Characterization and Identification of cis-Regulatory Elements in Arabidopsis Based on Single-Nucleotide Polymorphism Information
Characterization and Identification of cis-Regulatory Elements in Arabidopsis Based on Single-Nucleotide Polymorphism Information
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DOI：
10.1104/pp.113.229716
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发表时间：
2014-01-01
期刊：
影响因子：
7.4
通讯作者：
Walther, Dirk
中科院分区：
文献类型：
--
作者：
Korkuc, Paula;Schippers, Jos H. M.;Walther, Dirk
识别调控元件并揭示它们在基因表达调控中的作用仍然是植物基因组研究的中心目标。我们利用大量拟南芥 (Arabidopsis thaliana) 种质的详细基因组测序信息，通过依赖保守性作为功能相关性的标志信号来表征和鉴定拟南芥基因启动子区域中的已知顺式调控元件。根据基因组布局和转录起始位点上游序列区域中单核苷酸多态性 (SNP) 的密度分布，拟南芥启动子区域的平均长度可以确定为 500 bp。与其各自上游区域高度变异相关的基因优先参与环境响应和信号传导过程，而低水平的启动子SNP密度在管家基因中很常见。发现已知的顺式元件表现出比与已知基序不相关的序列区域更低的 SNP 密度。对于 15 个已知的顺式元件基序，根据其启动子 SNP 密度分布检测到相对于转录起始位点的强烈位置偏好。五个新的候选顺式元件基序被确定为 17 个序列六聚体的共有基序，表现出增加的序列保守性，并结合位置偏好、注释信息和诱导相关基因表达的功能相关性的证据。我们的研究表明，目前可用的 SNP 数据分辨率为识别功能基因组元件和表征基因启动子序列提供了新方法。
Identifying regulatory elements and revealing their role in gene expression regulation remains a central goal of plant genome research. We exploited the detailed genomic sequencing information of a large number of Arabidopsis (Arabidopsis thaliana) accessions to characterize known and to identify novel cis-regulatory elements in gene promoter regions of Arabidopsis by relying on conservation as the hallmark signal of functional relevance. Based on the genomic layout and the obtained density profiles of single-nucleotide polymorphisms (SNPs) in sequence regions upstream of transcription start sites, the average length of promoter regions in Arabidopsis could be established at 500 bp. Genes associated with high degrees of variability of their respective upstream regions are preferentially involved in environmental response and signaling processes, while low levels of promoter SNP density are common among housekeeping genes. Known cis-elements were found to exhibit a decreased SNP density than sequence regions not associated with known motifs. For 15 known cis-element motifs, strong positional preferences relative to the transcription start site were detected based on their promoter SNP density profiles. Five novel candidate cis-element motifs were identified as consensus motifs of 17 sequence hexamers exhibiting increased sequence conservation combined with evidence of positional preferences, annotation information, and functional relevance for inducing correlated gene expression. Our study demonstrates that the currently available resolution of SNP data offers novel ways for the identification of functional genomic elements and the characterization of gene promoter sequences.