Teif, Vladimir and Peng, Yunhui and Song, Wei and Ovcharenko, Ivan and Landsman, David and Panchenko, Anna (2024) Detection of new pioneer transcription factors as cell-type specific nucleosome binders. eLife, 12. RP88936-. DOI https://doi.org/10.7554/eLife.88936
Teif, Vladimir and Peng, Yunhui and Song, Wei and Ovcharenko, Ivan and Landsman, David and Panchenko, Anna (2024) Detection of new pioneer transcription factors as cell-type specific nucleosome binders. eLife, 12. RP88936-. DOI https://doi.org/10.7554/eLife.88936
Teif, Vladimir and Peng, Yunhui and Song, Wei and Ovcharenko, Ivan and Landsman, David and Panchenko, Anna (2024) Detection of new pioneer transcription factors as cell-type specific nucleosome binders. eLife, 12. RP88936-. DOI https://doi.org/10.7554/eLife.88936
Abstract
Wrapping of DNA into nucleosomes restricts DNA accessibility and the recognition of binding motifs by transcription factors. A certain class of transcription factors, so-called pioneer transcription factors, can specifically recognize their binding sites on nucleosomal DNA, initiate local chromatin opening and facilitate the binding of co-factors in a cell-type-specific manner. For the vast majority of human pioneer transcription factors, the locations of their binding sites, mechanisms of binding and regulation remain unknown. We have developed a computational method to predict the cell-type-specific ability of transcription factors to bind nucleosomes by integrating ChIP-seq, MNaseq-seq and DNase-seq data with the details of nucleosome structure. We have achieved classification accuracy with AUC=0.94 in discriminating pioneer factors from canonical transcription factors and predicted 32 potential pioneer transcription factors as nucleosome binders in embryonic cell differentiation. Lastly, we systemically analyzed the interaction modes between various pioneer factors and detected several clusters of distinctive binding sites on nucleosomal DNA.
Item Type: | Article |
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Uncontrolled Keywords: | DNA binding; DNA-protein binding; nucleosome; TF; transcription factor |
Divisions: | Faculty of Science and Health Faculty of Science and Health > Life Sciences, School of |
SWORD Depositor: | Unnamed user with email elements@essex.ac.uk |
Depositing User: | Unnamed user with email elements@essex.ac.uk |
Date Deposited: | 30 Apr 2024 11:51 |
Last Modified: | 16 May 2024 21:59 |
URI: | http://repository.essex.ac.uk/id/eprint/36223 |
Available files
Filename: elife-88936-v1.pdf
Licence: Creative Commons: Attribution 4.0