title: Characterization of transcription start sites of putative non-coding RNAs by multifaceted use of massively paralleled sequencer.
abstract: On the basis of integrated transcriptome analysis, we show that not all transcriptional start site clusters (TSCs) in the intergenic regions (iTSCs) have the same properties; thus, it is possible to discriminate the iTSCs that are likely to have biological relevance from the other noise-level iTSCs. We used a total of 251,933,381 short-read sequence tags generated from various types of transcriptome analyses in order to characterize 6039 iTSCs, which have significant expression levels. We analyzed and found that 23% of these iTSCs were located in the proximal regions of the RefSeq genes. These RefSeq-linked iTSCs showed similar expression patterns with the neighboring RefSeq genes, had widely fluctuating transcription start sites and lacked ordered nucleosome positioning. These iTSCs seemed not to form independent transcriptional units, simply representing the by-products of the neighboring RefSeq genes, in spite of their significant expression levels. Similar features were also observed for the TSCs located in the antisense regions of the RefSeq genes. Furthermore, for the remaining iTSCs that were not associated with any RefSeq genes, we demonstrate that integrative interpretation of the transcriptome data provides essential information to specify their biological functions in the hypoxic responses of the cells.
authors.affiliation: Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8568, Japan.
authors.forename: Nuankanya
authors.initials: N
authors.lastname: Sathira
authors.forename: Riu
authors.initials: R
authors.lastname: Yamashita
authors.forename: Kousuke
authors.initials: K
authors.lastname: Tanimoto
authors.forename: Akinori
authors.initials: A
authors.lastname: Kanai
authors.forename: Takako
authors.initials: T
authors.lastname: Arauchi
authors.forename: Soutaro
authors.initials: S
authors.lastname: Kanematsu
authors.forename: Kenta
authors.initials: K
authors.lastname: Nakai
authors.forename: Yutaka
authors.initials: Y
authors.lastname: Suzuki
authors.forename: Sumio
authors.initials: S
authors.lastname: Sugano
mesh_terms: D002478:Cells, Cultured; D019295:Computational Biology; D021901:DNA, Intergenic / Q000235:genetics*; D020869:Gene Expression Profiling; D006801:Humans; D009707:Nucleosomes / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013347:Subcellular Fractions; D014018:Tissue Distribution; D024363:Transcription Initiation Site / Q000502:physiology*; D014158:Transcription, Genetic
chemical_list: D021901:DNA, Intergenic; D009707:Nucleosomes; D022661:RNA, Untranslated
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