ERH facilitates microRNA maturation through the interaction with the N-terminus of DGCR8

Abstract

The microprocessor complex cleaves the primary transcript of microRNA (pri-miRNA) to initiate miRNA maturation. Microprocessor is known to consist of RNase III DROSHA and dsRNA-binding DGCR8. Here, we identify Enhancer of Rudimentary Homolog (ERH) as a new component of Microprocessor. Through a crystal structure and biochemical experiments, we reveal that ERH uses its hydrophobic groove to bind to a conserved region in the N-terminus of DGCR8, in a 2:2 stoichiometry. Knock-down of ERH or deletion of the DGCR8 N-terminus results in a reduced processing of suboptimal pri-miRNAs in polycistronic miRNA clusters. ERH increases the processing of suboptimal pri-miR-451 in a manner dependent on its neighboring pri-miR-144. Thus, the ERH dimer may mediate ‘cluster assistance’ in which Microprocessor is loaded onto a poor substrate with help from a high-affinity substrate in the same cluster. Our study reveals a role of ERH in the miRNA biogenesis pathway.

Structural basis of PETISCO complex assembly during piRNA biogenesis inC. elegans

“…Finally, the human ERH homolog has recently been shown to support the microprocessor complex during microRNA (miRNA) processing (Fang and Bartel 2020; Hutter et al 2020; Kwon et al 2020). Microprocessor is a trimeric complex consisting of one copy of DROSHA and two copies of DGCR8 and dimerization of DGCR8 is necessary for miRNA processing (Faller et al 2007).…”

“…S4D). PID-3 pep shows well-ordered electron density for residues 177-193 (Chain C) and [179][180][181][182][183][184][185][186][187][188][189][190][191][192][193] and occupies a similar surface on ERH as DGCR8 in the human ERH/DGCR8 peptide complex (Kwon et al 2020), and Mmi1 in the fission yeast Erh1/Mmi1 peptide complex (Xie et al 2019) (Supplemental Fig. 4A).…”

“…Finally, ERH-2 is one of the two C. elegans paralogs of ‘enhancer of rudimentary’ (Erh), a factor that is conserved throughout eukaryotes (Weng and Luo 2013). Erh was shown to participate in the RNA exosome-mediated degradation of meiotic RNAs in Schizosaccharomyces pombe (S. pombe) (Sugiyama et al 2016) and to facilitate miRNA processing in human cells (Fang and Bartel 2020; Hutter et al 2020; Kwon et al 2020).…”

Cisregulation within a cluster of viral microRNAs

“…A second model would involve protein cofactors able to recruit the Microprocessor on the neighboring miRNA hairpin. Very recently, it was shown that ERH and SAFB2 can interact with the Microprocessor and their ability to dimerize may even mediate multimerization of the Microprocessor and allow its simultaneous binding to several hairpins (35, 38, 40, 44). However, this model remains to be clearly established.…”

“…Maturation of pri-miRNAs by the Microprocessor is controlled by sequence and structural features of miRNA hairpin, defining the basal level of pre-miRNAs excised (see (34) for a recent review). Recently, several studies demonstrated interdependent processing in the context of bicistronic pri-miRNA where an optimal miRNA hairpin assists the processing of a neighboring suboptimal one (35–40). Such interdependency has not yet been documented in the case of larger miRNA clusters.…”