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clones can of course also be transformed individually when particular pre-defined
interactions are to be examined ( Reece-Hoyes et al.,2009 ).
In addition to transformation into haploid DNA bait strains, AD-TF clones can
also be introduced by mating. For this, we have transformed the AD-TF clones
( 755 in the first iteration) into yeast of mating type a , which is compatible for
mating with the DNA bait strains that have the ''a'' mating type ( Vermeirssen et al.,
2007b ). DNA bait strains are mated with the AD-TF clone array and positives are
examined in diploids. Each of these different methods for introducing AD-TFs into
DNA bait strains has advantages and disadvantages ( Vermeirssen et al., 2007b ).
Generally, transformation detects more interacting TFs than mating. However, mat-
ing is fast, less labor-intensive, and much less costly. Further, interactions detected
by mating are highly reproducible. When comparing library screens to more directed
experiments with smart pools or individual clones, it is clear that many more
protein-DNA interactions are found by the latter methods. However, with directed
experiments only cloned TFs can by definition be found, which in our current
collection is about 850 ( 90%) ( Vermeirssen et al., 2007b ) (unpublished data).
Proteins that do not have a recognizable DNA binding domain can only be retrieved
in unbiased cDNA library screens ( Deplancke et al., 2006a; Vermeirssen et al.,
2007a ). However, we do include these in TF resources after confirming their capa-
bility of interacting with C. elegans promoters and obtaining a suitable clone.
4. MicroRNA - mRNA Interactions
Putative interactions between the 3 0 UTRs of mRNAs and microRNAs are mostly
identified genetically or computationally predicted using one or more algorithms
that are publicly available. These include PicTar ( Lall et al., 2006 ), MiRanda
( Griffiths-Jones et al., 2006 ), TargetScan ( Lewis et al., 2005 ), RNA hybrid
( Rehmsmeier et al., 2004 ), and mirWIP ( Hammell et al., 2008 ). These algorithms
are challenging to use because they are often too greedy (high rate of false positive
predictions), or too stringent (high rate of false negative predictions). In order to
alleviate this, at least to some extent, we have previously used predictions that were
found by at least two of the four algorithms used ( Martinez et al., 2008a ). Future
experimental approaches will shed light onto physical and functional microRNA-
mRNA interactions that occur in vivo ( Lall et al., 2006; Zisoulis et al., 2010 ).
5. Other Regulatory Interactions
In addition to protein-DNA and microRNA-mRNA interactions, other relation-
ships are involved in gene control. An important class involves sequence-specific
RNA binding proteins that interact with the 3 0 UTR of mRNAs. It is not yet clear how
many sequence-specific RNA binding proteins are encoded by the C. elegans
genome, and only few have been studied genetically or biochemically. For instance,
detailed binding sites have been determined in vitro for MEX-3, MEX-5, and a
handful of other RNA binding proteins ( Farley et al., 2008; Pagano et al., 2007,
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