In Silico Identification of Short Nucleotide Sequences Associated with Gene Expression of Pollen Development in Rice
In Silico Identification of Short Nucleotide Sequences Associated with Gene Expression of Pollen Development in Rice
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DOI：
10.1093/pcp/pcn129
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发表时间：
2008-10-01
影响因子：
4.9
通讯作者：
Izawa, Takeshi
中科院分区：
文献类型：
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作者：
Mihara, Motohiro;Itoh, Takeshi;Izawa, Takeshi
从激光显微切割（LM）制备的植物切片样品中提取的微量RNA的微阵列分析可以提供特定植物细胞在发育的各个阶段的基因表达的高质量信息。加入LM-微阵列分析项目后，我们利用来自发育中的水稻花粉细胞的全基因组基因表达数据来鉴定这些细胞中特定基因表达的顺式调控元件的候选者。我们首先发现了几个集群的基因表达模式的基础上的数据从LM微阵列。在一个基因簇中的成员在双细胞和成熟花粉有丝分裂阶段特异性表达，我们确定了基因簇指纹（GCF），其中每一个由一个短的核苷酸代表的基因簇。我们预计这些GCF将包含阶段和组织特异性基因表达的顺式调控元件，我们进一步确定了具有共同核心序列的GCF组。一些标准，如出现在基因簇中的频率，相对于总的测试基因集，侧翼序列的偏好和组合GCF集的基因区域中的分布，允许我们限制候选人的顺式调控序列在水稻花粉细胞中的特定基因表达的至少20套组合GCF。这种方法应该提供一个通用的算法，用于识别与特定基因表达相关的短核苷酸。
Microarray analysis of tiny amounts of RNA extracted from plant section samples prepared by laser microdissection (LM) can provide high-quality information on gene expression in specified plant cells at various stages of development. Having joined the LM-microarray analysis project, we utilized such genome-wide gene expression data from developing rice pollen cells to identify candidates for cis-regulatory elements for specific gene expression in these cells. We first found a few clusters of gene expression patterns based on the data from LM-microarrays. On one gene cluster in which the members were specifically expressed at the bicellular and mature pollen mitotic stages, we identified gene cluster fingerprints (GCFs), each of which consists of a short nucleotide representing the gene cluster. We expected that these GCFs would contain cis-regulatory elements for stage- and tissue-specific gene expression, and we further identified groups of GCFs with common core sequences. Some criteria, such as frequency of occurrence in the gene cluster in contrast to the total tested gene set, flanking sequence preference and distribution of combined GCF sets in the gene regions, allowed us to limit candidates for cis-regulatory sequences for specific gene expression in rice pollen cells to at least 20 sets of combined GCFs. This approach should provide a general purpose algorithm for identifying short nucleotides associated with specific gene expression.