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Expression profiling of antisense transcripts on DNA arrays.

Andreas Werner1, Gabriele Schmutzler, Mark Carlile

  • 1Epithelial Research Group, Institute for Cell and Molecular Biosciences. andreas.werner@ncl.ac.uk

Physiological Genomics
|November 16, 2006
PubMed
Summary
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Commercial DNA arrays can detect natural antisense transcripts (NATs) in mouse tissues. This study demonstrates NATs are tissue-specific and linked to sense transcripts, paving the way for large-scale NAT analysis.

Area of Science:

  • Genomics
  • Molecular Biology
  • Gene Expression

Background:

  • Bidirectional transcription is common in mouse genes, but tissue-specific patterns and functions of natural antisense transcripts (NATs) are poorly understood.
  • Assessing NAT expression at scale is challenging due to limited methodologies.

Purpose of the Study:

  • To evaluate the utility of commercial DNA arrays for large-scale assessment of antisense transcription in mouse tissues.
  • To investigate the tissue-specific distribution and relationship of NATs with their sense counterparts.

Main Methods:

  • Utilized Affymetrix U74 mouse genome arrays with reversely annotated oligonucleotides to detect NATs in kidney and brain RNA samples.
  • Confirmed antisense RNA transcription using real-time PCR across multiple tissues (kidney, brain, heart, thymus, liver).

Related Experiment Videos

Main Results:

  • Detected potential NATs in 11.9% of kidney and 10.1% of brain samples, with approximately half found in both tissues.
  • Found that most detected NATs (92.5% in kidney, 74.5% in brain) had corresponding sense transcripts.
  • Observed tissue-specific expression patterns and varying sense/antisense ratios for randomly selected transcripts.

Conclusions:

  • Commercial DNA arrays are sufficiently sensitive for assessing NATs in total RNA from whole organs.
  • Antisense transcriptomes exhibit tissue-specific characteristics, with a strong association with the sense transcriptome.
  • This study provides a proof-of-principle for using DNA arrays to study NATs on a large scale.