Together, these findings define the molecular and functional basis of N3-DRE-mediated mRNA regulation in germ cell development. Moreover, we provide a paradigm of two RNA-binding proteins with low (DND1) or no (NANOS3) intrinsic sequence-specificity, jointly building a high-information-content RNA sequence motif that is different from the sum of their individual preferences. Because RNA-binding protein specificities are typically studied individually, rather than in the context of ribonucleoproteins, this type of “two-factor authorization” may be an underappreciated mechanism to protect posttranscriptional gene regulatory networks from aberrant expression of an individual ribonucleoprotein component.