A General Introduction to MicroRNAs,Their Investigation and Exploitation in CHO Cell Lines - MicroRNAs as Tools in Biopharmaceutical Production - page 3

55%of C. elegans miRNAs are related to human miRNAs and 55 % Drosophila

miRNAs are related to human (Ibanez-Ventoso et al. 2008 ) indicating that miRNAs
have had important roles throughout animal evolution and implying that miRNAs are
conserved across several species and tightly regulate their target. Indeed, target genes
are more efficiently repressed by conserved miRNAs as opposed to less conserved
microRNAs (Huang and Gu 2011 ).
As described above, microRNAs can be found in both intergenic and intragenic
regions, sometimes in clusters. A detailed analysis of 60 microRNAs by Lagos-
Quintana et al ( 2003 ) revealed that 33 of these 60 resided in intergenic regions,
7 in sense orientation in non-coding genes/regions, and 13 in sense/7 in antisense
orientation within introns. The apparent discrepancy of microRNA loci of expression
raised at the time a question as to which promoter elements and RNA polymerases
controlled the transcription of microRNAs. It has since been ascertained that the
majority of pri-miRNAs are transcribed by RNA polymerase II (Cai et al. 2004 ), but
a fraction of these, notably residing upstream of tRNA sequences, Alu sequences or
mammalian-wide interspersed repeat (MWIR) sequences, are transcribed by RNA
polymerase III (Borchert et al. 2006 ).

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1.3 Informative Tools to Predict Targets of MicroRNAs

1.3.1 Target Binding and Specificity

Target genes can be paired to more than one miRNA, likewise a single miRNA could
in theory target hundreds of unrelated messages and as a result it is thought that
almost a third of genes are potentially regulated by microRNAs (Lewis et al. 2005 ).
This is essentially because in mammalian cells the target recognition is mediated
via imperfect Watson-Crick base pairing to the mRNA i.e. only 6-8 nucleotides
(called the seed region) near the 5 end of the miRNA show a perfect match (as
opposed to plants where there are few or no mismatches). Notably, the 3 region
may supplement seed matches or compensate for mismatches (Bartel 2009 ). Whilst
the sequence differs primarily at the 3 and 5 -end of the molecule, the biological
significance of these observations is unclear. Kiryu et al also suggested that miRNAs
have positive correlations with accessibilities in broad regions downstream of their
putative binding sites, which could indicate that downstream regions of the target
sites are bound by other proteins, assisting miRNA binding (Kiryu et al. 2011 ).
To date, only a fraction of miRNAs have been assigned a biological function and
therefore recent efforts have focused on developing prediction software to identify
additional miRNA targets in a specific host in order to further annotate pathways
of regulation. Current prediction tools differ in their approach and performance
and sometimes exhibit poor overlap. However, TargetScan (Friedman et al. 2009 ),
PicTar (Krek et al. 2005 ), Miranda (Betel et al. 2008 ), PITA Top (Kertesz et al.
2007 ), mIRGator (Nam et al. 2008 ) and the combined use of these software is a good
starting point to identify potential miRNA:mRNA interactions (for review, see Li