ArticleNucleic acids research2019
Co-SELECT reveals sequence non-specific contribution of DNA shape to transcription factor binding in vitro.
Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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15 citing papers in PubMed, 21 citations in OpenAlex.
- ShapeME: A Tool and Web Front-end for De Novo Discovery of Structural Motifs Underpinning Protein-DNA Interactions.Journal of molecular biology · 2026Article
- ShapeME: A tool and web front-end for de novo discovery of structural motifs underpinning protein-DNA interactions.bioRxiv : the preprint server for biology · 2025Article
- RiceSNP-ABST: a deep learning approach to identify abiotic stress-associated single nucleotide polymorphisms in rice.Briefings in bioinformatics · 2024Article
- RiceSNP-BST: a deep learning framework for predicting biotic stress-associated SNPs in rice.Briefings in bioinformatics · 2024Article
- Deep DNAshape webserver: prediction and real-time visualization of DNA shape considering extended k-mers.Nucleic acids research · 2024Article
- Noncanonical binding of transcription factors: time to revisitMolecular biology of the cell · 2023Review
- Article
- Transcription Factor-Binding Site Identification and Enrichment Analysis.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Article
- Insights gained from a comprehensive all-against-all transcription factor binding motif benchmarking study.Genome biology · 2020Article
- Bioinformatics pipeline using JUDI: Just Do It!Bioinformatics (Oxford, England) · 2020Article
- TFBSshape: an expanded motif database for DNA shape features of transcription factor binding sites.Nucleic acids research · 2020Article
- Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework.Nucleic acids research · 2019Article
- A De Novo Shape Motif Discovery Algorithm Reveals Preferences of Transcription Factors for DNA Shape Beyond Sequence Motifs.Cell systems · 2019Article
- Article
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Authors and funding
3 authors at 1 institution in 1 country.
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Abstract
Understanding the principles of DNA binding by transcription factors (TFs) is of primary importance for studying gene regulation. Recently, several lines of evidence suggested that both DNA sequence and shape contribute to TF binding. However, the following compelling question is yet to be considered: in the absence of any sequence similarity to the binding motif, can DNA shape still increase binding probability? To address this challenge, we developed Co-SELECT, a computational approach to analyze the results of in vitro HT-SELEX experiments for TF-DNA binding. Specifically, Co-SELECT leverages the presence of motif-free sequences in late HT-SELEX rounds and their enrichment in weak binders allows Co-SELECT to detect an evidence for the role of DNA shape features in TF binding. Our approach revealed that, even in the absence of the sequence motif, TFs have propensity to bind to DNA molecules of the shape consistent with the motif specific binding. This provides the first direct evidence that shape features that accompany the preferred sequence motifs also bestow an advantage for weak, sequence non-specific binding.
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