A General Introduction to MicroRNAs,Their Investigation and Exploitation in CHO Cell Lines - MicroRNAs as Tools in Biopharmaceutical Production - page 5

study by Arvey et al. examined several predictors of downregulation (A U con-

tent, 3 UTR length and the expression level of individual transcripts) and concluded
that the target binding by a miRNA was mostly influenced by the microRNA over
mRNA abundance ratio (Arvey et al. 2011 ). This ratio is also linked to the num-
ber of predicted targets. The “dilution factor” therefore means that endogenous or
plasmid-borne miRNAs ultimately may have a different influence on their specific
targets depending on the host, target expression level, and culture conditions and as
such these parameters must be considered when manipulating microRNAs. As stated
above, the length of the target 3 UTR can influence mRNA regulation by microR-
NAs and Hinske et al observed that for microRNAs that reside in intronic regions, the
3 UTR of host genes predicted to be targeted by their own microRNA (20 %) are sig-
nificantly longer and hold more adenylate/uridylate-rich elements (AREs) (Hinske
et al. 2010 ). Qiu et al ( 2010 ) also examined how miRNAs evolved with respect to
their target genes and transcription factors (TFs) and showed that microRNAs have
different evolutionary rules than TFs and protein-coding genes.

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1.4.2 RNA Editing

A-to-I RNA editing, which causes the conversion of single adenosines into inosines,
is mediated by adenosine deaminases acting on RNA (ADARs) (Yang et al. 2006 ),
a family of enzymes that recognise double-stranded RNA molecules. The process
can interfere with the efficiency of microRNA maturation and thus with the miRNA
homeostasis within a cell (Godfried Sie and Kuchka 2011 ; Gommans 2011 ). It
appears to affect 10 % of primiRNAs downstream processing by interfering with
Drosha-mediated cleavage. Interestingly, there are very few examples of mature
microRNAs influenced by RNA editing although this may be an artefact of the small
RNA sequences. Strikingly, RNA editing is also implicated in de novo generation of
miRNA binding sites in Alu sequences (Borchert et al. 2009).

1.4.3 Control of MicroRNA Expression

How miRNA levels are controlled is less well described and understood. The pro-
moter of protein-coding genes and microRNA are known to share common regulatory
elements (Lee et al. 2007 ). Putative binding sites for transcription factors of con-
served genomic regions can be found on the UCSC Genome Browser, JASPAR
(http://jaspar.binf.ku.dk/) and TESS (http://www.cbil.upenn.edu/cgi-bin/tess/tess). It
remains to be determined whether a set of mRNAs regulated by an individual miRNA
simply reflects a random set of functionally-independent genes or not. Interestingly,
Cui and colleagues ( 2007 ) concluded that genes with more transcription factor -
binding sites have a higher probability of being targeted by miRNAs and have more
miRNA-binding sites, suggesting that transcription factors and microRNAs might
act coordinately.