The fully linked HTML version of this article has now been published.
Development ePress online publication date 14 Dec 2005
doi: 10.1242/dev.02185
Research article
Chromosomal clustering and GATA transcriptional regulation of intestine-expressed genes in C. elegans
Florencia Pauli,
Yueyi Liu,
Yoona A. Kim,
Pei-Jiun Chen,
and
Stuart K. Kim*
* Author for correspondence (e-mail: kim{at}pmgm2.stanford.edu)
We used mRNA tagging to identify genes expressed in the intestine of C. elegans. Animals expressing an epitope-tagged protein that binds the poly-A tail of mRNAs (FLAG::PAB-1) from an intestine-specific promoter (ges-1) were used to immunoprecipitate FLAG::PAB-1/mRNA complexes from the intestine. A total of 1938 intestine-expressed genes (P<0.001) were identified using DNA microarrays. First, we compared the intestine-expressed genes with those expressed in the muscle and germline, and identified 510 genes enriched in all three tissues and 624 intestine-, 230 muscle- and 1135 germ line-enriched genes. Second, we showed that the 1938 intestine-expressed genes were physically clustered on the chromosomes, suggesting that the order of genes in the genome is influenced by the effect of chromatin domains on gene expression. Furthermore, the commonly expressed genes showed more chromosomal clustering than the tissue-enriched genes, suggesting that chromatin domains may influence housekeeping genes more than tissue-specific genes. Third, in order to gain further insight into the regulation of intestinal gene expression, we searched for regulatory motifs. This analysis found that the promoters of the intestine genes were enriched for the GATA transcription factor consensus binding sequence. We experimentally verified these results by showing that the GATA motif is required in cis and that GATA transcription factors are required in trans for expression of these intestinal genes.
CiteULike 
Complore 
Connotea 
Del.icio.us 
Digg 
Reddit 
Technorati 
Twitter What's this?
This article has been cited by other articles:
|
|
|
|
 
J. Takayama, S. Faumont, H. Kunitomo, S. R. Lockery, and Y. Iino
Single-cell transcriptional analysis of taste sensory neuron pair in Caenorhabditis elegans
Nucleic Acids Res.,
October 29, 2009;
(2009)
gkp868v1.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
H. C. Mak, L. Pillus, and T. Ideker
Dynamic reprogramming of transcription factors to and from the subtelomere
Genome Res.,
June 1, 2009;
19(6):
1014 - 1025.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
V. Reinke and A. D. Cutter
Germline Expression Influences Operon Organization in the Caenorhabditis elegans Genome
Genetics,
April 1, 2009;
181(4):
1219 - 1228.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S. G. Kuntz, E. M. Schwarz, J. A. DeModena, T. De Buysscher, D. Trout, H. Shizuya, P. W. Sternberg, and B. J. Wold
Multigenome DNA sequence conservation identifies Hox cis-regulatory elements
Genome Res.,
December 1, 2008;
18(12):
1955 - 1968.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S. Hellwig and B. L. Bass
A starvation-induced noncoding RNA modulates expression of Dicer-regulated genes
PNAS,
September 2, 2008;
105(35):
12897 - 12902.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
J. E Morabito, J. F Trott, D. M Korz, H. E Fairfield, S. H Buck, and R. C Hovey
A 5' distal palindrome within the mouse mammary tumor virus-long terminal repeat recruits a mammary gland-specific complex and is required for a synergistic response to progesterone plus prolactin
J. Mol. Endocrinol.,
August 1, 2008;
41(2):
75 - 90.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
S. J. Romney, C. Thacker, and E. A. Leibold
An Iron Enhancer Element in the FTN-1 Gene Directs Iron-dependent Expression in Caenorhabditis elegans Intestine
J. Biol. Chem.,
January 11, 2008;
283(2):
716 - 725.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
A. Neves, K. English, and J. R. Priess
Notch-GATA synergy promotes endoderm-specific expression of ref-1 in C. elegans
Development,
December 15, 2007;
134(24):
4459 - 4468.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
H. Feng, M. Ren, L. Chen, and C. S. Rubin
Properties, Regulation, and in Vivo Functions of a Novel Protein Kinase D: CAENORHABDITIS ELEGANS DKF-2 LINKS DIACYLGLYCEROL SECOND MESSENGER TO THE REGULATION OF STRESS RESPONSES AND LIFE SPAN
J. Biol. Chem.,
October 26, 2007;
282(43):
31273 - 31288.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
E. S. Motakis, G. P. Nason, P. Fryzlewicz, and G. A. Rutter
Variance stabilization and normalization for one-color microarray data using a data-driven multiscale approach
Bioinformatics,
October 15, 2006;
22(20):
2547 - 2553.
[Abstract]
[Full Text]
[PDF]
|
|
|
|
|
|
|
M. Shapira, B. J. Hamlin, J. Rong, K. Chen, M. Ronen, and M.-W. Tan
A conserved role for a GATA transcription factor in regulating epithelial innate immune responses
PNAS,
September 19, 2006;
103(38):
14086 - 14091.
[Abstract]
[Full Text]
[PDF]
|
|
|
© The Company of Biologists Ltd 2005
