title: Mice and men: their promoter properties.
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 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.
authors: Knowledge Extraction Laboratory, Institute for Infocomm Research, Singapore. vlad@sanbi.ac.za
authors: Vladimir B
authors: VB
authors: Bajic
authors: Sin Lam
authors: SL
authors: Tan
authors: Alan
authors: A
authors: Christoffels
authors: Christian
authors: C
authors: Schönbach
authors: Leonard
authors: L
authors: Lipovich
authors: Liang
authors: L
authors: Yang
authors: Oliver
authors: O
authors: Hofmann
authors: Adele
authors: A
authors: Kruger
authors: Winston
authors: W
authors: Hide
authors: Chikatoshi
authors: C
authors: Kai
authors: Jun
authors: J
authors: Kawai
authors: David A
authors: DA
authors: Hume
authors: Piero
authors: P
authors: Carninci
authors: Yoshihide
authors: Y
authors: Hayashizaki