Journal Article

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 and Sumio Sugano

in DNA Research

Published on behalf of Kazusa DNA Research Institute

Volume 17, issue 3, pages 169-183
Published in print June 2010 | ISSN: 1340-2838
Published online April 2010 | e-ISSN: 1756-1663 | DOI:

Show Summary Details


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.

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

Journal Article.  7019 words.  Illustrated.

Subjects: Genetics and Genomics

Users without a subscription are not able to see the full content. Please, subscribe or login to access all content.