Review
Genome-wide expression analysis of plant cell cycle modulated genes

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Abstract

Genome-wide expression analysis is rapidly becoming an essential tool for identifying and analysing genes involved in, or controlling, various biological processes ranging from development to responses to environmental cues. The control of cell division involves the temporal expression of different sets of genes, allowing the dividing cell to progress through the different phases of the cell cycle. A landmark study using DNA microarrays to follow the patterns of gene expression in synchronously dividing yeast cells has allowed the identification of several hundreds of genes that are involved in the cell cycle. Although DNA microarrays provide a convenient tool for genome-wide expression analysis, their use is limited to organisms for which the complete genome sequence or a large cDNA collection is available. For other organisms, including most plant species, DNA fragment analysis based methods, such as cDNA-AFLP, provide a more appropriate tool for genome-wide expression analysis. Furthermore, cDNA-AFLP exhibits properties that complement DNA microarrays and, hence, constitutes a useful tool for gene discovery.

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 26ā€ˆ000 genes have been studied experimentally to date, and the challenge for the coming decade will be to determine the function of the remaining 23ā€ˆ000 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:

  • radical dot of special interest

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