Abstract: MicroRNAs are an important class of gene expression
regulators that are involved in many biological processes including
embryogenesis. miR-125b is a conserved microRNA that is enriched
in the nervous system. We have previously reported the function of
miR-125b in neuronal differentiation of human cell lines. We also
discovered the function of miR-125b in regulating p53 in human and
zebrafish. Here we further characterize the brain defects in zebrafish
embryos injected with morpholinos against miR-125b. Our data
confirm the essential role of miR-125b in brain morphogenesis
particularly in maintaining the balance between proliferation, cell
death and differentiation. We identified lunatic fringe (lfng) as an
additional target of miR-125b in human and zebrafish and suggest
that lfng may mediate the function of miR-125b in neurogenesis.
Together, this report reveals new insights into the function of miR-
125b during neural development of zebrafish.
Abstract: It has been established that microRNAs (miRNAs) play
an important role in gene expression by post-transcriptional regulation
of messengerRNAs (mRNAs). However, the precise relationships
between microRNAs and their target genes in sense of numbers,
types and biological relevance remain largely unclear. Dissecting the
miRNA-target relationships will render more insights for miRNA
targets identification and validation therefore promote the understanding
of miRNA function. In miRBase, miRanda is the key
algorithm used for target prediction for Zebrafish. This algorithm
is high-throughput but brings lots of false positives (noise). Since
validation of a large scale of targets through laboratory experiments
is very time consuming, several computational methods for miRNA
targets validation should be developed. In this paper, we present an
integrative method to investigate several aspects of the relationships
between miRNAs and their targets with the final purpose of extracting
high confident targets from miRanda predicted targets pool. This is
achieved by using the techniques ranging from statistical tests to
clustering and association rules. Our research focuses on Zebrafish.
It was found that validated targets do not necessarily associate with
the highest sequence matching. Besides, for some miRNA families,
the frequency of their predicted targets is significantly higher in the
genomic region nearby their own physical location. Finally, in a case
study of dre-miR-10 and dre-miR-196, it was found that the predicted
target genes hoxd13a, hoxd11a, hoxd10a and hoxc4a of dre-miR-
10 while hoxa9a, hoxc8a and hoxa13a of dre-miR-196 have similar
characteristics as validated target genes and therefore represent high
confidence target candidates.