A gene expression map for the euchromatic genome of Drosophila melanogaster
A gene expression map for the euchromatic genome of Drosophila melanogaster
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DOI：
10.1126/science.1101312
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发表时间：
2004-10-22
期刊：
影响因子：
56.9
通讯作者：
White, KP
中科院分区：
文献类型：
--
作者：
Stolc, V;Gauhar, Z;White, KP
我们使用了无掩模光刻法生产DNA寡核苷酸微阵列与独特的探针序列平铺在整个基因组的果蝇和跨预测的剪接点。RNA表达的蛋白质编码和非蛋白质编码序列的生命周期的每个主要阶段，包括成年配偶和女性。我们检测到93%的注释基因的转录活性和41%的探针在内含子和基因间序列的RNA表达。与全基因组RNA干扰数据和基因注释的比较揭示了不同类别基因的可区分的表达水平和具有基本细胞功能的基因的更高表达水平。在约40%的预测基因中观察到差异剪接，并检测到5440种以前未知的剪接形式。与D. pseudobscura具有高度相关的表达;这些区域的长度范围从10到900个酶对。表达的基因间序列和内含子序列比不表达的序列更可能是进化上保守的，并且其中约15%似乎是发育调节的。我们的研究结果提供了一个草案的整个非重复基因组的表达图谱，揭示了一个更广泛和多样化的表达序列比以前预测的。
We used a maskless photolithography method to produce DNA oligonucleotide microarrays with unique probe sequences tiled throughout the genome of Drosophila melanogaster and across predicted splice junctions. RNA expression of protein coding and nonprotein coding sequences was determined for each major stage of the life cycle, including adult mates and females. We detected transcriptional activity for 93% of annotated genes and RNA expression for 41% of the probes in intronic and intergenic sequences. Comparison to genome-wide RNA interference data and to gene annotations revealed distinguishable levels of expression for different classes of genes and higher levels of expression for genes with essential cellular functions. Differential splicing was observed in about 40% of predicted genes, and 5440 previously unknown splice forms were detected. Genes within, conserved regions of synteny with D. pseudoobscura had highly correlated expression; these regions ranged in length from 10 to 900 kilobase pairs. The expressed intergenic and intronic sequences are more likely to be evolutionarily conserved than nonexpressed ones, and about 15% of them appear to be developmentally regulated. Our results provide a draft expression map for the entire nonrepetitive genome, which reveals a much more extensive and diverse set of expressed sequences than was previously predicted.