Use of Serial Analysis of Gene Expression (SAGE) for transcript profiling in plants

Abstract

Serial Analysis of Gene Expression (SAGE) is a powerful technique for genome wide analysis of gene expression. The SAGE technique quantifies a 'tag' which represents the transcriptome product of a gene. A tag for the purpose of SAGE, is a nucleotide sequence of a defined length, directly adjacent to the 3'-most restriction site for a particular restriction enzyme. Thus, data product of SAGE is a list of tags with their count values, providing a digital representation of cellular gene expression. Several technical modifications have been made to the original SAGE protocol to improve its efficiency, reducing the amount of input RNA, increasing the length of SAGE tags, and allowing further use of SAGE results. This chapter deals with the methodology of SAGE, problems associated with SAGE, various SAGE modifications attempted, comparison with other contemporary high-throughput methods like microarrays, and current applications of SAGE in plant transcript profiling. In plants, SAGE has been used to analyse: (1) host-pathogen interactions, (2) plant responses to various environmental and nutritional stresses, (3) metabolism of toxic compounds, and (4) transcript profiling of a particular tissue/organ. Although majority of these studies have confined to model plants i.e. rice and Arabidopsis thaliana, a few recent efforts have extended the use of SAGE to other plant species also.