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Vol. 12, Issue 5, 701-712, May 2002
Identification of a Novel cis-Regulatory Element Involved in the Heat Shock Response in Caenorhabditis elegans Using Microarray Gene Expression and Computational Methods
Debraj
GuhaThakurta,1,5
Lisanne
Palomar,1
Gary D.
Stormo,1
Pat
Tedesco,2
Thomas E.
Johnson,2
David W.
Walker,3,6
Gordon
Lithgow,3,7
Stuart
Kim,4 and
Christopher D.
Link2,8
1 Department of Genetics, Washington University School of
Medicine, St. Louis, Missouri 63114, USA; 2 Institute for
Behavioral Genetics, University of Colorado, Boulder, Colorado 80309, USA; 3 School of Biological Sciences, University of
Manchester, Manchester M13 9PT, United Kingdom; 4 Department
of Developmental Biology, Stanford University School of Medicine,
Stanford, California 94305, USA.
We report here the identification of a previously unknown
transcription regulatory element for heat shock (HS) genes in
Caenorhabditis elegans. We monitored the expression pattern of
11,917 genes from C. elegans to determine the genes that were
up-regulated on HS. Twenty eight genes were observed to be consistently
up-regulated in several different repetitions of the experiments. We
analyzed the upstream regions of these genes using computational DNA
pattern recognition methods. Two potential cis-regulatory
motifs were identified in this way. One of these motifs (TTCTAGAA) was
the DNA binding motif for the heat shock factor (HSF), whereas the other (GGGTGTC) was previously unreported in the literature. We determined the significance of these motifs for the HS genes using different statistical tests and parameters. Comparative sequence analysis of orthologous HS genes from C. elegans and
Caenorhabditis briggsae indicated that the identified DNA
regulatory motifs are conserved across related species. The role of the
identified DNA sites in regulation of HS genes was tested by in vitro
mutagenesis of a green fluorescent protein (GFP) reporter
transgene driven by the C. elegans hsp-16-2
promoter. DNA sites corresponding to both motifs are shown to play a
significant role in up-regulation of the hsp-16-2
gene on HS. This is one of the rare instances in which a novel
regulatory element, identified using computational methods, is shown to
be biologically active. The contributions of individual sites toward
induction of transcription on HS are nonadditive, which indicates
interaction and cross-talk between the sites, possibly through the
transcription factors (TFs) binding to these sites.
[The
following individuals kindly provided reagents, samples, or unpublished
information as indicated in the paper: L. Hillier.]
Present addresses:
5Informatics Department, Rosetta
Inpharmatics, Inc., 12040 115th Avenue, N.E., Kirkland. WA 98034, USA;
6Division of Biology, Caltech, Pasadena, CA 91125, USA;
7Buck Institute, 8001 Redwood Blvd., Novato, CA 94945, USA.
8
Corresponding author.
12:701-712 ©2002 by Cold Spring Harbor Laboratory Press ISSN 1088-9051/02 $5.00
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