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Computational Reconstruction of Transcriptional Relationships from ChIP-Chip Data

Content Provider	ACM Digital Library
Author	Ho, Bich Hai Ho, Tu Bao Le, Ngoc Tu
Abstract	Eukaryotic gene transcription is a complex process, which requires the orchestrated recruitment of a large number of proteins, such as sequence-specific DNA binding factors, chromatin remodelers and modifiers, and general transcription machinery, to regulatory regions. Previous works have shown that these regulatory proteins favor specific organizational theme along promoters. Details about how they cooperatively regulate transcriptional process, however, remain unclear. We developed a method to reconstruct a Bayesian network (BN) model representing functional relationships among various transcriptional components. The positive/negative influence between these components was measured from protein binding and nucleosome occupancy data and embedded into the model. Application on S.cerevisiae ChIP-Chip data showed that the proposed method can recover confirmed relationships, such as Isw1-Pol II, TFIIH-Pol II, TFIIB-TBP, Pol II-H3K36Me3, H3K4Me3-H3K14Ac, etc. Moreover, it can distinguish colocating components from functionally related ones. Novel relationships, e.g., ones between Mediator and chromatin remodeling complexes (CRCs), and the combinatorial regulation of Pol II recruitment and activity by CRCs and general transcription factors (GTFs), were also suggested. Conclusion: protein binding events during transcription positively influence each other. Among contributing components, GTFs and CRCs play pivotal roles in transcriptional regulation. These findings provide insights into the regulatory mechanism.
Starting Page	300
Ending Page	307
Page Count	8
File Format	PDF
ISSN	15455963
DOI	10.1109/TCBB.2012.102
Volume Number	10
Issue Number	2
Journal	IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2013-03-01
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Bioinformatics,Proteins,Stability analysis,Genomics,Machinery,Bayesian methods,Data models,nucleosome positioning,Bioinformatics,Proteins,Stability analysis,Genomics,Machinery,Bayesian methods,Data models,chromatin remodeling complex,Transcriptional relationship,Bayesian network,ChIP-Chip data,histone modification
Content Type	Text
Resource Type	Article
Subject	Genetics Biotechnology Applied Mathematics

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

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