Strong conservation of inbred mouse strain microRNA loci but broad variation in brain microRNAs due to RNA editing and isomiR expression

Abstract

Diversity in the structure and expression of microRNAs, important regulators of gene expression, arises from SNPs, duplications followed by divergence, production of isomiRs, and RNA editing. Inbred mouse strains and crosses using them are important reference populations for genetic mapping, and as models of human disease. We determined the nature and extent of interstrain miRNA variation by (i) identifying miRNA SNPs in whole-genome sequence data from 36 strains, and (ii) examining miRNA editing and expression in hippocampus (Hpc) and frontal cortex (FCx) of six strains, to facilitate the study of miRNAs in neurobehavioral phenotypes. miRNA loci were strongly conserved among the 36 strains, but even the highly conserved seed region contained 16 SNPs. In contrast, we identified RNA editing in 58.9% of miRNAs, including 11 consistent editing events in the seed region. We confirmed the functional significance of three conserved edits in the miR-379/410 cluster, demonstrating that edited miRNAs gained novel target mRNAs not recognized by the unedited miRNAs. We found significant interstrain differences in miRNA and isomiR expression: Of 779 miRNAs expressed in Hpc and 719 in FCx, 262 were differentially expressed (190 in Hpc, 126 in FCx, 54 in both). We also identified 32 novel miRNA candidates using miRNA prediction tools. Our studies provide the first comprehensive analysis of SNP, isomiR, and RNA editing variation in miRNA loci across inbred mouse strains, and a detailed catalog of expressed miRNAs in Hpc and FCx in six commonly used strains. These findings will facilitate the molecular analysis of neurological and behavioral phenotypes in this model organism.

Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API

“…Finally, post-transcriptional processing of miRNAs can generate nucleotide changes at any position of the sequence by RNA processing enzymes, such as A-to-I editing by ADAR enzymes [30]. The specific function of isomiRs is still not well understood, but multiple studies have suggested a context-specific effect of isomiRs on gene regulation [26,28,31,32]. This is further supported by the fact that different isomiRs from the same mature miRNA can target virtually non-overlapping sets of transcripts [10,[33][34][35].…”

A comprehensive overview of bull sperm-borne small non-coding RNAs and their diversity across breeds

“…Whether the relative frequency of classic vs non-classic editing in sperm may also be associated with APOBEC3A and impact bull fertility in cattle warrants future investigation. Furthermore, ADAR A > I editing has been previously described as the major driver of seed polymorphisms in the mouse brain, accounting for about 40% of changes within the seed [84]. This finding seems to be far from general, and in bull sperm G > A and C > U transitions are the most frequent changes within the seed.…”

Population variation in miRNAs and isomiRs and their impact on human immunity to infection

“…Fueled by the advent of deep sequencing technologies, growing evidence has emerged that mature miRNAs undergo important post-transcriptional modifications [22][23][24][25][26]. These include nucleotide substitutions (miRNA editing) [27,28], 3′ adenylation or urydilation by terminal nucleotidyl transferases [29,30], shortening of their 3′ end by poly(A)-specific ribonuclease [31], and, more rarely, shifts in their 5′ start sites [24].…”