Novel determinants of mammalian primary microRNA processing revealed by systematic evaluation of hairpin-containing transcripts and human genetic variation

Abstract

Mature microRNAs (miRNAs) are processed from hairpin-containing primary miRNAs (pri-miRNAs). However, rules that distinguish pri-miRNAs from other hairpin-containing transcripts in the genome are incompletely understood. By developing a computational pipeline to systematically evaluate 30 structural and sequence features of mammalian RNA hairpins, we report several new rules that are preferentially utilized in miRNA hairpins and govern efficient pri-miRNA processing. We propose that a hairpin stem length of 36 ± 3 nt is optimal for pri-miRNA processing. We identify two bulge-depleted regions on the miRNA stem, located ∼16-21 nt and ∼28-32 nt from the base of the stem, that are less tolerant of unpaired bases. We further show that the CNNC primary sequence motif selectively enhances the processing of optimal-length hairpins. We predict that a small but significant fraction of human single-nucleotide polymorphisms (SNPs) alter pri-miRNA processing, and confirm several predictions experimentally including a disease-causing mutation. Our study enhances the rules governing mammalian pri-miRNA processing and suggests a diverse impact of human genetic variation on miRNA biogenesis.

MuStARD: Deep Learning for intra- and inter-species scanning of functional genomic patterns

“…The model trained on secondary structure and conservation was the best performing two-input model. This result aligns with the identification of pre-miRNA hairpins by the Microprocessor complex during the biogenesis of miRNAs primarily by characteristics of their secondary structure rather than sequence (Roden et al 2017) and the fact that pre-miRNAs have highly conserved regions corresponding to the mature miRNA sequences. Surprisingly, the non-balanced model (MuStARD-mirSFC-U) performs best out of all model combinations including the balanced three input model (All comparisons Suppl.…”

Genetic variation and RNA structure regulate microRNA biogenesis

“…A recent study aiming to identify novel determinants of mammalian primary microRNA processing confirmed that the CNNC primary sequence motif selectively enhances the processing of optimal-length hairpins. This study, also predicted that a fraction of human SNPs will lead to alterations of pri-miRNA processing57.…”

Non-coding RNAs: long non-coding RNAs and microRNAs in endocrine-related cancers

“…HOTAIRM1 SOX9 is a stem cell factor involved in tamoxifen resistant BCa (Jeselsohn, et al 2017). HOTAIR and BCL2 expression were correlated in breast tumors and HOTAIR was shown to act as a ceRNA by base-pairing with miR-206, thus relieving mIR-206's repression of BCL2 expression (Ding, et al 2017). HOTAIRM1 expression increased in recurrent ovarian cancer ), but acts as a tumor suppressor in colorectal cancer (Wan, et al 2016) Another group performed a similar analysis on RNAseq data in the TCGA using ~ 1,000 breast tumors, an independent RNA-seq dataset of 50 pairs of matched tumors and adjacent normal tissues from BCa patients, and 23 normal breast tissues from healthy women .…”

“…The microprocessor complex of DROSHA (an RNAse III endonuclease) and DGCR8, plus additional proteins, cleaves hairpin-loop-containing pri-miR into 60-70 nucleotide (nt) precursor (pre)-miRNAs. The efficiency of pri-miRNA processing depends on stem length (36 ± 3 nt) and the appearance of bulges in the structure (Roden, et al 2017). DGCR8 acts as an oncogene in prostate cancer whereas DROSHA has oncogenic or tumor suppressor activity depending on the cancer type (reviewed in (Hata and Kashima 2016)).…”