Upstream regulatory architecture of rice genes: summarizing the baseline towards genus-wide comparative analysis of regulatory networks and allele mining.
Upstream regulatory architecture of rice genes: summarizing the baseline towards genus-wide comparative analysis of regulatory networks and allele mining.
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DOI：
10.1186/s12284-015-0041-x
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发表时间：
2015
期刊：
影响因子：
--
通讯作者：
Lee DY
中科院分区：
文献类型：
--
作者：
de Los Reyes BG;Mohanty B;Yun SJ;Park MR;Lee DY
研究水稻基因及其同源调控蛋白的上游调控结构是网络生物学及其在比较功能基因组学中应用的核心。随着稻属比较基因组学资源的快速发展，必须建立一个参考基因组注释，定义各种顺式元件和反式作用因子，这些元件和反式作用因子将每个基因位点与生长、发育、繁殖和适应的各种内在和外在信号连接起来，以促进在调控网络背景下对表型变异的理解。这些信息对于建立挖掘非编码序列变异的基础也很重要，非编码序列变异定义了水稻种质中巨大的表型多样性中的新等位基因和表观等位基因。本文介绍了一个综合的知识和共识的趋势，关于各种顺式作用和反式作用的组件，定义的时空调控水稻基因的基础上，在其他模式和非模式植物的基础研究的代表性例子，和最近的研究在水稻。目的是总结快速发展的稻属基因组序列资源的系统性上游序列注释的基线，为全属功能基因组学做准备。展望了这些信息在基因发现、网络工程和基因组育种中的潜在应用。
Dissecting the upstream regulatory architecture of rice genes and their cognate regulator proteins is at the core of network biology and its applications to comparative functional genomics. With the rapidly advancing comparative genomics resources in the genus Oryza, a reference genome annotation that defines the various cis-elements and trans-acting factors that interface each gene locus with various intrinsic and extrinsic signals for growth, development, reproduction and adaptation must be established to facilitate the understanding of phenotypic variation in the context of regulatory networks. Such information is also important to establish the foundation for mining non-coding sequence variation that defines novel alleles and epialleles across the enormous phenotypic diversity represented in rice germplasm. This review presents a synthesis of the state of knowledge and consensus trends regarding the various cis-acting and trans-acting components that define spatio-temporal regulation of rice genes based on representative examples from both foundational studies in other model and non-model plants, and more recent studies in rice. The goal is to summarize the baseline for systematic upstream sequence annotation of the rapidly advancing genome sequence resources in Oryza in preparation for genus-wide functional genomics. Perspectives on the potential applications of such information for gene discovery, network engineering and genomics-enabled rice breeding are also discussed.
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影响因子：
10.5
作者：
Butler, JEF;Kadonaga, JT
通讯作者：
Kadonaga, JT
影响因子：
4.4
作者：
Cheng C;Yun KY;Ressom HW;Mohanty B;Bajic VB;Jia Y;Yun SJ;de los Reyes BG
通讯作者：
de los Reyes BG
影响因子：
3.5
作者：
Bodenhausen, Natacha;Reymond, Philippe
通讯作者：
Reymond, Philippe
DOI：
10.1073/pnas.92.10.4114
发表时间：
1995-05-09
影响因子：
11.1
作者：
CREELMAN, RA;MULLET, JE
通讯作者：
MULLET, JE
影响因子：
11.4
作者：
BARANOWSKIJ, N;FROHBERG, C;WILLMITZER, L
通讯作者：
WILLMITZER, L