Conserved genomic organisation of Group B Sox genes in insects.

BACKGROUND: Sox domain containing genes are important metazoan transcriptional regulators implicated in a wide rage of developmental processes. The vertebrate B subgroup contains the Sox1, Sox2 and Sox3 genes that have early functions in neural development. Previous studies show that Drosophila Group B genes have been functionally conserved since they play essential roles in early neural specification and mutations in the Drosophila Dichaete and SoxN genes can be rescued with mammalian Sox genes. Despite their importance, the extent and organisation of the Group B family in Drosophila has not been fully characterised, an important step in using Drosophila to examine conserved aspects of Group B Sox gene function. RESULTS: We have used the directed cDNA sequencing along with the output from the publicly-available genome sequencing projects to examine the structure of Group B Sox domain genes in Drosophila melanogaster, Drosophila pseudoobscura, Anopheles gambiae and Apis mellifora. All of the insect genomes contain four genes encoding Group B proteins, two of which are intronless, as is the case with vertebrate group B genes. As has been previously reported and unusually for Group B genes, two of the insect group B genes, Sox21a and Sox21b, contain introns within their DNA-binding domains. We find that the highly unusual multi-exon structure of the Sox21b gene is common to the insects. In addition, we find that three of the group B Sox genes are organised in a linked cluster in the insect genomes. By in situ hybridisation we show that the pattern of expression of each of the four group B genes during embryogenesis is conserved between D. melanogaster and D. pseudoobscura. CONCLUSION: The DNA-binding domain sequences and genomic organisation of the group B genes have been conserved over 300 My of evolution since the last common ancestor of the Hymenoptera and the Diptera. Our analysis suggests insects have two Group B1 genes, SoxN and Dichaete, and two Group B2 genes. The genomic organisation of Dichaete and another two Group B genes in a cluster, suggests they may be under concerted regulatory control. Our analysis suggests a simple model for the evolution of group B Sox genes in insects that differs from the proposed evolution of vertebrate Group B genes.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Genomic mapping of Suppressor of Hairy-wing binding sites in Drosophila.

BACKGROUND: Insulator elements are proposed to play a key role in the organization of the regulatory architecture of the genome. In Drosophila, one of the best studied is the gypsy retrotransposon insulator, which is bound by the Suppressor of Hairy-wing (Su [Hw]) transcriptional regulator. Immunolocalization studies suggest that there are several hundred Su(Hw) sites in the genome, but few of these endogenous Su(Hw) binding sites have been identified. RESULTS: We used chromatin immunopurification with genomic microarray analysis to identify in vivo Su(Hw) binding sites across the 3 megabase Adh region. We find 60 sites, and these enabled the construction of a robust new Su(Hw) binding site consensus. In contrast to the gypsy insulator, which contains tightly clustered Su(Hw) binding sites, endogenous sites generally occur as isolated sites. These endogenous sites have three key features. In contrast to most analyses of DNA-binding protein specificity, we find that strong matches to the binding consensus are good predictors of binding site occupancy. Examination of occupancy in different tissues and developmental stages reveals that most Su(Hw) sites, if not all, are constitutively occupied, and these isolated Su(Hw) sites are generally highly conserved. Analysis of transcript levels in su(Hw) mutants indicate widespread and general changes in gene expression. Importantly, the vast majority of genes with altered expression are not associated with clustering of Su(Hw) binding sites, emphasizing the functional relevance of isolated sites. CONCLUSION: Taken together, our in vivo binding and gene expression data support a role for the Su(Hw) protein in maintaining a constant genomic architecture

Conserved genomic organisation of Group B Sox genes in insects.

BACKGROUND: Sox domain containing genes are important metazoan transcriptional regulators implicated in a wide rage of developmental processes. The vertebrate B subgroup contains the Sox1, Sox2 and Sox3 genes that have early functions in neural development. Previous studies show that Drosophila Group B genes have been functionally conserved since they play essential roles in early neural specification and mutations in the Drosophila Dichaete and SoxN genes can be rescued with mammalian Sox genes. Despite their importance, the extent and organisation of the Group B family in Drosophila has not been fully characterised, an important step in using Drosophila to examine conserved aspects of Group B Sox gene function. RESULTS: We have used the directed cDNA sequencing along with the output from the publicly-available genome sequencing projects to examine the structure of Group B Sox domain genes in Drosophila melanogaster, Drosophila pseudoobscura, Anopheles gambiae and Apis mellifora. All of the insect genomes contain four genes encoding Group B proteins, two of which are intronless, as is the case with vertebrate group B genes. As has been previously reported and unusually for Group B genes, two of the insect group B genes, Sox21a and Sox21b, contain introns within their DNA-binding domains. We find that the highly unusual multi-exon structure of the Sox21b gene is common to the insects. In addition, we find that three of the group B Sox genes are organised in a linked cluster in the insect genomes. By in situ hybridisation we show that the pattern of expression of each of the four group B genes during embryogenesis is conserved between D. melanogaster and D. pseudoobscura. CONCLUSION: The DNA-binding domain sequences and genomic organisation of the group B genes have been conserved over 300 My of evolution since the last common ancestor of the Hymenoptera and the Diptera. Our analysis suggests insects have two Group B1 genes, SoxN and Dichaete, and two Group B2 genes. The genomic organisation of Dichaete and another two Group B genes in a cluster, suggests they may be under concerted regulatory control. Our analysis suggests a simple model for the evolution of group B Sox genes in insects that differs from the proposed evolution of vertebrate Group B genes.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

Genes with expression changes in su(Hw) mutant larvae (L3) and wing discs

A cluster diagram showing changes in gene expression in a () null condition compared with changes in the heterozygous controls (fold change ≥ 1.7, ≤ 10for the mutants and approximately half the fold change at ≤ 10for the heterozygotes). The table lists those genes with greater than 1.7-fold expression change that have predicted Suppressor of Hairy-wing (Su [Hw]) binding sites within 30 kilobases (kb). The Expression column shows the absolute fold change for each gene. The Distance column indicates the distance between the gene model and Su(Hw) sites(s); for those genes with predicted sites within the gene model, the number of sites are indicated. If there is more than one site, the distance between them is given. The Location column indicates where the predicted sites lie with respect to the gene models. UTR, untranslated region.<p><b>Copyright information:</b></p><p>Taken from "Genomic mapping of Suppressor of Hairy-wing binding sites in "</p><p>http://genomebiology.com/2007/8/8/R167</p><p>Genome Biology 2007;8(8):R167-R167.</p><p>Published online 16 Aug 2007</p><p>PMCID:PMC2374998.</p><p></p

Correlation of ChIP enrichment using either anti-Su(Hw) on wild-type chromatin or anti-GFP on chromatin from Su(Hw)-GFP transgenic

The enrichment values are plotted as the arsinh transformation (approximately equivalent to the log2 scale) of the ratio of specific versus control ChIP. Correlation coefficient is 0.66. ChIP, chromatin immunoprecipitation; GFP, green fluorescent protein; Su(Hw), Suppressor of Hairy-wing.<p><b>Copyright information:</b></p><p>Taken from "Genomic mapping of Suppressor of Hairy-wing binding sites in "</p><p>http://genomebiology.com/2007/8/8/R167</p><p>Genome Biology 2007;8(8):R167-R167.</p><p>Published online 16 Aug 2007</p><p>PMCID:PMC2374998.</p><p></p

Closeness of match to the Su(Hw) binding site consensus is associated with binding

The Patser value for each Patser match is plotted against the enrichment (arsinh transformation; approximately equal to logratio) of the fragment containing the matching sequence. The enrichment value is the highest mean value from the three chromatin sources. The vertical line indicates the Patser = e; for matches with < e, 63% show enrichment greater than 0.5 (1.4-fold) and 53% show enrichment greater than 0.8 (1.7-fold). Su(Hw), Suppressor of Hairy-wing.<p><b>Copyright information:</b></p><p>Taken from "Genomic mapping of Suppressor of Hairy-wing binding sites in "</p><p>http://genomebiology.com/2007/8/8/R167</p><p>Genome Biology 2007;8(8):R167-R167.</p><p>Published online 16 Aug 2007</p><p>PMCID:PMC2374998.</p><p></p

Expression changes in the 3 Mb region with respect to Su(Hw) binding sites

Expression changes (as absolute fold change according to the scale bar) are indicated by the bars above the gene models, with upregulated genes in orange and downregulated genes in blue. The bars mark the 5' end of each gene. The location of Su(Hw) binding sites are plotted on the three rows All sites, Cluster 1, and Cluster 2. Cluster 2 indicates the two sites within 100 base pairs of each other. Cluster 1 indicates the six pairs of sites within 1 kilobase of each other. All sites plots the locations of the remaining 83 sites in the region. The maps are plotted and rendered using the Affymetrix Integrated Genome Browser.<p><b>Copyright information:</b></p><p>Taken from "Genomic mapping of Suppressor of Hairy-wing binding sites in "</p><p>http://genomebiology.com/2007/8/8/R167</p><p>Genome Biology 2007;8(8):R167-R167.</p><p>Published online 16 Aug 2007</p><p>PMCID:PMC2374998.</p><p></p