Biology Reference
In-Depth Information
B. Regulators
1. Transcription Factors
TFs provide the first level of gene control. They bind directly to DNA through
their sequence-specific DNA binding domain and can be grouped into families
based on the type of DNA binding domain they possess (
Reece-Hoyes et al.,
2005
). Well-known DNA binding domains include the homeodomain, the basic
helix-loop-helix (bHLH) domain, C2H2 zinc fingers, the ETS domain, the bZIP
domain, and C4-type zinc fingers found in nuclear hormone receptors (NHRs). TFs
can be predicted in a genome of interest by searching the complete collection of
proteins for the presence of a known DNA binding domain. This is usually done by
computational methods, for instance using Interpro (
Mulder et al., 2003
) or SMART
(
Letunic et al., 2004
) databases. However, we have found that visual inspection of
predicted DNA binding domains using knowledge of their sequence and structure is
highly useful as well. Indeed, by doing sowe increased the predicted set of C. elegans
TFs from
600 (
Ruvkun and Hobert, 1998
) to 940, or
5% of all protein-coding
genes (
Reece-Hoyes et al., 2005; Vermeirssen et al., 2007b
). Most C. elegans TF-
encoding genes encode a single splice variant; however in some cases multiple
variants are present, and some of these may encode proteins with different DNA
binding domains (
Reece-Hoyes et al., 2005
). Interestingly, different TF variants can
have different biological functions. For instance, different variants of the forkhead
protein DAF-16 were recently found to be expressed in distinct patterns and to confer
different functions related to metabolism and aging (
Kwon et al., 2010
). Several
proteins have been identified that can bind C. elegans gene promoters but that do not
possess a known DNA binding domain (
Deplancke et al., 2006a; Vermeirssen et al.,
2007a
). Thus, the total collection of C. elegans TFs may be slightly larger, but is
likely not to exceed 1000 (unpublished data).
More than 12,000 C. elegans full-length open reading frames (ORFs) have been
cloned into a Gateway-compatible resource called the ORFeome (
Lamesch et al.,
2004; Reboul et al., 2003
). We obtained the TF-encoding ORFs from this resource
and supplemented that with TF-encoding ORFs that we cloned ab initio (
Deplancke
et al., 2004; Vermeirssen et al., 2007b
). The resulting clone collection currently
contains
90% of all full-length TFs and can be directly used in assays for the
delineation of gene regulatory networks such as Y1H assays (unpublished data, see
below).
2. MicroRNAs
MicroRNAs regulate gene expression post-transcriptionally by sequence-specific
but imperfect basepairing with the 3
0
UTR of their target mRNAs. It has been
estimated that the C. elegans genome encodes more than 110 microRNAs
(
Lehrbach and Miska, 2008
). Some of these have been identified genetically (e.g.,
lin-4, let-7), some have been predicted computationally (
Lim et al., 2003
), and others
were more recently found by deep sequencing small RNA populations purified from
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