Saccharomyces cerevisiae
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA279980 | ENA |
REPOSITORIES: ENA
Similar Datasets
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
Project description:In vivo RNA binding sites of the yeast ribosome biogenesis factor Utp23
| PRJNA343936 | ENA
Project description:Intrinsically disordered regions direct transcription factor in-vivo binding specificity
| PRJNA573518 | ENA
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
Project description:Genome-wide mapping of the binding sites of transcription factor Cst6p in Saccharomyces cerevisiae
| PRJNA306490 | ENA
Project description:Genomic regions flanking E-box sites influence DNA binding specificity of bHLH transcription factors through DNA shape (validation)
| PRJNA190630 | ENA
Project description:Genomic regions flanking E-box sites influence DNA binding specificity of bHLH transcription factors through DNA shape (different concentrations)
| PRJNA190629 | ENA
Project description:ChIP-exo analysis of the DNA-binding sites of the yeast transcription factor Yfl052w sequenced by SOLiD
| PRJNA248391 | ENA
Project description:ChIP-exo analysis of the DNA-binding sites of the yeast transcription factor Yfl052w sequenced by Illumina
| PRJNA248390 | ENA
Project description:GATA transcription factors are highly conserved among eukaryotes and play roles in transcription of genes implicated in cancer progression and hematopoiesis. However, although their consensus binding sites have been well defined in vitro, the in vivo selectivity for recognition by GATA factors remains poorly characterized. Using ChIP-Seq, we identified the Dal80 GATA factor targets in yeast. Our data reveal Dal80 binding to a large set of promoters, sometimes independently of GATA sites, correlating with nitrogen- and/or Dal80-sensitive gene expression. Strikingly, Dal80 was also detected across the body of promoter-bound genes, correlating with high expression. Mechanistic single-gene experiments showed that Dal80 spreading across gene bodies requires active transcription. Consistently, Dal80 co-immunoprecipitated with the initiating and post-initiation forms of RNA Polymerase II. Our work suggests that GATA factors could play dual, synergistic roles during transcription initiation and post-initiation steps, promoting efficient remodeling of the gene expression program in response to environmental changes.
2019-02-06 | GSE86325 | GEO