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  Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers

Jankowski, A., Szczurek, E., Jauch, R., Tiuryn, J., & Prabhakar, S. (2013). Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers. Genome Research, 23(8), 1307-1318. doi:10.1101/gr.154922.113.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-7C2B-8 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0014-7C2C-6
Genre: Journal Article

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© 2013 by Cold Spring Harbor Laboratory Press
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Jankowski, Aleksander, Author
Szczurek, Ewa1, Author              
Jauch, Ralf, Author
Tiuryn, Jerzy, Author
Prabhakar, Shyam, Author
Affiliations:
1Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433547              

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 Abstract: The binding of transcription factors (TFs) to their specific motifs in genomic regulatory regions is commonly studied in isolation. However, in order to elucidate the mechanisms of transcriptional regulation, it is essential to determine which TFs bind DNA cooperatively as dimers and to infer the precise nature of these interactions. So far, only a small number of such dimeric complexes are known. Here, we present an algorithm for predicting cell-type-specific TF-TF dimerization on DNA on a large scale, using DNase I hypersensitivity data from 78 human cell lines. We represented the universe of possible TF complexes by their corresponding motif complexes, and analyzed their occurrence at cell-type-specific DNase I hypersensitive sites. Based on approximately 1.4 billion tests for motif complex enrichment, we predicted 603 highly significant cell-type-specific TF dimers, the vast majority of which are novel. Our predictions included 76% (19/25) of the known dimeric complexes and showed significant overlap with an experimental database of protein-protein interactions. They were also independently supported by evolutionary conservation, as well as quantitative variation in DNase I digestion patterns. Notably, the known and predicted TF dimers were almost always highly compact and rigidly spaced, suggesting that TFs dimerize in close proximity to their partners, which results in strict constraints on the structure of the DNA-bound complex. Overall, our results indicate that chromatin openness profiles are highly predictive of cell-type-specific TF-TF interactions. Moreover, cooperative TF dimerization seems to be a widespread phenomenon, with multiple TF complexes predicted in most cell types.

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Language(s): eng - English
 Dates: 2013-04-032013-08
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Method: Peer
 Identifiers: DOI: 10.1101/gr.154922.113
ISSN: 1549-5469 (Electronic)1088-9051 (Print)
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Title: Genome Research
Source Genre: Journal
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Publ. Info: Cold Spring Harbor, N.Y. : Cold Spring Harbor Laboratory Press
Pages: - Volume / Issue: 23 (8) Sequence Number: - Start / End Page: 1307 - 1318 Identifier: ISSN: 1088-9051
CoNE: https://pure.mpg.de/cone/journals/resource/954926997202