Gene-Centered Regulatory Network Mapping - Caenorhabditis Elegans: Molecular Genetics and Development - page 271

short compared to more complex organisms such as humans, and for practical
purposes, promoters can therefore be defined as the region immediately upstream
of the translational start site. It is difficult to determine the 5 0 start point of gene
promoters. However, since most intergenic regions are shorter than 2 kb, most
studies have limited their analyses to this length ( Deplancke et al., 2004; Dupuy
et al., 2004; Hunt-Newbury et al., 2007 ). Importantly, it has been shown that this
region, when fused to a reporter gene such as that encoding the green fluorescent
protein (GFP) often drives gene expression in a manner that recapitulates the
expression of the endogenous gene ( Dupuy et al., 2004; Grove et al., 2009; Hunt-
Newbury et al., 2007; Martinez et al., 2008b; Reece-Hoyes et al., 2007 ).
To facilitate the system-level analysis of gene expression, a clone resource com-
prised of 6000 C. elegans promoters, referred to as the Promoterome, has been
generated ( Dupuy et al., 2004 ). This resource is based on the Gateway cloning
system and consists of promoter Entry clones that can be easily transferred to various
Destination vectors by a simple recombination reaction ( Hartley et al., 2000;
Walhout et al., 2000b ). Destination vectors that can be used to analyze gene regu-
latory networks include a GFP vector for the creation of transgenic animals to study
promoter activity in vivo, and Y1H vectors for the identification of TFs that can
interact with the promoter (see below). So far, systematic efforts have determined the
in vivo activity of 350 TF-encoding gene promoters ( Grove et al., 2009; Reece-
Hoyes et al., 2007 ), 1800 additional gene promoters ( Hunt-Newbury et al., 2007 ),
and 73 microRNA gene promoters ( Martinez et al., 2008b ). Many of the correspond-
ing transgenic lines are available to the community through the C. elegans genetics
center (CGC).
2. 3 0 UTRs
The 3 0 UTR is the untranslated region in the mRNA, immediately downstream of
the stop codon. This region is subject to post-transcriptional control by microRNAs
and RNA binding proteins. Recently, a comprehensive collection of 3 0 UTRs has
been delineated for most C. elegans genes ( Mangone et al., 2010 ). Cloning these
3 0 UTRs into Gateway-compatible vectors will provide a resource for experimental
gene regulatory network mapping that is similar to the ORFeome (see below) and
Promoterome resources.
3. Other Genic Regulatory Regions
It is not clear to what extent other regulatory regions function in gene regulatory
networks in C. elegans. So far, transcriptional studies have mostly focused on
promoters. However, it is clear that other regions, such as introns and sequences
downstream of the gene, can also play a role. Similarly, microRNAs and RNA
binding proteins could target regions outside 3 0 UTRs within their mRNA targets.
Systematic studies are required to elucidate the relative role different genic regions
play in complex gene regulatory networks.