Identification of transcription factor binding sites using ATAC-seq. Li, Z., Schulz, M. H., Look, T., Begemann, M., Zenke, M., & Costa, I. G. Genome Biology, 20(1):45, February, 2019. doi abstract bibtex Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of open chromatin. Computational footprinting, the search for regions with depletion of cleavage events due to transcription factor binding, is poorly understood for ATAC-seq. We propose the first footprinting method considering ATAC-seq protocol artifacts. HINT-ATAC uses a position dependency model to learn the cleavage preferences of the transposase. We observe strand-specific cleavage patterns around transcription factor binding sites, which are determined by local nucleosome architecture. By incorporating all these biases, HINT-ATAC is able to significantly outperform competing methods in the prediction of transcription factor binding sites with footprints.
@article{li_identification_2019,
title = {Identification of transcription factor binding sites using {ATAC}-seq},
volume = {20},
issn = {1474-760X},
doi = {10.1186/s13059-019-1642-2},
abstract = {Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) is a simple protocol for detection of open chromatin. Computational footprinting, the search for regions with depletion of cleavage events due to transcription factor binding, is poorly understood for ATAC-seq. We propose the first footprinting method considering ATAC-seq protocol artifacts. HINT-ATAC uses a position dependency model to learn the cleavage preferences of the transposase. We observe strand-specific cleavage patterns around transcription factor binding sites, which are determined by local nucleosome architecture. By incorporating all these biases, HINT-ATAC is able to significantly outperform competing methods in the prediction of transcription factor binding sites with footprints.},
language = {eng},
number = {1},
journal = {Genome Biology},
author = {Li, Zhijian and Schulz, Marcel H. and Look, Thomas and Begemann, Matthias and Zenke, Martin and Costa, Ivan G.},
month = feb,
year = {2019},
pmid = {30808370},
pmcid = {PMC6391789},
keywords = {Animals, ATAC-seq, Cleavage bias, Computational footprinting, Dendritic Cells, DNA Footprinting, Genomics, Humans, K562 Cells, Mice, Models, Genetic, Nucleosomes, Open chromatin, Sequence Analysis, DNA, Transcription Factors, Transposases},
pages = {45},
file = {Volltext:/Users/mschulz/Zotero/storage/UGQILYCY/Li et al. - 2019 - Identification of transcription factor binding sit.pdf:application/pdf},
}
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