GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE67453 Query DataSets for GSE67453
Status Public on Oct 22, 2015
Title ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo
Organism Saccharomyces cerevisiae
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
Overall design We adapted ChEC to a genome-wide sequencing readout (ChEC-seq) to map the genome-wide distributions of the budding yeast transcription factors Abf1, Rap1 and Reb1 without the limitations associated with ChIP-based methods.
Contributor(s) Zentner GE, Kasinathan S, Henikoff S
Citation(s) 26490019
Submission date Mar 31, 2015
Last update date May 15, 2019
Contact name Jorja Henikoff
Phone 206-667-4850
Organization name Fred Hutchinson Cancer Research Center
Department Basic Sciences
Lab Henikoff
Street address 1100 Fairview AV N, A1-162
City Seattle
State/province WA
ZIP/Postal code 98109-1024
Country USA
Platforms (2)
GPL13821 Illumina HiSeq 2000 (Saccharomyces cerevisiae)
GPL17342 Illumina HiSeq 2500 (Saccharomyces cerevisiae)
Samples (57)
GSM1647289 Free_MNase_ChEC_seq_no_calcium_(20141114_11)
GSM1647290 Free_MNase_ChEC_seq_10s_(20141114_8)
GSM1647291 Free_MNase_ChEC_seq_20m_(20141114_1)
BioProject PRJNA279980
SRA SRP056746

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE67453_ChEC-seq.rtf.gz 1.1 Kb (ftp)(http) RTF
GSE67453_RAW.tar 1.1 Gb (http)(custom) TAR (of BED, BEDGRAPH, WIG)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap