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Title: Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array

Author
item Coram, Tristan
item SETTLES, MATTHEW - WASHINGTON STATE UNIV
item Chen, Xianming

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/29/2009
Publication Date: 5/29/2009
Citation: Coram, T., Settles, M.L., Chen, X. 2009. Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array. BMC Genomics 10:253.

Interpretive Summary: Natural antisense transcripts (NATs) are transcripts of the opposite DNA strand to the sense-strand either at the same locus or a different locus. They can affect gene expression at multiple stages including transcription, RNA processing and transport, and translation. Traditionally, NATs were identified by the alignment of full-length cDNAs or expressed sequence tags to genome sequences, but an alternative method for large-scale detection of sense-antisense transcript pairs involves the use of microarrays. In this study we developed a novel protocol to assay sense- and antisense-strand transcription on the 55K Affymetrix GeneChip Wheat Genome Array. We selected five different tissue types for assay to enable maximum discovery, and used the ‘Chinese Spring’ wheat genotype because most of the wheat GeneChip probe sequences were based on its genomic sequence. We identified 110 sense-antisense transcript pairs and validated the microarray observations using strand-specific RT-PCR. The results show that antisense transcription is relatively abundant in wheat, and may affect the expression of valuable agronomic phenotypes. This study is the first report of using an expression array to discover the expression of natural sense-antisense transcript pairs, and may be considered as proof-of-concept.

Technical Abstract: Natural antisense transcripts (NATs) are transcripts of the opposite DNA strand to the sense-strand either at the same locus (cis-encoded) or a different locus (trans-encoded). They can affect gene expression at multiple stages including transcription, RNA processing and transport, and translation. NATs give rise to sense-antisense transcript pairs and the number of these identified has escalated greatly with the availability of DNA sequencing resources and public databases. Traditionally, NATs were identified by the alignment of full-length cDNAs or expressed sequence tags to genome sequences, but an alternative method for large-scale detection of sense-antisense transcript pairs involves the use of microarrays. In this study we developed a novel protocol to assay sense- and antisense-strand transcription on the 55K Affymetrix GeneChip Wheat Genome Array, which is a 3’ in vitro transcription (3’IVT) expression array. We selected five different tissue types for assay to enable maximum discovery, and used the ‘Chinese Spring’ wheat genotype because most of the wheat GeneChip probe sequences were based on its genomic sequence. This study is the first report of using a 3’IVT expression array to discover the expression of natural sense-antisense transcript pairs, and may be considered as proof-of-concept.