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Non-coding antisense transcription detected by conventional and single-stranded cDNA microarray

Vallon-Christersson, Johan LU ; Staaf, Johan LU ; Kvist, Anders LU ; Medstrand, Patrik LU ; Borg, Åke LU and Rovira, Carlos LU (2007) In BMC Genomics 8.
Abstract
Background: Recent studies revealed that many mammalian protein- coding genes also transcribe their complementary strands. This phenomenon raises questions regarding the validity of data obtained from double-stranded cDNA microarrays since hybridization to both strands may occur. Here, we wanted to analyze experimentally the incidence of antisense transcription in human cells and to estimate their influence on protein coding expression patterns obtained by double-stranded microarrays. Therefore, we profiled transcription of sense and antisense independently by using strand-specific cDNA microarrays. Results: Up to 88% of expressed protein coding loci displayed concurrent expression from the complementary strand. Antisense transcription is... (More)
Background: Recent studies revealed that many mammalian protein- coding genes also transcribe their complementary strands. This phenomenon raises questions regarding the validity of data obtained from double-stranded cDNA microarrays since hybridization to both strands may occur. Here, we wanted to analyze experimentally the incidence of antisense transcription in human cells and to estimate their influence on protein coding expression patterns obtained by double-stranded microarrays. Therefore, we profiled transcription of sense and antisense independently by using strand-specific cDNA microarrays. Results: Up to 88% of expressed protein coding loci displayed concurrent expression from the complementary strand. Antisense transcription is cell specific and showed a strong tendency to be positively correlated to the expression of the sense counterparts. Even if their expression is widespread, detected antisense signals seem to have a limited distorting effect on sense profiles obtained with double-stranded probes. Conclusion: Antisense transcription in humans can be far more common than previously estimated. However, it has limited influence on expression profiles obtained with conventional cDNA probes. This can be explained by a biological phenomena and a bias of the technique: a) a co-ordinate sense and antisense expression variation and b) a bias for sense-hybridization to occur with more efficiency, presumably due to variable exonic overlap between antisense transcripts. (Less)
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author
organization
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type
Contribution to journal
publication status
published
subject
in
BMC Genomics
volume
8
publisher
BioMed Central
external identifiers
  • wos:000250091700001
  • scopus:35248844540
ISSN
1471-2164
DOI
10.1186/1471-2164-8-295
project
CREATE Health
language
English
LU publication?
yes
id
424beb0c-9d11-4b6e-9bbe-b6d3530cc278 (old id 655438)
date added to LUP
2007-12-19 11:42:30
date last changed
2017-10-29 04:08:33
@article{424beb0c-9d11-4b6e-9bbe-b6d3530cc278,
  abstract     = {Background: Recent studies revealed that many mammalian protein- coding genes also transcribe their complementary strands. This phenomenon raises questions regarding the validity of data obtained from double-stranded cDNA microarrays since hybridization to both strands may occur. Here, we wanted to analyze experimentally the incidence of antisense transcription in human cells and to estimate their influence on protein coding expression patterns obtained by double-stranded microarrays. Therefore, we profiled transcription of sense and antisense independently by using strand-specific cDNA microarrays. Results: Up to 88% of expressed protein coding loci displayed concurrent expression from the complementary strand. Antisense transcription is cell specific and showed a strong tendency to be positively correlated to the expression of the sense counterparts. Even if their expression is widespread, detected antisense signals seem to have a limited distorting effect on sense profiles obtained with double-stranded probes. Conclusion: Antisense transcription in humans can be far more common than previously estimated. However, it has limited influence on expression profiles obtained with conventional cDNA probes. This can be explained by a biological phenomena and a bias of the technique: a) a co-ordinate sense and antisense expression variation and b) a bias for sense-hybridization to occur with more efficiency, presumably due to variable exonic overlap between antisense transcripts.},
  author       = {Vallon-Christersson, Johan and Staaf, Johan and Kvist, Anders and Medstrand, Patrik and Borg, Åke and Rovira, Carlos},
  issn         = {1471-2164},
  language     = {eng},
  publisher    = {BioMed Central},
  series       = {BMC Genomics},
  title        = {Non-coding antisense transcription detected by conventional and single-stranded cDNA microarray},
  url          = {http://dx.doi.org/10.1186/1471-2164-8-295},
  volume       = {8},
  year         = {2007},
}