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Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Drosophila yakuba Drosophila virilis Drosophila melanogaster Drosophila pseudoobscura

PROVIDER: GSE50773 | GEO | 2013/09/12

SECONDARY ACCESSION(S): PRJNA218867

REPOSITORIES: GEO

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Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression.

Project description:To better characterize how variation in regulatory sequences drives divergence in gene expression, we undertook a systematic study of transcription factor binding and gene expression in blastoderm embryos of four species, which sample much of the diversity in the 40 million-year old genus Drosophila: D. melanogaster, D. yakuba, D. pseudoobscura and D. virilis. We compared gene expression, measured by mRNA-seq, to the genome-wide binding, measured by ChIP-seq, of four transcription factors involved in early anterior-posterior patterning. We found that mRNA levels are much better conserved than individual transcription factor binding events, and that changes in a gene's expression were poorly explained by changes in adjacent transcription factor binding. However, highly bound sites, sites in regions bound by multiple factors and sites near genes are conserved more frequently than other binding, suggesting that a considerable amount of transcription factor binding is weakly or non-functional and not subject to purifying selection.

| S-EPMC3772039 | biostudies-literature

Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-09-12 | E-GEOD-50773 | biostudies-arrayexpress

Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression (part 2)

Project description:To better characterize how variation in regulatory sequences drives divergence in gene expression, we undertook a systematic study of transcription factor binding and gene expression in blastoderm embryos of four species, which sample much of the diversity in the 40 million-year old genus Drosophila: D. melanogaster, D. yakuba, D. pseudoobscura and D. virilis. We compared gene expression, measured by mRNA-seq, to the genome-wide binding, measured by ChIP-seq, of four transcription factors involved in early anterior-posterior patterning. We found that mRNA levels are much better conserved than individual transcription factor binding events, and that changes in a gene’s expression were poorly explained by changes in adjacent transcription factor binding. However highly bound sites, sites in regions bound by multiple factors and sites near genes are conserved more frequently than other binding, suggesting that a considerable amount of transcription factor binding is weakly or non-functional and not subject to purifying selection

2013-09-12 | GSE50771 | GEO

Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression (part 1)

Project description:We sequenced mRNA from blastoderm embryos of Drosophila melanogaster, Drosophila yakuba, Drosophila pseudoobscura and Drosophila virilis. Two samples contain pooled mRNA from several species, and the remaining 24 samples contain mRNA from a single species. Methods: Retinal mRNA profiles of Blastoderm embryos

2013-09-12 | GSE50766 | GEO

Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression (part 1)

2013-09-12 | E-GEOD-50766 | biostudies-arrayexpress

Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression

Project description:Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression

| PRJNA218867 | ENA

Extensive DNA-binding specificity divergence of a conserved transcription regulator.

Project description:The DNA sequence recognized by a transcription regulator can be conserved across large evolutionary distances. For example, it is known that many homologous regulators in yeasts and mammals can recognize the same (or closely related) DNA sequences. In contrast to this paradigm, we describe a case in which the DNA-binding specificity of a transcription regulator has changed so extensively (and over a much smaller evolutionary distance) that its cis-regulatory sequence appears unrelated in different species. Bioinformatic, genetic, and biochemical approaches were used to document and analyze a major change in the DNA-binding specificity of Mat?1, a regulator of cell-type specification in ascomycete fungi. Despite this change, Mat?1 controls the same core set of genes in the hemiascomycetes because its DNA recognition site has evolved with it, preserving the protein-DNA interaction but significantly changing its molecular details. Mat?1 and its recognition sequence diverged most dramatically in the common ancestor of the CTG-clade (Candida albicans, Candida lusitaniae, and related species), apparently without the aid of a gene duplication event. Our findings suggest that DNA-binding specificity divergence between orthologous transcription regulators may be more prevalent than previously thought and that seemingly unrelated cis-regulatory sequences can nonetheless be homologous. These findings have important implications for understanding transcriptional network evolution and for the bioinformatic analysis of regulatory circuits.

| S-EPMC3088634 | biostudies-literature

Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression (part 2)

Project description:Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression (part 2)

| PRJNA218869 | ENA

Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression (part 1)

Project description:Extensive divergence of transcription factor binding in Drosophila embryos with highly conserved gene expression (part 1)

| PRJNA218868 | ENA

Stable Binding of the Conserved Transcription Factor Grainy Head to its Target Genes Throughout Drosophila melanogaster Development.

Project description:It has been suggested that transcription factor binding is temporally dynamic, and that changes in binding determine transcriptional output. Nonetheless, this model is based on relatively few examples in which transcription factor binding has been assayed at multiple developmental stages. The essential transcription factor Grainy head (Grh) is conserved from fungi to humans, and controls epithelial development and barrier formation in numerous tissues. Drosophila melanogaster, which possess a single grainy head (grh) gene, provide an excellent system to study this conserved factor. To determine whether temporally distinct binding events allow Grh to control cell fate specification in different tissue types, we used a combination of ChIP-seq and RNA-seq to elucidate the gene regulatory network controlled by Grh during four stages of embryonic development (spanning stages 5-17) and in larval tissue. Contrary to expectations, we discovered that Grh remains bound to at least 1146 genomic loci over days of development. In contrast to this stable DNA occupancy, the subset of genes whose expression is regulated by Grh varies. Grh transitions from functioning primarily as a transcriptional repressor early in development to functioning predominantly as an activator later. Our data reveal that Grh binds to target genes well before the Grh-dependent transcriptional program commences, suggesting it sets the stage for subsequent recruitment of additional factors that execute stage-specific Grh functions.

| S-EPMC5289840 | biostudies-literature

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