RiceAntherNet: a gene co‐expression network for identifying anther and pollen development genes

In plants, normal anther and pollen development involves many important biological events and complex molecular regulatory coordination. Understanding gene regulatory relationships during male reproductive development is essential for fundamental biology and crop breeding. In this work, we developed a rice gene co‐expression network for anther development (RiceAntherNet) that allows prediction of gene regulatory relationships during pollen development. RiceAntherNet was generated from 57 rice anther tissue microarrays across all developmental stages. The microarray datasets from nine rice male sterile mutants, including msp1‐4, ostdl1a, gamyb‐2, tip2, udt1‐1, tdr, eat1‐1, ptc1 and mads3‐4, were used to explore and test the network. Among the changed genes, three clades showing differential expression patterns were constructed to identify genes associated with pollen formation. Many of these have known roles in pollen development, for example, seven genes in Clade 1 (OsABCG15, OsLAP5, OsLAP6, DPW, CYP703A3, OsNP1 and OsCP1) are involved in rice pollen wall formation. Furthermore, Clade 1 contained 12 genes whose predicted orthologs in Arabidopsis have been reported as key during pollen development and may play similar roles in rice. Genes in Clade 2 are expressed earlier than Clade 1 (anther stages 2–9), while genes in Clade 3 are expressed later (stages 10–12). RiceAntherNet serves as a valuable tool for identifying novel genes during plant anther and pollen development. A website is provided ( https://www.cpib.ac.uk/anther/riceindex.html ) to present the expression profiles for gene characterization. This will assist in determining the key relationships between genes, thus enabling characterization of critical genes associated with anther and pollen regulatory networks.     

水稻花粉发育的分子机理

水稻的小孢子母细胞在花粉囊中进行减数分裂产生小孢子, 小孢子进一步发育成花粉粒。当花粉成熟时, 花粉粒从花粉囊中释放出来进行受精。分子生物学的研究已经发现了一些参与这一过程的基因, 包括控制花粉囊组织的分化、小孢子母细胞的减数分裂、小孢子的发育和花药的开裂等。本文旨在总结水稻花粉发育过程及其调控分子机制的研究进展。     

水稻花粉发育的分子机理

水稻的小孢子母细胞在花粉囊中进行减数分裂产生小孢子,小孢子进一步发育成花粉粒。当花粉成熟时,花粉粒从花粉囊中释放出来进行受精。分子生物学的研究已经发现了一些参与这一过程的基因,包括控制花粉囊组织的分化、小孢子母细胞的减数分裂、小孢子的发育和花药的开裂等。本文旨在总结水稻花粉发育过程及其调控分子机制的研究进展。     

多组学整合网络: 一把精准解码玉米功能基因组的钥匙

高通量组学技术的快速发展使生命科学进入大数据时代。科学家们从基因组、转录组、蛋白质组和代谢组等多组学数据中剥茧抽丝, 逐步揭示生物体内复杂而巧妙的调控网络。近日, 华中农业大学李林课题组联合杨芳课题组和严建兵课题组构建了玉米(Zea mays)首个多组学整合网络。该网络包括3万个玉米基因在三维基因组水平、转录水平、翻译水平和蛋白质互作水平的调控关系, 由280万个网络连接组成, 构成1 412个调控模块。利用该整合网络, 研究团队预测并证实了5个调控玉米分蘖、侧生器官发育和籽粒皱缩的新基因。进一步结合机器学习方法, 他们预测出2 651个影响玉米开花期的候选基因, 鉴定到8条可能参与玉米开花期的调控通路, 并利用基因编辑技术和EMS突变体证实了20个候选基因的生物学功能。此外, 通过对整合调控网络的进化分析, 他们发现玉米两套亚基因组在转录组、翻译组和蛋白互作组水平上存在渐进式的功能分化。这套集合多组学数据构建的整合网络图谱是玉米功能基因组学研究的重大进展, 为玉米重要性状新基因克隆、分子调控通路解析和玉米基因组进化分析提供了新工具, 是解锁玉米功能基因组学的一把新钥匙。     

Systematic discovery of functional modules and context-specific functional annotation of human genome

MOTIVATION: The rapid accumulation of microarray datasets provides unique opportunities to perform systematic functional characterization of the human genome. We designed a graph-based approach to integrate cross-platform microarray data, and extract recurrent expression patterns. A series of microarray datasets can be modeled as a series of co-expression networks, in which we search for frequently occurring network patterns. The integrative approach provides three major advantages over the commonly used microarray analysis methods: (1) enhance signal to noise separation (2) identify functionally related genes without co-expression and (3) provide a way to predict gene functions in a context-specific way. RESULTS: We integrate 65 human microarray datasets, comprising 1105 experiments and over 11 million expression measurements. We develop a data mining procedure based on frequent itemset mining and biclustering to systematically discover network patterns that recur in at least five datasets. This resulted in 143,401 potential functional modules. Subsequently, we design a network topology statistic based on graph random walk that effectively captures characteristics of a gene's local functional environment. Function annotations based on this statistic are then subject to the assessment using the random forest method, combining six other attributes of the network modules. We assign 1126 functions to 895 genes, 779 known and 116 unknown, with a validation accuracy of 70%. Among our assignments, 20% genes are assigned with multiple functions based on different network environments. AVAILABILITY: http://zhoulab.usc.edu/ContextAnnotation.     

拟南芥花药基因的共表达分析

运用图论中最大团算法,对ATTED-Ⅱ数据库中提供的拟南芥共表达数据进行分析,为进一步研究基因功能提供了较为可靠的数据。文中提出的算法首先根据芯片数据鉴定拟南芥花药基因,然后以ATTED-Ⅱ数据库为基础构建每一个花药基因的共表达网络,最后利用最大团算法从共表达网络中挖掘共表达数据。基于这种方法,系统地分析了每一个拟南芥花药基因的共表达情况,有助于拟南芥花药发育分子机理和基因转录调控的深入研究。实验验证这种方法对拟南芥花药共表达基因的提取十分有效。     

Microarray Analysis of Gene Expression Involved in Anther Development in rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.)

In flowering plants, anthers bear male gametophytes whose development is regulated by the elaborate coordination of many genes. In addition, both gibberellic acid (GA₃) and jasmonic acid (JA) play important roles in anther development and pollen fertility. To facilitate the analysis of anther development genes and how GA₃ and JA regulate anther development, we performed microarray experiments using a 10-K cDNA microarray with probes derived from seedlings, meiotic anthers, mature anthers and GA₃- or JA-treated suspension cells of rice. The expression level change of 2155 genes was significantly (by 2-fold or greater) detected in anthers compared with seedlings. Forty-seven genes, representing genes with potential function in cell cycle and cell structure regulation, hormone response, photosynthesis, stress resistance and metabolism, were differentially expressed in meiotic and mature anthers. Moreover, 314 genes responded to either GA₃ or JA treatment, and 24 GA₃- and 82 JA-responsive genes showed significant changes in expression between meiosis and the mature anther stages. RT-PCR demonstrated that gene y656d05 was not only highly expressed in meiotic anthers but also induced by GA₃. Strong RNA signals of y656d05 were detected in pollen mother cells and tapetum in in situ hybridization. Further characterization of these candidate genes can contribute to the understanding of the molecular mechanism of anther development and the involvement of JA and GA₃ signals in the control of anther development in rice.     

Identifying candidate genes for wood formation in poplar based on microarray network analysis and graph theory

In poplar, genetic research on wood properties is very important for the improvement of wood quality. Studies of wood formation genes at each developmental stage using modern biotechnology have often been limited to several genes or gene families. Because of the complex regulatory network involved in the co-expression and interactions of thousands of genes, however, the genetic mechanisms of wood formation must be surveyed on a genome-wide scale. In this study, we identified wood formation-related genes using a differentially co-expressed (DCE) gene subset approach based on biological networks inferred from microarray data. Gene co-expression networks in leaf, root, and wood tissues were first constructed and topologically analyzed using microarray data collected from the Gene Expression Omnibus. The DCE gene modules in wood-forming tissue were then detected based on graph theory, which was followed by gene ontology (GO) enrichment analysis and GO annotation of probe sets. Finally, 72 probe sets were identified in the largest cohesive subgroup of the DCE gene network in wood tissue, with most of the probe sets associated with wood formation-related biological processes and GO cellular component categories. The approach described in this paper provides an effective strategy to identify wood formation genes in poplar and should contribute to the better understanding of the genetic and molecular mechanisms underlying wood properties in trees.