Xue Yongtao, Haas Stefan A, Brino Laurent, Gusnanto Arief, Reimers Mark, Talibi Driss, Vingron Martin, Ekwall Karl, Wright Anthony P H
Natural Sciences Section, Södertörns University College, S-141 89 Huddinge, Sweden.
Yeast. 2004 Jan 15;21(1):25-39. doi: 10.1002/yea.1053.
Completion of the fission yeast genome sequence has opened up possibilities for post-genomic approaches. We have constructed a DNA microarray for genome-wide gene expression analysis in fission yeast. The microarray contains DNA fragments, PCR-amplified from a genomic DNA template, that represent > 99% of the 5000 or so annotated fission yeast genes, as well as a number of control sequences. The GenomePRIDE software used attempts to design similarly sized DNA fragments corresponding to gene regions within single exons, near the 3'-end of genes that lack homology to other fission yeast genes. To validate the design and utility of the array, we studied expression changes after a 2 h temperature shift from 25 degrees C to 36 degrees C, conditions widely used when studying temperature-sensitive mutants. Obligingly, the vast majority of genes do not change more than two-fold, supporting the widely held view that temperature-shift experiments specifically reveal phenotypes associated with temperature-sensitive mutants. However, we did identify a small group of genes that showed a reproducible change in expression. Importantly, most of these corresponded to previously characterized heat-shock genes, whose expression has been reported to change after more extreme temperature shifts than those used here. We conclude that the DNA microarray represents a useful resource for fission yeast researchers as well as the broader yeast community, since it will facilitate comparison with the distantly related budding yeast, Saccharomyces cerevisiae. To maximize the utility of this resource, the array and its component parts are fully described in On-line Supplementary Information and are also available commercially.
裂殖酵母基因组序列的完成开启了后基因组研究方法的可能性。我们构建了一个用于裂殖酵母全基因组基因表达分析的DNA微阵列。该微阵列包含从基因组DNA模板PCR扩增得到的DNA片段，这些片段代表了约5000个已注释的裂殖酵母基因中的99%以上，以及一些控制序列。所使用的GenomePRIDE软件试图设计大小相似的DNA片段，这些片段对应于单个外显子内的基因区域，位于与其他裂殖酵母基因缺乏同源性的基因的3'端附近。为了验证该阵列的设计和实用性，我们研究了在从25℃到36℃的2小时温度变化后的表达变化，这是研究温度敏感突变体时广泛使用的条件。幸运的是，绝大多数基因的变化不超过两倍，这支持了一种广泛持有的观点，即温度变化实验专门揭示与温度敏感突变体相关的表型。然而，我们确实鉴定出一小部分基因的表达有可重复的变化。重要的是，其中大多数对应于先前已表征的热休克基因，据报道，在比这里使用的温度变化更极端的情况下，这些基因的表达会发生变化。我们得出结论，DNA微阵列对于裂殖酵母研究人员以及更广泛的酵母群体来说是一种有用的资源，因为它将有助于与远缘的芽殖酵母酿酒酵母进行比较。为了最大限度地利用这一资源，该阵列及其组成部分在在线补充信息中进行了全面描述，并且也可商业获得。
