脚印
转录因子
生物
染色质
计算生物学
劈理(地质)
核小体
转座酶
遗传学
基因组
转座因子
DNA
基因
断裂(地质)
古生物学
作者
Zhijian Li,Marcel H. Schulz,Thomas Look,Matthias Begemann,Martin Zenke,Ivan G. Costa
出处
期刊:Genome Biology
[Springer Nature]
日期:2019-02-26
卷期号:20 (1)
被引量:230
标识
DOI:10.1186/s13059-019-1642-2
摘要
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.
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