ReviewGenome-wide expression analysis of plant cell cycle modulated genes
Introduction
The recent completion of the genome sequence of the flowering plant Arabidopsisthaliana (L.) Heynh. [1] will have a tremendous impact on plant molecular genetic research. Despite intensive research efforts, fewer than 10% of Arabidopsisā nearly 26ā000 genes have been studied experimentally to date, and the challenge for the coming decade will be to determine the function of the remaining 23ā000 genes. To this end, the global analysis of gene expression, often referred to as genome-wide expression profiling, is rapidly becoming recognised as one of the most promising tools in functional genomics. In the past years, a number of landmark papers, such as those describing the transcriptional program regulating the cell cycle or the identification of genes involved in cancer, have convincingly demonstrated that genome-wide expression profiling is an efficient tool for the large-scale identification of gene functions.
Although DNA microarrays are rapidly becoming the standard tool for genome-wide expression analysis, their application is still limited to a restricted number of experimental systems. Several alternative technologies for expression profiling based on DNA sequencing or cDNA fragment analysis have been developed and successfully used in other biological systems. In this review, we discuss and compare the merits and limitations of the different genome-wide expression analysis technologies available today. Particular attention will be given to the cDNA- AFLP (amplified fragment-length polymorphism) technology, and its usefulness in gene discovery and transcript profiling will be illustrated.
Section snippets
Technologies for genome-wide expression analysis
The first attempt to measure global levels of gene expression was based on large-scale expressed sequence tag (EST) sequencing [2]. This approach is particularly useful for discovering novel genes but is far too laborious and costly for routine analysis of gene expression. In the course of the past five years, different powerful approaches for detecting and quantifying gene expression levels have been developed. In essence, these methods depend on three different principles each having their
Screening for cell cycle modulated genes
The precise execution of the molecular processes of DNA replication, chromosome segregation and mitosis during the cell cycle is likely to be governed by a precise regulation of gene activity. This makes the study of cell cycle dependent gene expression an attractive system for genome-wide expression analysis. Earlier studies using traditional methods revealed that a large number of messages are cell cycle regulated. The first genome-wide expression analyses of cell cycle modulated genes were
Conclusions
In plants, as in other organisms, microarray-based analysis will likely continue to be widely used to study different biological processes. With the availability of the complete genomic sequence of Arabidopsis, it will be possible to build a microarray containing all ORFs from this plant. Furthermore, technological improvements will most probably enhance the sensitivity and specificity of transcript detection within microarrays. Nevertheless, the high levels of redundancy in plant genomes will
References and recommended reading
Papers of particular interest, published within the annual period of review, have been highlighted as:
of special interest
of outstanding interest
References (48)
- et al.
A comparison of gel-based, nylon filter and microarray techniques to detect differential RNA expression in plants
Curr Opin Plant Biol
(1999) - et al.
Chasing the dream: plant EST microarrays
Curr Opin Plant Biol
(2000) - et al.
Monitoring genome-wide expression in plants
Curr Opin Biotechnol
(2000) - et al.
Functional discovery via a compendium of expression profiles
Cell
(2000) - et al.
Analysing uncharted transcriptomes with SAGE
Trends Genet
(2000) - et al.
Molecular phenotype of the human oocyte by PCR-SAGE
Genomics
(2000) - et al.
A genome-wide transcriptional analysis of the mitotic cell cycle
Mol Cell
(1998) Microarrays and cell cycle transcription in yeast
Curr Opin Cell Biol
(2000)- et al.
Chemical inhibitors: a tool for plant cell cycle studies
FEBS Lett
(2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
Nature
(2000)