Program of the 2001 International Worm Meeting - Sternberg Lab ...

1019
1019. Computer prediction of
cis-acting elements from co-regulated
genes.
Archana Sharma-Oates, Ian A.
Hope
School of Biology, University of Leeds, Leeds,
LS2 9JT, UK.
The complete nucleic acid sequence of a
genome provides new opportunities to study
gene regulation. cis-regulatory elements are
required for the correct developmental
activation (spatially, temporally as well as
appropriate level of expression) of genes.
Identification and analysis of these sites are
crucial for advancing our appreciation of
genome regulation.
The ultimate goal of the research is to construct
specific promoter models containing a
combination of several regulatory elements. As
a first step towards this goal, it is necessary to
focus on the detection of single motifs
(representing transcription factor binding sites)
common to the promoter sequences of
putatively co-regulated genes. However, this
problem is complex: putative regulatory motifs
will be of unknown size with variable sequence
and ill-defined position.
Analysis of gene expression using a reporter
gene fusion approach [http://129.11.204.86:591]
has identified groups of genes with similar
expression patterns. Many if not all these genes
are likely to be co-regulated and contain
cis-elements recognized by a common
regulatory system. The regions of these genes
able to drive this expression pattern has been
analyzed using two software packages, MEME
[http://meme.sdsc.edu/meme/website/] and
SPEXS [http://ep.ebi.ac.uk/EP/SPEXS/] to
identify cis-regulatory elements. The
significance of the MEME results was difficult
to assess as many motifs were detected but the
low sequence complexity of many of them
raised questions about the significance of the
output. In contrast the SPEXS output was
simpler although the number of motifs
generated was greater. The output is being
further processed to include other characteristics
in a score for identified motifs. The motifs with
the highest scores should be the strongest
candidates for experimental verification.
1020. Regulation of the C. elegans
posterior Hox paralogs nob-1 and
php-3
Ellen Kress 1 , Kimberly Van Auken 1 ,
Jacqueline Schein 2 , William B.
Wood 1
1 Dept. of MCD Biology, University of
Colorado, Boulder, CO 80309
2 B.C. Cancer Agency, Vancouver, B.C.,
Canada V5Z 4E6
1020
During metazoan embryonic development,
regional differences along the anterior-posterior
axis are specified by Hox gene products, which
are highly conserved homeodomain
transcription factors. We have recently
described two previously unknown C. elegans
posterior Hox paralogs, nob-1 and php-3 (Van
Auken et al., PNAS 97:4499-4503, 2000), and
are now undertaking a study of their regulatory
regions. The two genes are 232bp apart;
however, they probably do not form an operon
because php-3, the downstream gene, is
SL1-spliced. nob-1 and php-3 are 47% identical
at the nucleotide level, and preliminary evidence
suggests that they have redundant functions. A
genetic null allele, ct223, contains a 25kb
deletion upstream of nob-1 that is likely to
remove most or all of the regulatory region for
both genes. We are currently making constructs
to rescue nob-1 and php-3 together as well as
individually. We have cloned the C. briggsae
nob-1 region for comparison to the C. elegans
nob-1 region and identification of putative
conserved regulatory elements. We will
eventually use GFP reporters to functionally test
these elements and correlate them to expression
patterns. Knowledge of the regulation of nob-1
and php-3 will provide an interesting
comparison to the regulation of the mouse and
Drosophila posterior Hox paralogs.