| dc.description.abstract | With the advancement of deep-sequencing technologies, it has become clear that
individual miRNAs show varying degrees of heterogeneity in the expressed mature
sequence. Recent evidence has suggested isomiR variants may be biologically
relevant, and that small sequence variations can affect e.g. miRNA stability and
RISC loading.
The goal of this work was to investigate and characterize such isomiRs to
determine 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 expression
changes for isomiRs in Ago2-knockout cells. The classifier is constructed from
miRNA sequence features, and is trained and tested using the observed read data
for individual isomiRs, thus handling the possibility that highly similar isomiRs
can experience different expression changes. The classifier is not successful, sug-
gesting expression changes in Ago2-knockout is determined by other factors. I
also 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 was
set off from the discovery of a group of short ∼ 10 nt reads that align to the
3 end of mature miRNAs. I initially searched for such reads with the goal of
finding products of Ago2 cleavage, but interestingly the reads are found in both
wildtype and Ago2-knockout samples. I present an analysis of these reads and
their corresponding miRNAs, and suggest they are produced by a previously
undescribed regulated miRNA degradation process. In light of this, I also study
the project data for isomiRs with non-templated 3 A/U-tails, which previously
has been reported to affect miRNA degradation. I find both A- and U-tailing is
common in the studied samples, but find neither a strong correlation nor a lack of
overlap between miRNAs targeted by 3 tailing and miRNAs with corresponding
short 3 -aligning reads. | |
