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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
agricultural and biological sciences
Mice and men: Their promoter properties
PLoS Genetics, Volume 2, No. 4, Article e54, Year 2006
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Description
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 cis-elements. 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. © 2006 Bajic et al.
Available Materials
https://efashare.b-cdn.net/share/pmc/articles/PMC1449896/bin/pgen.0020054.sd001.zip
https://efashare.b-cdn.net/share/pmc/articles/PMC1449896/bin/pgen.0020054.sg001.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC1449896/bin/pgen.0020054.sg002.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC1449896/bin/pgen.0020054.st001.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC1449896/bin/pgen.0020054.st002.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC1449896/bin/pgen.0020054.st003.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC1449896/bin/pgen.0020054.st004.pdf
https://efashare.b-cdn.net/share/pmc/articles/PMC1449896/bin/pgen.0020054.st005.pdf
Authors & Co-Authors
Bajic, Vladimir B.
Singapore, Singapore City
A-star, Institute for Infocomm Research
South Africa, Bellville
University of the Western Cape
Sin, Lam Tan
Singapore, Singapore City
A-star, Institute for Infocomm Research
South Africa, Bellville
University of the Western Cape
Christoffels, Alan G.
Singapore, Singapore City
National University of Singapore
Singapore, Singapore City
School of Biological Sciences
Schönbach, Christian
Japan, Yokohama
Riken Yokohama Institute
Lipovich, Leonard
Singapore, Singapore City
A-star, Genome Institute of Singapore
Yang, Liang
Singapore, Singapore City
National University Hospital
Hofmann, Oliver M.
South Africa, Bellville
University of the Western Cape
Kruger, Adele
South Africa, Bellville
University of the Western Cape
Hide, Winston A.
South Africa, Bellville
University of the Western Cape
Kai, Chikatoshi
Japan, Yokohama
Riken Yokohama Institute
Kawai, Jun
Japan, Yokohama
Riken Yokohama Institute
Japan, Wako
Riken Wako Insititute
Hume, David A.
Australia, Brisbane
The University of Queensland
Carninci, Piero
Japan, Yokohama
Riken Yokohama Institute
Japan, Wako
Riken Wako Insititute
Hayashizaki, Yoshihide
Japan, Yokohama
Riken Yokohama Institute
Japan, Wako
Riken Wako Insititute
Statistics
Citations: 120
Authors: 14
Affiliations: 9
Identifiers
Doi:
10.1371/journal.pgen.0020054
e-ISSN:
15537404
Research Areas
Genetics And Genomics
Participants Gender
Male