Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Saccharomyces cerevisiae

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

PROVIDER: PRJNA279980 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR1947780_1.fastq.gz	Fastqsanger.gz
	SRR1947780_2.fastq.gz	Fastqsanger.gz
	SRR1947790_1.fastq.gz	Fastqsanger.gz
	SRR1947790_2.fastq.gz	Fastqsanger.gz
	SRR1947800_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 114

Similar Datasets

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.

2015-10-22 | GSE67453 | GEO

Saccharomyces cerevisiae

Project description:In vivo RNA binding sites of the yeast ribosome biogenesis factor Utp23

| PRJNA343936 | ENA

Saccharomyces cerevisiae BY4741

Project description:Intrinsically disordered regions direct transcription factor in-vivo binding specificity

| PRJNA573518 | ENA

Saccharomyces cerevisiae

Project description:Genome-wide mapping of the binding sites of transcription factor Cst6p in Saccharomyces cerevisiae

| PRJNA306490 | ENA

Saccharomyces cerevisiae

Project description:Genomic regions flanking E-box sites influence DNA binding specificity of bHLH transcription factors through DNA shape (validation)

| PRJNA190630 | ENA

Saccharomyces cerevisiae

Project description:Genomic regions flanking E-box sites influence DNA binding specificity of bHLH transcription factors through DNA shape (different concentrations)

| PRJNA190629 | ENA

ChEC-Seq: a robust method to identify protein-DNA interactions genome-wide

Project description:Here we show that the ChEC-Seq technique is able to differentiate the binding specificities of Esa1 and Gcn5 two chromatin-binding factors displaying widespread genome-wide associations. We also show that the ChEC-Seq technique reveals strong binding of the transcription factor Sfp1 at Ribi gene promoters. Furthermore, our data provide the first evidence that a specific DNA motif previously identified by ChEC-Seq (Albert 2019 PMID: 30804227) is in fact an in vivo binding site for Sfp1.

2020-07-01 | GSE133645 | GEO

Saccharomyces cerevisiae

Project description:ChIP-exo analysis of the DNA-binding sites of the yeast transcription factor Yfl052w sequenced by SOLiD

| PRJNA248391 | ENA

Saccharomyces cerevisiae

Project description:ChIP-exo analysis of the DNA-binding sites of the yeast transcription factor Yfl052w sequenced by Illumina

| PRJNA248390 | ENA

Saccharomyces cerevisiae

Project description:Genome wide Mms1-binding sites in S. cerevisiae

| PRJNA385333 | ENA