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Comparative Study
. 2004 Oct;136(2):3223-33.
doi: 10.1104/pp.104.043406.

Maximizing the efficacy of SAGE analysis identifies novel transcripts in Arabidopsis

Stephen J Robinson  1 , Dustin J Cram, Christopher T Lewis, Isobel A P Parkin
Affiliations
Comparative Study

Maximizing the efficacy of SAGE analysis identifies novel transcripts in Arabidopsis

Stephen J Robinson et al. Plant Physiol. 2004 Oct.

Abstract

The efficacy of using Serial Analysis of Gene Expression (SAGE) to analyze the transcriptome of the model dicotyledonous plant Arabidopsis was assessed. We describe an iterative tag-to-gene matching process that exploits the availability of the whole genome sequence of Arabidopsis. The expression patterns of 98% of the annotated Arabidopsis genes could theoretically be evaluated through SAGE and using an iterative matching process 79% could be identified by a tag found at a unique site in the genome. A total of 145,170 reliable experimental tags from two Arabidopsis leaf tissue SAGE libraries were analyzed, of which 29,632 were distinct. The majority (93%) of the 12,988 experimental tags observed greater than once could be matched within the Arabidopsis genome. However, only 78% were matched to a single locus within the genome, reflecting the complexities associated with working in a highly duplicated genome. In addition to a comprehensive assessment of gene expression in Arabidopsis leaf tissue, we describe evidence of transcription from pseudo-genes as well as evidence of alternative mRNA processing and anti-sense transcription. This collection of experimental SAGE tags could be exploited to assist in the on-going annotation of the Arabidopsis genome.

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Figures

Figure 1.
Figure 1.
Distributions for the length of TIGR defined Arabidopsis UTR sequences. A, 5′ UTRs; B, 3′ UTRs.
Figure 2.
Figure 2.
Comparison of the number of genes with anti-sense transcripts detected by three expression profiling technologies. Total number of annotated Arabidopsis genes with anti-sense transcripts expressed in leaf tissue detected using SAGE (247), MPSS (5,200), and microarray (7,544) technologies.
Figure 3.
Figure 3.
Comparison of the number of genes detected by three expression profiling technologies. Total number of annotated Arabidopsis genes with sense transcripts expressed in leaf tissue detected using SAGE (12,934), MPSS (15,759), and microarray (13,317) technologies.
See this image and copyright information in PMC

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