title: Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics.
abstract: Although the knowledge accumulated on the transcriptional regulations of eukaryotes is significant, the knowledge on their translational regulations remains limited. Thus, we performed a comprehensive detection of terminal oligo-pyrimidine (TOP), which is one of the well-characterized cis-regulatory motifs for translational controls located immediately downstream of the transcriptional start sites of mRNAs. Utilizing our precise 5'-end information of the full-length cDNAs, we could screen 1645 candidate TOP genes by position specific matrix search. Among them, not only 75 out of 78 ribosomal protein genes but also eight previously identified non-ribosomal-protein TOP genes were included. We further experimentally validated the translational activities of 83 TOP candidate genes. Clear translational regulations exerted on the stimulation of 12-O-tetradecanoyl-1-phorbol-13-acetate for at least 41 of them was observed, indicating that there should be a few hundreds of human genes which are subjected to regulation at translation levels via TOPs. Our result suggests that TOP genes code not only formerly characterized ribosomal proteins and translation-related proteins but also a wider variety of proteins, such as lysosome-related proteins and metabolism-related proteins, playing pivotal roles in gene expression controls in the majority of cellular mRNAs.
authors.affiliation: Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan.
authors.forename: Riu
authors.initials: R
authors.lastname: Yamashita
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Suzuki
authors.forename: Nono
authors.initials: N
authors.lastname: Takeuchi
authors.forename: Hiroyuki
authors.initials: H
authors.lastname: Wakaguri
authors.forename: Takuya
authors.initials: T
authors.lastname: Ueda
authors.forename: Sumio
authors.initials: S
authors.lastname: Sugano
authors.forename: Kenta
authors.initials: K
authors.lastname: Nakai
mesh_terms: D000818:Animals; D020869:Gene Expression Profiling; D005786:Gene Expression Regulation; D015894:Genome, Human; D018922:HL-60 Cells; D006801:Humans; D051379:Mice; D014176:Protein Biosynthesis; D038641:RNA 5' Terminal Oligopyrimidine Sequence; D012333:RNA, Messenger / Q000737:chemistry; D012269:Ribosomal Proteins / Q000235:genetics; D024363:Transcription Initiation Site
chemical_list: D012333:RNA, Messenger; D012269:Ribosomal Proteins