Identification of transcription factor binding sites using ATAC-seq
By Zhijian Li, Marcel H. Schulz, T. Look, M. Begemann, Martin Zenke, I. Costa. Genome Biology, 2018
393 citations recorded by the source corpus.
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.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/17f34c4bc9111d6bb1efe934e5d93fdacff6b007
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In Molecular Biology
- Syuzo Kaneko
- Masaaki Komatsu
- Ken Asada
- Ken Takasawa
- Ryuji Hamamoto
- Yusuke Nakamura
- N. Dohmae
- Takehiro Suzuki
Citations in the corpus
- Epigenetics Analysis and Integrated Analysis of Multiomics Data, Including Epigenetic Data, Using Artificial Intelligence in the Era of Precision Medicine (2019, methodology): “This method has been applied to defining the genome-wide chromatin accessibility landscape in human cancers [82], and computational footprinting methods can be performed on ATAC-seq to identify cell specific binding sites of transcription factors and their cell specific activity [83].”