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Fig. 4.2 Conservation of CHO miRNAs . 365 CHO miRNAs and the respective 212 precursor-
miRNAs (pre-miRNAs) that gave an unambiguous BLAST alignment in the CHO-K1 genome were
mapped against miRNAs from human, mouse and rat as available in the latest update of miRBase
(version 18, Nov. 2011). a Out of 365 mature miRNAs, 257 (70.4 %) possess a 100 % identical
(full-length alignment and no mismatches) human or rodent homolog. On the primary y-axis the
fraction of the CHO miRNA in percent that could be aligned to a human or rodent ortholog is
shown, while the secondary y-axis shows the number of mismatches observed for the respective
alignment. b An analogous analysis for the 212 CHO pre-miRNAs identified 53 (25 %) sequences
with perfectly identical human or rodent ortholog
hits for 365 mature miRNAs (
94 %) were observed, corresponding to 212 miRNA
hairpins or miRNA gene loci. The respective sequences of both mature and precur-
sor miRNAs were subsequently compared to their human, mouse and rat orthologs
available in miRBase version 18 to find that 257 mature miRNAs (70.4 %) possess
a 100 % identical (full-length alignment and no mismatches) human or rodent ho-
molog (Fig. 4.2 a). A similar analysis for precursor miRNA sequences identified 53
pre-miRNAs (25 % of CHO pre-miRNAs) in human, mouse or rat that are 100 %
identical to the CHO ortholog (Fig. 4.2 b). Thus, by the use of cross-species microar-
ray platforms, which most commonly comprise combined probe-sets against human,
mouse and rat miRNAs, more than 70 % of the currently annotated CHO miRNAs
can be reliably detected.
Expansion of currently reported CHO miRNA sequences can be achieved by
identification of novel and CHO-specific miRNAs, which was done by mapping
small RNA reads to the mouse reference genome (Hackl et al. 2011 ). Initially 11
potential miRNA loci were thus identified, of which two miRNAs (cgr-miR-6091
and cgr-miR-6092) gave an unambiguous BLAST hit in the CHO-K1 reference
genome, exhibited a canonical miRNA-like secondary structure and can therefore
be considered as the first CHO-specific miRNAs.
To sum up, the currently available miRNA-seq data from CHO cells point to a high
conservation of mature miRNA sequences compared to human and several rodent
species. Consequently, this raises the question whether miRNA functions are equally
well conserved. The presence of most (80 %) of the so far reported and validated
miRNA binding sites for miR-17-92 in CHO cDNA sequence data suggests a similar
biologic function at least for this miRNA cluster. However, comprehensvie studies
of miRNA binding sites in CHO cDNA sequences have not yet been performed.
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