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

Masahiro Uesaka, Osamu Nishimura, Yasuhiro Go, Kinichi Nakashima, Kiyokazu Agata, Takuya Imamura

Research output: Contribution to journalArticle

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Abstract

Background: The 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.Results: We 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.Conclusions: We propose that single-stranded ncRNA resulting from head-to-head transcription at GC-rich sequences regulates tissue-specific gene expression.

Original languageEnglish
Article number35
JournalBMC Genomics
Volume15
Issue number1
DOIs
Publication statusPublished - Jan 17 2014

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Untranslated RNA
Transcriptional Activation
Mammals
Long Noncoding RNA
Messenger RNA
Transcription Initiation Site
RNA
GC Rich Sequence
Genome
CpG Islands
Pan troglodytes
Genes
Down-Regulation
Gene Expression
Proteins

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Genetics

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Bidirectional promoters are the major source of gene activation-associated non-coding RNAs in mammals. / Uesaka, Masahiro; Nishimura, Osamu; Go, Yasuhiro; Nakashima, Kinichi; Agata, Kiyokazu; Imamura, Takuya.

In: BMC Genomics, Vol. 15, No. 1, 35, 17.01.2014.

Research output: Contribution to journalArticle

Uesaka, Masahiro ; Nishimura, Osamu ; Go, Yasuhiro ; Nakashima, Kinichi ; Agata, Kiyokazu ; Imamura, Takuya. / Bidirectional promoters are the major source of gene activation-associated non-coding RNAs in mammals. In: BMC Genomics. 2014 ; Vol. 15, No. 1.
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