Mice and men: Their promoter properties

Simple item page
dc.contributor.authorBajic, Vladimir B.
dc.contributor.authorTan, Sin lam
dc.contributor.authorChristoffels, Alan
dc.contributor.authorSchonbach, Christian
dc.contributor.authorLipovich, Leonard
dc.contributor.authorYang, Liang
dc.contributor.authorHofmann, Oliver
dc.contributor.authorKruger, Adele
dc.contributor.authorHide, Winston
dc.contributor.authorKai, Chikatoshi
dc.contributor.authorKawai, Jun
dc.contributor.authorHume, David, A.
dc.contributor.authorCarninci, Piero
dc.contributor.authorHayashizaki, Yoshihide
dc.date.accessioned2015-09-08T13:42:13Z
dc.date.available2015-09-08T13:42:13Z
dc.date.issued2006
dc.description.abstractUsing 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.en_US
dc.description.accreditationWeb of Scienceen_US
dc.description.sponsorshipRIKEN Genome Exploration Research Project grant Grant of the genome network project grant for the strategic program for R&D of RIKENen_US
dc.identifier.citationBajic, V.B. et al. (2006). Mice and men: Their promoter properties. PLoS Genetics 2(4): e54en_US
dc.identifier.issn1553-7404
dc.identifier.urihttp://hdl.handle.net/10566/1588
dc.language.isoenen_US
dc.privacy.showsubmitterfalse
dc.publisherPLoS Geneticsen_US
dc.rightsOpen Access copyright Bajic et al.
dc.source.uridx.doi.org/10.1371/journal.pgen.0020054
dc.status.ispeerreviewedtrue
dc.subjectMus musculusen_US
dc.subjectHomo sapiensen_US
dc.subjectPromoter propertiesen_US
dc.subjectGene-finding toolsen_US
dc.subjectGene ontologyen_US
dc.subjectDrosophila melanogasteren_US
dc.subjectFugu rubripesen_US
dc.subjectDNAen_US
dc.titleMice and men: Their promoter propertiesen_US
dc.typeArticleen_US

Files

Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
bajic_mice_plos_2006.pdf
Size:
681.35 KB
Format:
Adobe Portable Document Format
Description:
Article
Download
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
1.55 KB
Format:
Item-specific license agreed upon to submission
Description:
Download

Collections

Research Articles (SANBI)
Prof. Alan Christoffels