Bidirectional promoters are the major source of gene activation-associated non-coding RNAs in mammals

BMC Genomics

Research Article

Kiyokazu Agata¹  Masahiro Uesaka²  Takuya Imamura²  Osamu Nishimura³  Yasuhiro Go⁴  Kinichi Nakashima⁵ 

[1] Department of Biophysics and Global COE Program, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, 606-8502, Sakyo-ku, Kyoto, Japan;Department of Biophysics and Global COE Program, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, 606-8502, Sakyo-ku, Kyoto, Japan;Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, 812-8581, Higashi-ku, Fukuoka, Japan;Department of Biophysics and Global COE Program, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, 606-8502, Sakyo-ku, Kyoto, Japan;Genome Resource and Analysis Unit, RIKEN Center for Developmental Biology, 2-2-3 Minatojima-Minamimachi, 650-0047, Chuo-ku, Kobe, Japan;Department of Cellular and Molecular Biology, Primate Research Institute, Kyoto University, 41-2 Kanrin, 484-8506, Inuyama, Aichi, Japan;Department of Brain Sciences, Center for Novel Science Initiatives, National Institutes of Natural Sciences, 38 Nishigonaka Myodaiji, 444-8585, Okazaki, Aichi, Japan;Department of Stem Cell Biology and Medicine, Graduate School of Medical Sciences, Kyushu University, 3-1-1 Maidashi, 812-8581, Higashi-ku, Fukuoka, Japan;

关键词: Bidirectional promoter;    Non-coding RNA;    CpG island;    Directional RNA-Seq;    Gene activation;   

DOI  :  10.1186/1471-2164-15-35

 received in 2013-06-16, accepted in 2014-01-15,  发布年份 2014

来源: Springer

【 摘 要 】

BackgroundThe majority of non-coding RNAs (ncRNAs) involved in mRNA metabolism in mammals have been believed to downregulate the corresponding mRNA expression level in a pre- or post-transcriptional manner by forming short or long ncRNA-mRNA duplex structures. Information on non-duplex-forming long ncRNAs is now also rapidly accumulating. To examine the directional properties of transcription at the whole-genome level, we performed directional RNA-seq analysis of mouse and chimpanzee tissue samples.ResultsWe found that there is only about 1% of the genome where both the top and bottom strands are utilized for transcription, suggesting that RNA-RNA duplexes are not abundantly formed. Focusing on transcription start sites (TSSs) of protein-coding genes revealed that a significant fraction of them contain switching-points that separate antisense- and sense-biased transcription, suggesting that head-to-head transcription is more prevalent than previously thought. More than 90% of head-to-head type promoters contain CpG islands. Moreover, CCG and CGG repeats are significantly enriched in the upstream regions and downstream regions, respectively, of TSSs located in head-to-head type promoters. Genes with tissue-specific promoter-associated ncRNAs (pancRNAs) show a positive correlation between the expression of their pancRNA and mRNA, which is in accord with the proposed role of pancRNA in facultative gene activation, whereas genes with constitutive expression generally lack pancRNAs.ConclusionsWe propose that single-stranded ncRNA resulting from head-to-head transcription at GC-rich sequences regulates tissue-specific gene expression.

【 授权许可】

Unknown   
© Uesaka et al.; licensee BioMed Central Ltd. 2014. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.