HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) Supplemental Data All Versions of this Article: 28/3/294    most recent 00127.2006v1 Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in ISI Web of Science Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via ISI Web of Science (1) Citing Articles via Google Scholar Google Scholar Articles by Werner, A. Articles by Peters, H. Search for Related Content PubMed PubMed Citation Articles by Werner, A. Articles by Peters, H.

Expression profiling of antisense transcripts on DNA arrays

¹ Epithelial Research Group, Institute for Cell and Molecular Biosciences
² International Centre for Life, Newcastle University, Newcastle upon Tyne, United Kingdom

The majority of mouse genes are estimated to undergo bidirectional transcription; however, their tissue-specific distribution patterns and physiological significance are largely unknown. This is in part due to the lack of methodology to routinely assess the expression of natural antisense transcripts (NATs) on a large scale. Here we tested whether commercial DNA arrays can be used to monitor antisense transcription in mouse kidney and brain. We took advantage of the reversely annotated oligonucleotides on the U74 mouse genome array from Affymetrix that hybridize to NATs overlapping with the sense transcript in the area of the probe set. In RNA samples from mouse kidney and brain, 11.9% and 10.1%, respectively, of 5,652 potential NATs returned positive and about half of the antisense RNAs were detected in both tissues, which was similar to the fraction of sense transcripts expressed in both tissues. Notably, we found that the majority of NATs are related to the sense transcriptome since corresponding sense transcripts were detected for 92.5% (kidney) and 74.5% (brain) of the detected antisense RNAs. Antisense RNA transcription was confirmed by real-time PCR and included additional RNA samples from heart, thymus, and liver. The randomly selected transcripts showed tissue specific expression patterns and varying sense/antisense ratios. The results indicate that antisense transcriptomes are tissue specific, and although pairing of sense/antisense transcripts are known to result in rapid degradation, our data provide proof of principle that the sensitivity of commercial DNA arrays is sufficient to assess NATs in total RNA of whole organs.

natural antisense transcript; DNA array; RNA; antisense transcriptome

This article has been cited by other articles:

				P. A. C. 't Hoen, Y. Ariyurek, H. H. Thygesen, E. Vreugdenhil, R. H. A. M. Vossen, R. X. de Menezes, J. M. Boer, G.-J. B. van Ommen, and J. T. den Dunnen Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms Nucleic Acids Res., October 31, 2008; (2008) gkn705v2. [Abstract] [Full Text] [PDF]

				A. Matsui, J. Ishida, T. Morosawa, Y. Mochizuki, E. Kaminuma, T. A. Endo, M. Okamoto, E. Nambara, M. Nakajima, M. Kawashima, et al. Arabidopsis Transcriptome Analysis under Drought, Cold, High-Salinity and ABA Treatment Conditions using a Tiling Array Plant Cell Physiol., August 1, 2008; 49(8): 1135 - 1149. [Abstract] [Full Text] [PDF]

				M. Carlile, P. Nalbant, K. Preston-Fayers, G. S. McHaffie, and A. Werner Processing of naturally occurring sense/antisense transcripts of the vertebrate Slc34a gene into short RNAs Physiol Genomics, June 1, 2008; 34(1): 95 - 100. [Abstract] [Full Text] [PDF]