Structural atlas of human primary microRNAs generated by SHAPE-MaP

MicroRNA (miRNA) maturation is critically dependent on structural features of primary transcripts (pri-miRNAs). However, the scarcity of determined pri-miRNA structures has limited our understanding of miRNA maturation. Here we employed SHAPE-MaP, a high-throughput RNA structure probing method, to unravel the secondary structures of 476 high-confidence human pri-miRNAs. Our SHAPE-based structures diverge substantially from those inferred solely from computation, particularly in the apical loop and basal segments, underlining the need for experimental data in RNA structure prediction. By comparing the structures with high-throughput processing data, we determined the optimal structural features of pri-miRNAs. The sequence determinants are influenced substantially by their structural contexts. Moreover, we identified an element termed the bulged GWG motif (bGWG) with a 3′ bulge in the lower stem, which promotes processing. Our structure-function mapping better annotates the determinants of pri-miRNA processing and offers practical implications for designing small hairpin RNAs and predicting the impacts of miRNA mutations. SHAPE-MaP experiments were performed on all 519 high-confidence human pri-miRNAs curated by MirGeneDB (v1). The pri-miRNAs were synthesized by in vitro transcription using minigene constructs of 125 nt, which contain a miRNA hairpin in the middle. As structural probing controls, we included three well-defined RNAs: human U1 snRNA, yeast tRNAAsp, and HCV IRES domain II. The pooled RNAs, including the controls, were incubated with 1M7. The acylated residues cause base substitutions or indels during reverse transcription. Through high-throughput sequencing, we obtained mutational rates for each nucleotide, which allowed us to quantify the reactivity of 1M7, referred to as “SHAPE reactivity.” This reactivity was then used to model the RNA secondary structure.