ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo
- PMID: 26490019
- PMCID: PMC4618392
- DOI: 10.1038/ncomms9733
ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo
Erratum in
-
Corrigendum: ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo.Nat Commun. 2015 Dec 16;6:10264. doi: 10.1038/ncomms10264. Nat Commun. 2015. PMID: 26669278 Free PMC article. No abstract available.
Abstract
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.
Conflict of interest statement
The authors declare no competing financial interests.
Figures
Similar articles
-
Genome-wide Mapping of Protein-DNA Interactions with ChEC-seq in Saccharomyces cerevisiae.J Vis Exp. 2017 Jun 3;(124):55836. doi: 10.3791/55836. J Vis Exp. 2017. PMID: 28605389 Free PMC article.
-
Genome-Wide Profiling of Protein-DNA Interactions with Chromatin Endogenous Cleavage and High-Throughput Sequencing (ChEC-Seq ).Methods Mol Biol. 2021;2351:289-303. doi: 10.1007/978-1-0716-1597-3_16. Methods Mol Biol. 2021. PMID: 34382196
-
ChEC-Seq: A Comprehensive Guide for Scalable and Cost-Efficient Genome-Wide Profiling in Saccharomyces cerevisiae.Methods Mol Biol. 2024;2846:263-283. doi: 10.1007/978-1-0716-4071-5_16. Methods Mol Biol. 2024. PMID: 39141241
-
A conserved role for transcription factor sumoylation in binding-site selection.Curr Genet. 2019 Dec;65(6):1307-1312. doi: 10.1007/s00294-019-00992-w. Epub 2019 May 15. Curr Genet. 2019. PMID: 31093693 Review.
-
Noncanonical binding of transcription factors: time to revisit specificity?Mol Biol Cell. 2023 Aug 1;34(9):pe4. doi: 10.1091/mbc.E22-08-0325. Mol Biol Cell. 2023. PMID: 37486893 Free PMC article. Review.
Cited by
-
Transcription factor chromatin profiling genome-wide using uliCUT&RUN in single cells and individual blastocysts.Nat Protoc. 2021 May;16(5):2633-2666. doi: 10.1038/s41596-021-00516-2. Epub 2021 Apr 28. Nat Protoc. 2021. PMID: 33911257 Free PMC article.
-
Genetic and epigenetic determinants establish a continuum of Hsf1 occupancy and activity across the yeast genome.Mol Biol Cell. 2018 Dec 15;29(26):3168-3182. doi: 10.1091/mbc.E18-06-0353. Epub 2018 Oct 17. Mol Biol Cell. 2018. PMID: 30332327 Free PMC article.
-
Fine-Resolution Mapping of TF Binding and Chromatin Interactions.Cell Rep. 2018 Mar 6;22(10):2797-2807. doi: 10.1016/j.celrep.2018.02.052. Cell Rep. 2018. PMID: 29514105 Free PMC article.
-
Emerging Single-Cell Technological Approaches to Investigate Chromatin Dynamics and Centromere Regulation in Human Health and Disease.Int J Mol Sci. 2021 Aug 16;22(16):8809. doi: 10.3390/ijms22168809. Int J Mol Sci. 2021. PMID: 34445507 Free PMC article. Review.
-
Correspondence: DNA shape is insufficient to explain binding.Nat Commun. 2017 Jun 5;8:15643. doi: 10.1038/ncomms15643. Nat Commun. 2017. PMID: 28580956 Free PMC article. No abstract available.
References
Publication types
MeSH terms
Substances
Associated data
- Actions
Grants and funding
- R01GM106056/GM/NIGMS NIH HHS/United States
- P30 CA015704/CA/NCI NIH HHS/United States
- F30CA186458/CA/NCI NIH HHS/United States
- R01ES020116/ES/NIEHS NIH HHS/United States
- F30 CA186458/CA/NCI NIH HHS/United States
- T32 CA009657/CA/NCI NIH HHS/United States
- T32CA009657/CA/NCI NIH HHS/United States
- HHMI/Howard Hughes Medical Institute/United States
- R01 GM106056/GM/NIGMS NIH HHS/United States
- R01 ES020116/ES/NIEHS NIH HHS/United States
- S10 OD020069/OD/NIH HHS/United States
- T32 GM007266/GM/NIGMS NIH HHS/United States
LinkOut - more resources
Full Text Sources
Other Literature Sources
Molecular Biology Databases
Research Materials
Miscellaneous
