Characterization of transcription start sites of putative non-coding RNAs by multifaceted use of massively paralleled sequencer

Nuankanya Sathira, Riu Yamashita, Kousuke Tanimoto, Akinori Kanai, Takako Arauchi, Soutaro Kanematsu, Kenta Nakai, Yutaka Suzuki, Sumio Sugano

Research output: Contribution to journalArticle

3 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)169-183
Number of pages15
JournalDNA Research
Volume17
Issue number3
DOIs
Publication statusPublished - 2010 Jun 1

Keywords

  • antisense transcript
  • integrated transcriptome analysis
  • intergenic transcript
  • non-coding RNA
  • transcriptional start site cluster (TSC)

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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    Sathira, N., Yamashita, R., Tanimoto, K., Kanai, A., Arauchi, T., Kanematsu, S., Nakai, K., Suzuki, Y., & Sugano, S. (2010). Characterization of transcription start sites of putative non-coding RNAs by multifaceted use of massively paralleled sequencer. DNA Research, 17(3), 169-183. https://doi.org/10.1093/dnares/dsq007