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Evolution of Reduced Co-Activator Dependence Led to Target Expansion of a Starvation Response Pathway

ABSTRACT: Evolution of Reduced Co-Activator Dependence Led to Target Expansion of a Starvation Response Pathway

PROVIDER: PRJNA382942 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5448390.fastq.gz	Fastqsanger.gz
	SRR5448400.fastq.gz	Fastqsanger.gz
	SRR5448410.fastq.gz	Fastqsanger.gz
	SRR5448420.fastq.gz	Fastqsanger.gz
	SRR5448430.fastq.gz	Fastqsanger.gz

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Evolution of Reduced Co-Activator Dependence Led to Target Expansion of a Starvation Response Pathway [Cgla RNA-seq]

Project description:In S. cerevisiae, the phosphate starvation (PHO) responsive transcription factors Pho4 and Pho2 are jointly required for induction of phosphate response genes and survival in phosphate starvation conditions. In the related human commensal and pathogen C. glabrata, Pho4 is required but Pho2 is dispensable for survival in phosphate-limited conditions and is only partially required for inducing the phosphate response genes. This reduced dependence on Pho2 evolved in C. glabrata and closely related species. Pho4 orthologs that are less dependent on Pho2 induce more genes when introduced into the S. cerevisiae background, and Pho4 in C. glabrata both binds to more sites and induces more genes with expanded functional roles compared to Pho4 in S. cerevisiae. We used RNA-seq to profile the transcriptome of wild type and mutants of Pho4 / Pho2 in C. glabrata, to identify genes induced by Pho4.

2017-04-15 | GSE97800 | GEO

Evolution of Reduced Co-Activator Dependence Led to Target Expansion of a Starvation Response Pathway [Scer RNA-seq]

Project description:In S. cerevisiae, the phosphate starvation (PHO) responsive transcription factors Pho4 and Pho2 are jointly required for induction of phosphate response genes and survival in phosphate starvation conditions. In the related human commensal and pathogen C. glabrata, Pho4 is required but Pho2 is dispensable for survival in phosphate-limited conditions and is only partially required for inducing the phosphate response genes. This reduced dependence on Pho2 evolved in C. glabrata and closely related species. Pho4 orthologs that are less dependent on Pho2 induce more genes when introduced into the S. cerevisiae background, and Pho4 in C. glabrata both binds to more sites and induces more genes with expanded functional roles compared to Pho4 in S. cerevisiae. We used RNA-seq to profile the transcriptome of wild type and mutants of Pho4 / Pho2, or Pho4 ortholog swap in S. cerevisiae, to identify genes induced by Pho4 or its orthologs in S. cerevisiae background.

2017-04-15 | GSE97799 | GEO

Evolution of Reduced Co-Activator Dependence Led to Target Expansion of a Starvation Response Pathway [Cgla ChIP-seq]

Project description:In S. cerevisiae, the phosphate starvation (PHO) responsive transcription factors Pho4 and Pho2 are jointly required for induction of phosphate response genes and survival in phosphate starvation conditions. In the related human commensal and pathogen C. glabrata, Pho4 is required but Pho2 is dispensable for survival in phosphate-limited conditions and is only partially required for inducing the phosphate response genes. This reduced dependence on Pho2 evolved in C. glabrata and closely related species. Pho4 orthologs that are less dependent on Pho2 induce more genes when introduced into the S. cerevisiae background, and Pho4 in C. glabrata both binds to more sites and induces more genes with expanded functional roles compared to Pho4 in S. cerevisiae. We used Chromatin-ImmunoPrecipitation with exonucleas followed by high-throughput sequencing (BioChIP-seq) to identify the binding locations of Pho4 from both S. cerevisiae and C. glabrata in the S. cerevisiae background lacking the negative regulator Pho80, and either with or without Pho2.

2017-04-15 | GSE97798 | GEO

Evolution of Reduced Co-Activator Dependence Led to Target Expansion of a Starvation Response Pathway [Scer ChIP-seq]

Project description:In S. cerevisiae, the phosphate starvation (PHO) responsive transcription factors Pho4 and Pho2 are jointly required for induction of phosphate response genes and survival in phosphate starvation conditions. In the related human commensal and pathogen C. glabrata, Pho4 is required but Pho2 is dispensable for survival in phosphate-limited conditions and is only partially required for inducing the phosphate response genes. This reduced dependence on Pho2 evolved in C. glabrata and closely related species. Pho4 orthologs that are less dependent on Pho2 induce more genes when introduced into the S. cerevisiae background, and Pho4 in C. glabrata both binds to more sites and induces more genes with expanded functional roles compared to Pho4 in S. cerevisiae. We used Biotin-assisted Chromatin-ImmunoPrecipitation followed by high-throughput sequencing (BioChIP-seq) to identify the binding locations of Pho4 from both S. cerevisiae and C. glabrata in the S. cerevisiae background lacking the negative regulator Pho80, and either with or without Pho2.

2017-04-15 | GSE97797 | GEO

Evolution of reduced co-activator dependence led to target expansion of a starvation response pathway.

Project description:Although combinatorial regulation is a common feature in gene regulatory networks, how it evolves and affects network structure and function is not well understood. In S. cerevisiae, the phosphate starvation (PHO) responsive transcription factors Pho4 and Pho2 are required for gene induction and survival during phosphate starvation. In the related human commensal C. glabrata, Pho4 is required but Pho2 is dispensable for survival in phosphate starvation and is only partially required for inducing PHO genes. Phylogenetic survey suggests that reduced dependence on Pho2 evolved in C. glabrata and closely related species. In S. cerevisiae, less Pho2-dependent Pho4 orthologs induce more genes. In C. glabrata, its Pho4 binds to more locations and induces three times as many genes as Pho4 in S. cerevisiae does. Our work shows how evolution of combinatorial regulation allows for rapid expansion of a gene regulatory network's targets, possibly extending its physiological functions.

| S-EPMC5446240 | biostudies-literature

Evolution of Reduced Co-Activator Dependence Led to Target Expansion of a Starvation Response Pathway

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-04-15 | GSE97801 | GEO

Saccharomyces cerevisiae

Project description:Evolution of Reduced Co-Activator Dependence Led to Target Expansion of a Starvation Response Pathway [Scer RNA-seq]

| PRJNA382955 | ENA

Nakaseomyces glabratus

Project description:Evolution of Reduced Co-Activator Dependence Led to Target Expansion of a Starvation Response Pathway [Cgla ChIP-seq]

| PRJNA382951 | ENA

Saccharomyces cerevisiae

Project description:Evolution of Reduced Co-Activator Dependence Led to Target Expansion of a Starvation Response Pathway [Scer ChIP-seq]