ArticleBMC genomics2008
Genome-wide analysis of antisense transcription with Affymetrix exon array.
Article in BMC genomics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Review
- OverGeneDB: a database of 5' end protein coding overlapping genes in human and mouse genomes.Nucleic acids research · 2018Article
- Article
- Identification of expressed and conserved human noncoding RNAs.RNA (New York, N.Y.) · 2014Article
- Integrated detection of natural antisense transcripts using strand-specific RNA sequencing data.Genome research · 2013Article
- Non-polyadenylated transcription in embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation.Nucleic acids research · 2013Article
- Conserved expression of natural antisense transcripts in mammals.BMC genomics · 2013Article
- Development of a rapid and inexpensive method to reveal natural antisense transcripts.Plant methods · 2012Article
- Identification of potential antisense transcripts in rice using conventional microarray.Molecular biotechnology · 2012Article
- Regulation of an antisense RNA with the transition of neonatal to IIb myosin heavy chain during postnatal development and hypothyroidism in rat skeletal muscle.American journal of physiology. Regulatory, integrative and comparative physiology · 2012Article
- Repression of meiotic genes by antisense transcription and by Fkh2 transcription factor in Schizosaccharomyces pombe.PloS one · 2012Article
- Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism.Genome biology · 2011Article
- Article
- What are natural antisense transcripts good for?Biochemical Society transactions · 2010Review
- The expression of ELK transcription factors in adult DRG: Novel isoforms, antisense transcripts and upregulation by nerve damage.Molecular and cellular neurosciences · 2010Article
- High-resolution profiling of gammaH2AX around DNA double strand breaks in the mammalian genome.The EMBO journal · 2010Article
- Regulatory roles of natural antisense transcripts.Nature reviews. Molecular cell biology · 2009Review
- Identification of novel endogenous antisense transcripts by DNA microarray analysis targeting complementary strand of annotated genes.BMC genomics · 2009Article
- Identification of differentially expressed sense and antisense transcript pairs in breast epithelial tissues.BMC genomics · 2009Article
- Long antisense non-coding RNAs function to direct epigenetic complexes that regulate transcription in human cells.Epigenetics · 2009Review
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Authors and funding
4 authors.
Funding
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Abstract
backgroundA large number of natural antisense transcripts have been identified in human and mouse genomes. Study of their potential functions clearly requires cost-efficient method for expression analysis.
resultsHere we show that Affymetrix Exon arrays, which were designed to detect conventional transcripts in the sense orientation, can be used to monitor antisense expression across all exonic loci in mammalian genomes. Through modification of the cDNA synthesis protocol, we labeled single-strand cDNA in the reverse orientation as in the standard protocol, thus enabling the detection of antisense transcripts using the same array. Applying this technique to human Jurkat cells, we identified antisense transcription at 2,088 exonic loci of 1,516 UniGene clusters. Many of these antisense transcripts were not observed previously and some were validated by orientation-specific RT-PCR.
conclusionOur results suggest that with a modified protocol Affymetrix human, mouse and rat Exon arrays can be used as a routine method for genome-wide analysis of antisense transcription in these genomes.
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