The advent of deep sequencing has revealed marked differences in microRNA
(miRNA) expression profiles between cell types. We focus on how miRNAs are
regulated in embryonic stem cells (ESCs) and their differentiated neural
progenitor stem cells (NPSCs). We discovered that 60% of miRNAs are regulated
b
y transcription. The remaining 40% of miRNAs were transcribed but not
processed in ESCs. Furthermore, systematic analysis of miRNAs on chromosome
1 and 2 helped to validate our results. We show that
43%
of these miRNAs,
which are highly expressed in differentiated cell types but poorly expressed in
ESCs, were transcribed but not processed in ESCs. Therefore we infer that post-
transcr
iptional regulation of miRNAs is prevalent in ESCs and could potentially
be a characteristic of this cell type.
Post-transcriptional regulation of miRNAs is also evident in miRNA clusters.
Clusters of miRNAs are transcribed together however individual mature miRNA
expression often differs between tissues and even within the same tissue type.
Following investigation into post-transcriptional regulation, we discovered
extensive alternative polyadenylation in three different miRNA clusters. We
suggest that alternative polyadenylation has the potential to influence regulation of individual miRNAs within a cluster contributing to their differential expression levels.