Contribution of transcriptional regulation to natural variations in Arabidopsis.
Contribution of transcriptional regulation to natural variations in Arabidopsis.
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DOI：
10.1186/gb-2005-6-4-r32
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发表时间：
2005
期刊：
影响因子：
12.3
通讯作者：
Zhu T
中科院分区：
文献类型：
--
作者：
Chen WJ;Chang SH;Hudson ME;Kwan WK;Li J;Estes B;Knoll D;Shi L;Zhu T
通过与拟南芥GeneChip微阵列的比较基因组杂交，在5个品种中鉴定出7508个未检测到基因组序列变异的探针集，并用于品种特异性转录组分析，鉴定出60个在不同品种背景下以器官依赖方式差异表达的基因。对这7508个基因的表达模式进行相关性分析，发现65个高可塑性基因在每个组合中具有不同的表达模式。基因转录的遗传控制是基因组进化的关键组成部分。为了了解自然变异的转录基础，我们研究了拟南芥全基因组的转录变异，并表征了调节元件的遗传变异。通过与拟南芥基因芯片（GeneChip）的比较基因组杂交，在5个菌株（Col-0、C24、Ler、WS-2和no -0）中鉴定出7508个未检测到基因组序列变异的探针集，并用于菌株特异性转录组分析。双向方差分析鉴定了60个基因，其mRNA水平在不同的加入背景下以器官依赖的方式存在差异。这些基因大多参与胁迫反应和植物发育的后期阶段，如种子发育。对这7508个基因的表达模式进行相关性分析，发现65个高可塑性基因在每个组合中具有不同的表达模式。在mRNA水平上表现出较大遗传变异的基因是那些具有信号转导、转录和应激反应功能的基因，表明这些基因在不同品种间的调控机制存在差异。这与基因组杂交鉴定的编码区具有显著多态性的基因形成对比，这些基因包括编码转座子相关蛋白、激酶和抗病蛋白的基因。虽然在这些基因的编码区平均检测到相对较少的序列变异，但在上游区域发现了许多差异，其中一些改变了潜在的顺式调控元件。我们的研究结果表明，编码控制因子的基因调控元件的核苷酸多态性可能是自然选择的主要目标，也是拟南芥遗传进化的驱动力。
Among five accessions 7,508 probe sets with no detectable genomic sequence variations were identified on the basis of the comparative genomic hybridization to the Arabidopsis GeneChip microarray, and used for accession-specific transcriptome analysis, identifying 60 genes that were differentially expressed in different accession backgrounds in an organ-dependent manner. Correlation analysis of expression patterns of these 7,508 genes between pairs of accessions identified a group of 65 highly plastic genes with distinct expression patterns in each accession. Genetic control of gene transcription is a key component in genome evolution. To understand the transcriptional basis of natural variation, we have studied genome-wide variations in transcription and characterized the genetic variations in regulatory elements among Arabidopsis accessions. Among five accessions (Col-0, C24, Ler, WS-2, and NO-0) 7,508 probe sets with no detectable genomic sequence variations were identified on the basis of the comparative genomic hybridization to the Arabidopsis GeneChip microarray, and used for accession-specific transcriptome analysis. Two-way ANOVA analysis has identified 60 genes whose mRNA levels differed in different accession backgrounds in an organ-dependent manner. Most of these genes were involved in stress responses and late stages of plant development, such as seed development. Correlation analysis of expression patterns of these 7,508 genes between pairs of accessions identified a group of 65 highly plastic genes with distinct expression patterns in each accession. Genes that show substantial genetic variation in mRNA level are those with functions in signal transduction, transcription and stress response, suggesting the existence of variations in the regulatory mechanisms for these genes among different accessions. This is in contrast to those genes with significant polymorphisms in the coding regions identified by genomic hybridization, which include genes encoding transposon-related proteins, kinases and disease-resistance proteins. While relatively fewer sequence variations were detected on average in the coding regions of these genes, a number of differences were identified from the upstream regions, several of which alter potential cis-regulatory elements. Our results suggest that nucleotide polymorphisms in regulatory elements of genes encoding controlling factors could be primary targets of natural selection and a driving force behind the evolution of Arabidopsis accessions.
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DOI：
10.1073/pnas.011404098
发表时间：
2001-01-02
影响因子：
11.1
作者：
Li, C;Wong, WH
通讯作者：
Wong, WH
影响因子：
11.6
作者：
Aukerman, MJ;Hirschfeld, M;Sharrock, RA
通讯作者：
Sharrock, RA
影响因子：
9.2
作者：
Freemont, PS
通讯作者：
Freemont, PS
DOI：
10.1073/pnas.172520999
发表时间：
2002-10-15
影响因子：
11.1
作者：
Cong, B;Liu, JP;Tanksley, SD
通讯作者：
Tanksley, SD
影响因子：
7.2
作者：
Jirage, D;Zhou, N;Glazebrook, J
通讯作者：
Glazebrook, J