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Related Experiment Videos

Antisense transcripts with FANTOM2 clone set and their implications for gene regulation.

Hidenori Kiyosawa1, Itaru Yamanaka, Naoki Osato

  • 1Laboratory for Genome Exploration Research Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.

Genome Research
|June 24, 2003
PubMed
Summary

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Researchers discovered 2,481 sense-antisense transcript pairs and 899 bidirectional transcription pairs in mice, expanding known mammalian examples. This suggests natural antisense transcripts play a more significant role in gene regulation than previously understood.

Area of Science:

  • Genomics
  • Transcriptomics
  • Mammalian Gene Expression

Background:

  • Mammalian genomes exhibit complex transcriptional patterns.
  • Understanding gene regulation requires identifying novel transcript types.

Purpose of the Study:

  • To identify and quantify sense-antisense (SA) and nonantisense bidirectional (NAB) transcription pairs in mammals.
  • To investigate the prevalence and genomic distribution of these transcript pairs.

Main Methods:

  • Utilized the FANTOM2 mouse cDNA set (60,770 clones).
  • Integrated public mRNA and mouse genome sequence data.
  • Performed genomic mapping to identify SA and NAB pairs.

Main Results:

  • Identified 2,481 SA pairs and 899 NAB pairs.

Related Experiment Videos

  • SA and NAB pairs were found at 15.1% and 5.4% of autosomal loci, respectively.
  • Lower prevalence of SA pairs on the X chromosome (6.3%) may relate to X chromosome inactivation.
  • SA transcripts were often co-isolated from libraries, unlike NAB pairs.

    • Conclusions:

    • The study significantly expands the known repertoire of SA and NAB transcripts in mammals.
    • The prevalence of natural antisense transcripts suggests a more widespread role in gene expression regulation.
    • A genome browser and statistical data are available online for further research.