Communication between layers in biological transcriptional networks

Chromatin-immunoprecipitation experiments in combination with microarrays (known as ChIP-chip) have recently allowed biologists to map where proteins bind in the yeast genome. The combinatorial binding of different proteins at or near a gene controls the transcription (copying) of a gene and the production of the functional RNA or protein that the gene encodes. Therefore, ChIP-chip data provides powerful insight on how genes and gene products (i.e., proteins, RNA) interact and regulate one another in the underlying network of the cell. Much of the current work in modeling yeast transcriptional networks focuses on the regulatory effect of a class of proteins known as transcription factors (TF). However, other sets of factors also influence transcription, including histone modifications and states (HS), histone modifiers (HM) and remodelers, nuclear processing (NP), and nuclear transport (NT) proteins. In order to gain a holistic understanding of the non-linear process of transcription, our work examines the communication between all five forementioned classes (or layers) of regulators. We use vastly available rich-media ChIP-chip data for various proteins within the five classes to model a multi-layered transcriptional network of the yeast species Saccharomyces cerevisiae.

Department dc:contributor.department

Massachusetts Institute of Technology. Dept. of Electrical Engineering and Computer Science.

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2005

Author dc:creator

• Tsankov, Alex

Advisor dc:contributor.advisor

• Moe Win and Pamela Silver.

• Electrical Engineering and Computer Science.

Statement dc:rights

• M.I.T. theses are protected by copyright. They may be viewed from this source for any purpose, but reproduction or distribution in any format is prohibited without written permission. See provided URL for inquiries about permission.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/1721.1/33208

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/33208