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)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/655438
- author
- Vallon-Christersson, Johan
LU
; Staaf, Johan
LU
; Kvist, Anders
LU
; Medstrand, Patrik
LU
; Borg, Åke
LU
and Rovira, Carlos
LU
- organization
- publishing date
- 2007
- type
- Contribution to journal
- publication status
- published
- subject
- in
- BMC Genomics
- volume
- 8
- publisher
- BioMed Central (BMC)
- external identifiers
-
- wos:000250091700001
- scopus:35248844540
- ISSN
- 1471-2164
- DOI
- 10.1186/1471-2164-8-295
- language
- English
- LU publication?
- yes
- additional info
- The information about affiliations in this record was updated in December 2015. The record was previously connected to the following departments: Stem Cell Center (013041110), Molecular Virology (013212007), Oncology, MV (013035000)
- id
- 424beb0c-9d11-4b6e-9bbe-b6d3530cc278 (old id 655438)
- date added to LUP
- 2016-04-01 15:24:43
- date last changed
- 2022-01-28 05:10:45
@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 (BMC)}},
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}},
doi = {{10.1186/1471-2164-8-295}},
volume = {{8}},
year = {{2007}},
}