Genome-wide analysis of clustered Dorsal binding sites identifies putative target genes in the Drosophila embryo

Abstract

Metazoan genomes contain vast tracts of cis-regulatory DNA that have been identified typically through tedious functional assays. As a result, it has not been possible to uncover a cis-regulatory code that links primary DNA sequences to gene expression patterns. In an initial effort to determine whether coordinately regulated genes share a common ''grammar,'' we have examined the distribution of Dorsal recognition sequences in the Drosophila genome. Dorsal is one of the best-characterized sequence-specific transcription factors in Drosophila. The homeobox gene zerknullt (zen) is repressed directly by Dorsal, and this repression is mediated by a 600-bp silencer, the ventral repression element (VRE), which contains four optimal Dorsal binding sites. The arrangement and sequence of the Dorsal recognition sequences in the VRE were used to develop a computational algorithm to search the Drosophila genome for clusters of optimal Dorsal binding sites. There are 15 regions in the genome that contain three or more optimal sites within a span of 400 bp or less. Three of these regions are associated with known Dorsal target genes: sog, zen, and Brinker. The Dorsal binding cluster in sog is shown to mediate lateral stripes of gene expression in response to low levels of the Dorsal gradient. Two of the remaining 12 clusters are shown to be associated with genes that exhibit asymmetric patterns of expression across the dorsoventral axis. These results suggest that bioinformatics can be used to identify novel target genes and associated regulatory DNAs in a gene network.

RNA polymerase stalling at developmental control genes in the Drosophila melanogaster embryo

“…1C,D). This is consistent with previous evidence that some genes such as sog are transiently activated but then repressed at later stages 26 , while other genes such as tup are never activated in Toll 10b mutants 19,20 .…”

Exploiting position effects and the gypsy retrovirus insulator to engineer precisely expressed transgenes

“…However, as every experiment in which this correlation has been reported is based on constructs using the HSP70 core promoter-which itself has been shown to contain sequences necessary for salivary gland expression 32 -it is possible that the gypsy insulator is not a salivary gland enhancer but instead protects or synergizes with the salivary gland enhancer in the HSP70 promoter. Thus, to determine whether the gypsy insulator itself acts as a salivary gland enhancer, we took advantage of previously published transgenes 33,34 built with the gypsy insulator flanking a lacZ reporter under the control of the widely used eve minimal promoter 35 . The eve promoter, like the HSP70 promoter, contains a strong TATA box and is commonly used as a generic promoter for tests of enhancer activity.…”

The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo

“…Many known enhancers of gene expression are bound by multiple transcription factors, suggesting that highly overlapping transcription factor binding may imply cis-regulatory potential. Supporting this hypothesis, clusters of transcription factor binding sites have been used to identify novel enhancers (Berman et al 2002;Markstein et al 2002), a method that is particularly powerful when combined with sequence conservation (Kazemian et al 2010), and which has proved useful even in the absence of experimentally determined transcription factor binding specificities ). Many, although not all, regions bound in vivo by multiple transcription factors confer enhancer activity and drive gene expression (Chen et al 2008;Ouyang et al 2009;Zinzen et al 2009;Negre et al 2011).…”