CCAT: Combinatorial Code Analysis Tool for transcriptional regulation

Peng Jiang, Mona Singh

Research output: Contribution to journalArticle

11 Scopus citations

Abstract

Combinatorial interplay among transcription factors (TFs) is an important mechanism by which transcriptional regulatory specificity is achieved. However, despite the increasing number of TFs for which either binding specificities or genome-wide occupancy data are known, knowledge about cooperativity between TFs remains limited. To address this, we developed a computational framework for predicting genome-wide co-binding between TFs (CCAT, Combinatorial Code Analysis Tool), and applied it to Drosophila melanogaster to uncover cooperativity among TFs during embryo development. Using publicly available TF binding specificity data and DNaseI chromatin accessibility data, we first predicted genome-wide binding sites for 324 TFs across five stages of D. melanogaster embryo development. We then applied CCAT in each of these developmental stages, and identified from 19 to 58 pairs of TFs in each stage whose predicted binding sites are significantly co-localized. We found that nearby binding sites for pairs of TFs predicted to cooperate were enriched in regions bound in relevant ChIP experiments, and were more evolutionarily conserved than other pairs. Further, we found that TFs tend to be co-localized with other TFs in a dynamic manner across developmental stages. All generated data as well as source code for our front-to-end pipeline are available at http://cat.princeton.edu.

Original languageEnglish (US)
Pages (from-to)2833-2847
Number of pages15
JournalNucleic acids research
Volume42
Issue number5
DOIs
StatePublished - 2014

All Science Journal Classification (ASJC) codes

  • Genetics

Fingerprint Dive into the research topics of 'CCAT: Combinatorial Code Analysis Tool for transcriptional regulation'. Together they form a unique fingerprint.

  • Cite this