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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 melanogaster Drosophila pseudoobscura Drosophila virilis

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 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 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)

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 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

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 functional divergence of the RosR transcription factor across haloarchaea

Project description:For microbial cells, an appropriate response to changing environmental conditions is critical for viability. Transcription regulatory proteins, or transcription factors (TFs) sense environmental signals to change gene expression. However, it remains unclear how TFs and their corresponding gene regulatory networks are selected for over evolutionary time scales. The function of TFs and how they evolve are particularly understudied in archaeal organisms. Here we identified, characterized, and compared the function of the RosR transcription factor across three related species of hypersaline adapted model archaea. RosR was previously characterized as a global regulator of gene expression during oxidative stress in the species Halobacterium salinarum (HsRosR). Here we use functional genomics and quantitative phenotyping to demonstrate that, despite strong conservation of HsRosR across species, its function diverges substantially. Surprisingly, RosR in Haloferax volcanii and Haloferax mediterranei regulates genes whose products function in motility and the outer membrane, leading to significant defects in motility when rosR is deleted. Given weak conservation and degeneration in the RosR cis-regulatory sequence across species, we hypothesize that the RosR regulatory network is easily rewired during evolution across related species of archaea.

2024-11-20 | GSE279016 | GEO

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