Predicting transcription factor binding motifs from DNA-binding domains, chromatin accessibility and gene expression data

• Mahdi Zamanighomi ^[1] ; Zhixiang Lin ^[1] ; Yong Wang ^[3] ; Rui Jiang ^[2] ; Wing Hung Wong ^[1]
  1. [1] Stanford University

     Stanford University

     Estados Unidos

     
  2. [2] Tsinghua University

     Tsinghua University

     China

     
  3. [3] Academy of Mathematics and Systems Science, National Center for Mathematics and Interdisciplinary Sciences, Chinese Academy of Sciences, Beijing 100190, China

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• Localización: Nucleic acids research, ISSN 0305-1048, Vol. 45, Nº. 10, 2017, págs. 5666-5677
• Idioma: inglés
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• Resumen

  • Transcription factors (TFs) play crucial roles in regulating gene expression through interactions with specific DNA sequences. Recently, the sequence motif of almost 400 human TFs have been identified using high-throughput SELEX sequencing. However, there remain a large number of TFs (∼800) with no high-throughput-derived binding motifs. Computational methods capable of associating known motifs to such TFs will avoid tremendous experimental efforts and enable deeper understanding of transcriptional regulatory functions. We present a method to associate known motifs to TFs (MATLAB code is available in Supplementary Materials). Our method is based on a probabilistic framework that not only exploits DNA-binding domains and specificities, but also integrates open chromatin, gene expression and genomic data to accurately infer monomeric and homodimeric binding motifs. Our analysis resulted in the assignment of motifs to 200 TFs with no SELEX-derived motifs, roughly a 50% increase compared to the existing coverage.