ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo.
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.
Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
Gabriel E
GE
Zentner
Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.|Medical Scientist Training Program, University of Washington School of Medicine, Seattle, Washington 98195, USA.|Molecular and Cellular Biology Graduate Program, University of Washington School of Medicine, Seattle, Washington 98195, USA.
Sivakanthan
S
Kasinathan
Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, California 90089, USA.
Beibei
B
Xin
Molecular and Computational Biology Program, Departments of Biological Sciences, Chemistry, Physics, and Computer Science, University of Southern California, Los Angeles, California 90089, USA.
Remo
R
Rohs
Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.|Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA.
Steven
S
Henikoff
D001665:Binding Sites / Q000235:genetics; D002843:Chromatin / Q000378:metabolism*; D004247:DNA / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing; D008836:Micrococcal Nuclease / Q000378:metabolism; D008968:Molecular Conformation; D059372:Nucleotide Motifs / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism; D000089804:Shelterin Complex; D034501:Telomere-Binding Proteins / Q000378:metabolism; D014157:Transcription Factors / Q000378:metabolism*
C061886:ABF1 protein, S cerevisiae; D002843:Chromatin; D004268:DNA-Binding Proteins; C440829:RAP1 protein, S cerevisiae; C065681:REB1 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D000089804:Shelterin Complex; D034501:Telomere-Binding Proteins; D014157:Transcription Factors; D004247:DNA; D008836:Micrococcal Nuclease