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DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP

Sneha Mitra, Anushua Biswas, Leelavati Narlikar
doi: https://doi.org/10.1101/122325
Sneha Mitra
Chemical Engineering Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
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Anushua Biswas
Chemical Engineering Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
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Leelavati Narlikar
Chemical Engineering Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
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  • For correspondence: l.narlikar@ncl.res.in
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Abstract

A high-throughput chromatin immunoprecipitation (ChIP) experiment is like a black-box: it reports all regions that are associated with the profiled protein based on the initial cross-linking step. These regions can be a highly diverse set of DNA sequences, with some making direct contact with the protein, some binding through intermediaries, and some being a result of long-range interactions involving the protein. We present diversity, a method that identifies the distinct components of such a mixture, leaving no data behind, while at the same time, using no prior motif knowledge. Using the example of the REST protein, we show that these different components give insights into the various complexes that may be forming along the chromatin and their regulatory functions.

http://diversity.ncl.res.in/ (webserver)

https://github.com/NarlikarLab/DIVERSITY (standalone for Mac OSX/Linux)

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted April 05, 2017.
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DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP
Sneha Mitra, Anushua Biswas, Leelavati Narlikar
bioRxiv 122325; doi: https://doi.org/10.1101/122325
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DIVERSITY in binding, regulation, and evolution revealed from high-throughput ChIP
Sneha Mitra, Anushua Biswas, Leelavati Narlikar
bioRxiv 122325; doi: https://doi.org/10.1101/122325

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