Mice and men: Their promoter properties

Bajic, Vladimir B., Tan, Sin Lam, Christoffels, Alan, Schonbach, Christian, Lilpovich, Leonard, Yang, Liang, Hofmann, Oliver, Kruger, Adele, Hide, Winston, Kai, Chikatoshi, Kawai, Jun, Hume, David A., Carninci, Piero and Hayashizaki, Yoshihide (2006) Mice and men: Their promoter properties. Plos Genetics, 2 4: 614-626. doi:10.1371/journal.pgen.0020054

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Author Bajic, Vladimir B.
Tan, Sin Lam
Christoffels, Alan
Schonbach, Christian
Lilpovich, Leonard
Yang, Liang
Hofmann, Oliver
Kruger, Adele
Hide, Winston
Kai, Chikatoshi
Kawai, Jun
Hume, David A.
Carninci, Piero
Hayashizaki, Yoshihide
Title Mice and men: Their promoter properties
Journal name Plos Genetics   Check publisher's open access policy
ISSN 1553-7390
Publication date 2006-06-28
Sub-type Article (original research)
DOI 10.1371/journal.pgen.0020054
Open Access Status DOI
Volume 2
Issue 4
Start page 614
End page 626
Total pages 13
Place of publication San Francisco, CA, United Sates
Publisher Public Library Science
Collection year 2006
Language eng
Subject 270202 Genome Structure
780106 Political science and public policy
Abstract Using the two largest collections of Mus musculus and Homo sapiens transcription start sites ( TSSs) determined based on CAGE tags, ditags, full- length cDNAs, and other transcript data, we describe the compositional landscape surrounding TSSs with the aim of gaining better insight into the properties of mammalian promoters. We classified TSSs into four types based on compositional properties of regions immediately surrounding them. These properties highlighted distinctive features in the extended core promoters that helped us delineate boundaries of the transcription initiation domain space for both species. The TSS types were analyzed for associations with initiating dinucleotides, CpG islands, TATA boxes, and an extensive collection of statistically significant cis- elements in mouse and human. We found that different TSS types show preferences for different sets of initiating dinucleotides and ciselements. Through Gene Ontology and eVOC categories and tissue expression libraries we linked TSS characteristics to expression. Moreover, we show a link of TSS characteristics to very specific genomic organization in an example of immune- response- related genes ( GO: 0006955). Our results shed light on the global properties of the two transcriptomes not revealed before and therefore provide the framework for better understanding of the transcriptional mechanisms in the two species, as well as a framework for development of new and more efficient promoter- and gene- finding tools.
Keyword Genetics & Heredity
Start Sites
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status UQ
Additional Notes Originally published as Citation: Bajic VB, Tan SL, Christoffels A, Schönbach C, Lipovich L, et al. (2006) Mice and Men: Their Promoter Properties. PLoS Genet 2(4): e54 doi:10.1371/journal.pgen.0020054 Received: August 15, 2005; Accepted: February 27, 2006; Published: April 28, 2006 Copyright: © 2006 Bajic et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

Document type: Journal Article
Sub-type: Article (original research)
Collections: 2007 Higher Education Research Data Collection
Institute for Molecular Bioscience - Publications
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Citation counts: TR Web of Science Citation Count  Cited 64 times in Thomson Reuters Web of Science Article | Citations
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Created: Wed, 15 Aug 2007, 08:55:43 EST