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Surprising mechanisms and regulatory roles of yeast transcription factors [ChEC-seq]

ABSTRACT: Surprising mechanisms and regulatory roles of yeast transcription factors [ChEC-seq]

PROVIDER: PRJNA993170 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25220300_1.fastq.gz	Fastqsanger.gz
	SRR25220300_2.fastq.gz	Fastqsanger.gz
	SRR25220400_1.fastq.gz	Fastqsanger.gz
	SRR25220400_2.fastq.gz	Fastqsanger.gz
	SRR25220500_1.fastq.gz	Fastqsanger.gz

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Surprising mechanisms and regulatory roles of yeast transcription factors

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Surprising mechanisms and regulatory roles of yeast transcription factors [ChEC-seq]

Project description:DNA sequence-specific transcription factors (TFs) modulate transcription and chromatin architecture, acting from regulatory sites in enhancers and promoters of eukaryotic genes. How multiple TFs cooperate to regulate individual genes is still unclear. Most yeast TFs are thought to regulate transcription via binding to Upstream Activating Sequences, situated within a few hundred base pairs upstream of the regulated gene1. While this model has been validated for individual TFs and specific genes, it has not been tested in a systematic way. We integrated information on the binding and expression targets for the near-complete set of yeast TFs. Here we show that, contrary to expectations, there are few TFs with dedicated activator or repressor functions with most TFs having a dual role. While nearly all protein coding genes are regulated by one or more TFs, our analysis revealed limited overlap between TF binding and gene regulation. Rapid depletion of many TFs also revealed numerous regulatory targets distant from detectable TF binding sites, suggesting unexpected regulatory mechanisms. Our study provides a comprehensive survey of TF functions, offering insights into interactions between the set of TFs expressed in a single cell type and how they contribute to the complex program of gene regulation.

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Surprising mechanisms and regulatory roles of yeast transcription factors

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

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High resolution genome-wide occupancy in Candida species using ChEC-seq

Project description:Chromatin endogenous cleavage (ChEC) uses fusion of a protein of interest to micrococcal nuclease (MNase) to target calcium-dependent cleavage to specific genomic loci in vivo. Here we report the combination of ChEC with high-throughput sequencing (ChEC-seq) to determine genomic occupancy of the generalist transcription factor Nsi1 and the catalytic subunit of the SWI/SNF chromatin remodelling complex Snf2 in the opportunistic yeast Candida albicans. Time-based analysis of ChEC-seq data reveals two classes of sites for each transcriptional regulator, one exhibiting rapid cleavage during the first 5 min with robust consensus motifs and the second showing slow cleavage at largely unique sites with low-scoring motifs. The ChEC-seq procedure described here will allow a high-resolution genomic location definition which will enable a better understanding of transcriptional regulatory circuits that govern fungal fitness and drug resistance in these medically important fungi.

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ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo

Project description:Chromatin endogenous cleavage (ChEC) uses fusion of a protein of interest to micrococcal nuclease (MNase) to target calcium-dependent cleavage to specific genomic loci in vivo. Here we report the combination of ChEC with high-throughput sequencing (ChEC-seq) to map budding yeast transcription factor (TF) binding. Temporal analysis of ChEC-seq data reveals two classes of sites for TFs, one displaying rapid cleavage at sites with robust consensus motifs and the second showing slow cleavage at largely unique sites with low-scoring motifs. Sites with high-scoring motifs also display asymmetric cleavage, indicating that ChEC-seq provides information on the directionality of TF-DNA interactions. Strikingly, similar DNA shape patterns are observed regardless of motif strength, indicating that the kinetics of ChEC-seq discriminates DNA recognition through sequence and/or shape. We propose that time-resolved ChEC-seq detects both high-affinity interactions of TFs with consensus motifs and sites preferentially sampled by TFs during diffusion and sliding.

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