Chromosomal clustering and GATA transcriptional regulation of intestine-expressed genes inC. elegans

Abstract

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.KEY WORDS: C. elegans, Intestine, Gene expression, GATA transcriptional regulation, Chromosomal clustering Development 133, 287-295 doi:10.1242 DEVELOPMENT 288The organogenesis of the C. elegans intestine has been detailed at the cellular level (Leung et al., 1999). It includes cytoplasmic polarization of cells in the intestinal primordium, intercalation of specific sets of cells, generation of an extracellular cavity within the primordium, and adherens junction formation. The adherens junctions present an ideal model with which to investigate epithelial cell polarity and several proteins involved in the process have been identified such as PAR-3, PAR-6, PKC-3, SMA-1, ERM-1, LET-413, DLG-1, AJM-1 and others (Knust and Bossinger, 2002). A molecular profile of the intestine would help to identify more genes involved in cell polarity and its development.By generating a profile of gene expression in the C. elegans intestine, we have identified the molecules that define intestinal function. The list of intestine-expressed genes includes genes of known and unknown function. The genes with known functions provide insight into mechanisms and pathways used in diverse intestinal functions, such as epithelial cell polarity, digestion, and resistance to pathogens and toxicity. The intestinal expression of genes with previously unknown function implies a role in intestinal processes.A genome-wide profile of intestinal gene expression can also be used to elucidate the regulatory networks that maintain intestinal differentiation. We have defined intestine-speci...

Direct examination of chromosomal clustering of organ‐specific genes in the chordate Ciona intestinalis

“…If so, the chromosomal proximity of the genes provides one possible mechanism that might explain this coordination. This has been demonstrated in genes that are preferentially expressed in muscle and intestine (Roy et al, 2002;Pauli et al, 2005), as well as in spermatogenesis-related genes (Miller et al, 2004) of Caenorhabditis elegans. A similar indication of clustering has been reported in testis-specific genes of Drosophila melanogaster (Boutanaev et al, 2002), and human placenta and skeletal muscle (Bortoluzzi et al, 1998).…”

“…We therefore next asked whether the chromosomal proximity of genes is responsible for facilitation of the temporally coordinated expression of the target genes of a specific transcription factor. This has been shown in GATA transcriptional regulation of intestine-expressed genes in Caenorhabditis elegans (Pauli et al, 2005). Forty-three genes that are thought to be downstream target of a T-box transcription factor Brachyury (Ci-Bra) and that are expressed in notochord cells of early embryo are distributed over the entire genome without showing any unusual pattern of chromosomal proximity (Takahashi et al, 2010).…”

“…It has been postulated that, with the exception of tandem duplicates, genes are randomly distributed throughout a given animal genome. On the other hand, several analyses have demonstrated that the genes expressed in a given tissue do not map to random locations, but instead resolve into clusters, suggesting a significant role of gene clustering in coordinate control of expression (e.g., Blanco et al, 2008;Boutanaev et al, 2002;Miller et al, 2004;Pauli et al, 2005;Roy et al, 2002). In addtion, the molecular mechanisms of coexpression and the functional significance between the gene neighbors is often not apparent, leading some workers to question the functional relevance of the observed coexpression (e.g., Batada et al, 2007;Lercher et al, 2003;Semon and Duret, 2006;Yanai et al, 2006).…”

In Silico Identification of Regulatory Elements in Promoters

“…Additionally in a C. elegans-C briggsae comparison, CompareProspector found the PHA-4 motif and the UNC-86 motif. Another C. Elegans CompareProspector analysis showed that intestine genes have GATA transcription factor binding motif that was latter experimentally validated (Pauli et al, 2006).…”

Development and Cell Polarity of the C. elegans Intestine

“…In brief, these events include the correct specification and asymmetric division of the intestinal founder cell EMS (Bossinger and Schierenberg, 1996;Goldstein, 1992;Han, 1997;Kormish et al, 2010;Schierenberg, 1987;see Fig.2 for further details), the ingression of the intestinal precusor cell Ea and Ep during gastrulation ( Fig.5B-C ;Chisholm, 2006;Putzke and Rothman, 2003;Rohrschneider and Nance, 2009;Sawyer et al, 2009;Schierenberg, 2005;Schierenberg, 2006), the cytoplasmic polarization of intestinal primordial cells ( Fig.5D; Achilleos et al, 2010;Bossinger et al, 2001;Leung et al, 1999;Totong et al, 2007), the formation of apical adherens junction and the generation of the future lumen within the primordium (Fig.5E'-E''; Leung et al, 1999), the intercalation of specific sets of cells (Hoffmann et al, 2010;Leung et al, 1999), the invariant 'twist' in the anterior of the intestinal primordium (Hermann et al, 2000), and finally the differentiation of the late embryonic, larval and adult intestine that has been proposed to be under the control of the GATA-factor ELT-2 (McGhee et al, 2009;McGhee et al, 2007;Pauli et al, 2006).…”