Studying differential isomiRs in high-throughput sequencing data identifies miRNA end-reads as a novel, putative miRNA degradation product
Abstract
With the advancement of deep-sequencing technologies, it has become clear thatindividual miRNAs show varying degrees of heterogeneity in the expressed maturesequence. Recent evidence has suggested isomiR variants may be biologicallyrelevant, and that small sequence variations can affect e.g. miRNA stability andRISC loading.The goal of this work was to investigate and characterize such isomiRs todetermine whether isomiRs of the same miRNA show biologically relevant differ-ences. The work can further be divided into two sub-studies.I first present a support-vector machine classifier for predicting expressionchanges for isomiRs in Ago2-knockout cells. The classifier is constructed frommiRNA sequence features, and is trained and tested using the observed read datafor individual isomiRs, thus handling the possibility that highly similar isomiRscan experience different expression changes. The classifier is not successful, sug-gesting expression changes in Ago2-knockout is determined by other factors. Ialso look more closely at whether there are isomiR variants that experience sig-nificantly different expression changes, but find no strong evidence of this.Working with the Ago2-knockout sequencing data, a second line of work wasset off from the discovery of a group of short ∼ 10 nt reads that align to the3 end of mature miRNAs. I initially searched for such reads with the goal offinding products of Ago2 cleavage, but interestingly the reads are found in bothwildtype and Ago2-knockout samples. I present an analysis of these reads andtheir corresponding miRNAs, and suggest they are produced by a previouslyundescribed regulated miRNA degradation process. In light of this, I also studythe project data for isomiRs with non-templated 3 A/U-tails, which previouslyhas been reported to affect miRNA degradation. I find both A- and U-tailing iscommon in the studied samples, but find neither a strong correlation nor a lack ofoverlap between miRNAs targeted by 3 tailing and miRNAs with correspondingshort 3 -aligning reads.