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Mice and Men: Their Promoter Properties

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...

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Autores principales: Bajic, Vladimir B, Tan, Sin Lam, Christoffels, Alan, Schönbach, Christian, Lipovich, Leonard, Yang, Liang, Hofmann, Oliver, Kruger, Adele, Hide, Winston, Kai, Chikatoshi, Kawai, Jun, Hume, David A, Carninci, Piero, Hayashizaki, Yoshihide
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449896/
https://www.ncbi.nlm.nih.gov/pubmed/16683032
http://dx.doi.org/10.1371/journal.pgen.0020054
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author Bajic, Vladimir B
Tan, Sin Lam
Christoffels, Alan
Schönbach, Christian
Lipovich, Leonard
Yang, Liang
Hofmann, Oliver
Kruger, Adele
Hide, Winston
Kai, Chikatoshi
Kawai, Jun
Hume, David A
Carninci, Piero
Hayashizaki, Yoshihide
author_facet Bajic, Vladimir B
Tan, Sin Lam
Christoffels, Alan
Schönbach, Christian
Lipovich, Leonard
Yang, Liang
Hofmann, Oliver
Kruger, Adele
Hide, Winston
Kai, Chikatoshi
Kawai, Jun
Hume, David A
Carninci, Piero
Hayashizaki, Yoshihide
author_sort Bajic, Vladimir B
collection PubMed
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.
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spelling pubmed-14498962006-05-08 Mice and Men: Their Promoter Properties Bajic, Vladimir B Tan, Sin Lam Christoffels, Alan Schönbach, Christian Lipovich, Leonard Yang, Liang Hofmann, Oliver Kruger, Adele Hide, Winston Kai, Chikatoshi Kawai, Jun Hume, David A Carninci, Piero Hayashizaki, Yoshihide PLoS Genet Research Article 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. Public Library of Science 2006-04 2006-04-28 /pmc/articles/PMC1449896/ /pubmed/16683032 http://dx.doi.org/10.1371/journal.pgen.0020054 Text en © 2006 Bajic et al. http://creativecommons.org/licenses/by/4.0/ 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 properly credited.
spellingShingle Research Article
Bajic, Vladimir B
Tan, Sin Lam
Christoffels, Alan
Schönbach, Christian
Lipovich, Leonard
Yang, Liang
Hofmann, Oliver
Kruger, Adele
Hide, Winston
Kai, Chikatoshi
Kawai, Jun
Hume, David A
Carninci, Piero
Hayashizaki, Yoshihide
Mice and Men: Their Promoter Properties
title Mice and Men: Their Promoter Properties
title_full Mice and Men: Their Promoter Properties
title_fullStr Mice and Men: Their Promoter Properties
title_full_unstemmed Mice and Men: Their Promoter Properties
title_short Mice and Men: Their Promoter Properties
title_sort mice and men: their promoter properties
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1449896/
https://www.ncbi.nlm.nih.gov/pubmed/16683032
http://dx.doi.org/10.1371/journal.pgen.0020054
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