title: The initiator motif is preferentially used as the core promoter element in ionizing radiation-responsive genes.
abstract: Recent improvements in DNA microarray technologies and bioinformatics have made it possible to look for common features of ionizing radiation-responsive genes and their regulatory regions. We analyzed the promoters of 217 radiation-responsive human genes, compiled from microarray databases available in the literature. Using the DBTSS database, the transcriptional start sites were determined, and the core promoter elements, such as the TATA-box, initiator (Inr), GC-box and CCAAT-box, were searched for in the -1000 bp/ +200 bp region of each gene by using MATCH. It was found that the frequency of Inr in radiation-responsive genes was higher than that in general genes, and the frequencies of the GC-box and CCAAT-box were significantly lower than those in general genes. Use of the GC-box and the CCAAT-box in radiation-responsive genes was found to be dependent on the TATA-box status; that is, GC-box frequency was low in TATA box-containing genes, and CCAAT-box frequency was also low in TATA-less genes. When correlations between gene functions and frequencies of core promoter elements were examined, no apparent biased use of the core promoter element in association with a specific gene function was observed. It may be speculated that use of Inr in the core promoter correlates with appearance of radiation-responsive enhancer (silencer) elements in the upstream (downstream) regulatory region.
authors.affiliation: Radiation Effect Mechanisms Research Group, National Institute of Radiological Sciences, Inage-ku, Chiba 263-8555, Japan.
authors.forename: Jianyu
authors.initials: J
authors.lastname: Wu
authors.forename: Kazuhiro
authors.initials: K
authors.lastname: Daino
authors.forename: Sachiko
authors.initials: S
authors.lastname: Ichimura
authors.forename: Mitsuru
authors.initials: M
authors.lastname: Nenoi
mesh_terms: D001798:Blood Proteins / Q000235:genetics* / Q000528:radiation effects*; D018387:Codon, Initiator / Q000235:genetics*; D006801:Humans; D011401:Promoter Regions, Genetic / Q000235:genetics*; D011836:Radiation Tolerance / Q000235:genetics*; D011839:Radiation, Ionizing; D035181:TATA-Box Binding Protein / Q000235:genetics*; D014158:Transcription, Genetic / Q000235:genetics* / Q000528:radiation effects
chemical_list: D001798:Blood Proteins; D018387:Codon, Initiator; D035181:TATA-Box Binding Protein