{"title":"拟南芥转录组分析预测干旱反应中的胁迫长度特异性调控网络","authors":"S. Akhtartavan, M. Talebi","doi":"10.21475/poj.11.01.18.pne735","DOIUrl":null,"url":null,"abstract":"Drought stress is one of the major environmental factors impairing crops productivity worldwide. Plants use various regulatory genes to reprogram genome activities to cope with such stresses. Among regulatory genes, transcription factors (TFs) function as terminal transducers and directly regulate the expression of wide spectrum of downstream genes. Multiplicity of the TF families and the complex interactions between TFs and cis-elements on the promoters of target genes as well as cross-talk between TFs in response to stress indicate the complexity of signaling networks involved in plant stress responses. This study aimed to use computational and statistical approaches to analyze a microarray dataset from Arabidopsis which covering different time periods of drought stress. After identifying and functional grouping of differentially expressed gens (DEGs), genes encoded TFs were determined and networked based on gene set enrichment analysis (GSE). Hierarchical regulatory network in each condition was assigned. After that, networks were used to conduct network topology analysis. Results indicated an obvious orientation in genome activity toward response to different cues; energy homeostasis and photosynthesis stability was occurred under drought stress. Also, 3787, 2931 and 5115 genes were differentially expressed under the early, moderate and prolonged drought stress, respectively, among them, 169, 140 and 261 TF were identified. Analysis of constructed regulatory networks of each drought condition revealed that plant recruits different but somewhat overlapping strategies to cope with stress in a long period of time. In each drought period, specific or common signaling pathways are activated using several numbers of transcription factors. It seems that among all identified TFs, ARR5, ARR6, ABF3, MYB29, MYB76 and SIGs genes are good candidate to manipulate plant stress tolerance.","PeriodicalId":54602,"journal":{"name":"Plant Omics","volume":"11 1","pages":"1-9"},"PeriodicalIF":0.0000,"publicationDate":"2018-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"1","resultStr":"{\"title\":\"Transcriptome analysis of Arabidopsis to predict stress length-specific regulatory networks involved in drought response\",\"authors\":\"S. Akhtartavan, M. Talebi\",\"doi\":\"10.21475/poj.11.01.18.pne735\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Drought stress is one of the major environmental factors impairing crops productivity worldwide. Plants use various regulatory genes to reprogram genome activities to cope with such stresses. Among regulatory genes, transcription factors (TFs) function as terminal transducers and directly regulate the expression of wide spectrum of downstream genes. Multiplicity of the TF families and the complex interactions between TFs and cis-elements on the promoters of target genes as well as cross-talk between TFs in response to stress indicate the complexity of signaling networks involved in plant stress responses. This study aimed to use computational and statistical approaches to analyze a microarray dataset from Arabidopsis which covering different time periods of drought stress. After identifying and functional grouping of differentially expressed gens (DEGs), genes encoded TFs were determined and networked based on gene set enrichment analysis (GSE). Hierarchical regulatory network in each condition was assigned. After that, networks were used to conduct network topology analysis. Results indicated an obvious orientation in genome activity toward response to different cues; energy homeostasis and photosynthesis stability was occurred under drought stress. Also, 3787, 2931 and 5115 genes were differentially expressed under the early, moderate and prolonged drought stress, respectively, among them, 169, 140 and 261 TF were identified. Analysis of constructed regulatory networks of each drought condition revealed that plant recruits different but somewhat overlapping strategies to cope with stress in a long period of time. In each drought period, specific or common signaling pathways are activated using several numbers of transcription factors. It seems that among all identified TFs, ARR5, ARR6, ABF3, MYB29, MYB76 and SIGs genes are good candidate to manipulate plant stress tolerance.\",\"PeriodicalId\":54602,\"journal\":{\"name\":\"Plant Omics\",\"volume\":\"11 1\",\"pages\":\"1-9\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2018-02-20\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"1\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Plant Omics\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.21475/poj.11.01.18.pne735\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"Agricultural and Biological Sciences\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Plant Omics","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.21475/poj.11.01.18.pne735","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"Agricultural and Biological Sciences","Score":null,"Total":0}
Transcriptome analysis of Arabidopsis to predict stress length-specific regulatory networks involved in drought response
Drought stress is one of the major environmental factors impairing crops productivity worldwide. Plants use various regulatory genes to reprogram genome activities to cope with such stresses. Among regulatory genes, transcription factors (TFs) function as terminal transducers and directly regulate the expression of wide spectrum of downstream genes. Multiplicity of the TF families and the complex interactions between TFs and cis-elements on the promoters of target genes as well as cross-talk between TFs in response to stress indicate the complexity of signaling networks involved in plant stress responses. This study aimed to use computational and statistical approaches to analyze a microarray dataset from Arabidopsis which covering different time periods of drought stress. After identifying and functional grouping of differentially expressed gens (DEGs), genes encoded TFs were determined and networked based on gene set enrichment analysis (GSE). Hierarchical regulatory network in each condition was assigned. After that, networks were used to conduct network topology analysis. Results indicated an obvious orientation in genome activity toward response to different cues; energy homeostasis and photosynthesis stability was occurred under drought stress. Also, 3787, 2931 and 5115 genes were differentially expressed under the early, moderate and prolonged drought stress, respectively, among them, 169, 140 and 261 TF were identified. Analysis of constructed regulatory networks of each drought condition revealed that plant recruits different but somewhat overlapping strategies to cope with stress in a long period of time. In each drought period, specific or common signaling pathways are activated using several numbers of transcription factors. It seems that among all identified TFs, ARR5, ARR6, ABF3, MYB29, MYB76 and SIGs genes are good candidate to manipulate plant stress tolerance.
期刊介绍:
Plant OMICS is an international, peer-reviewed publication that gathers and disseminates fundamental and applied knowledge in almost all area of molecular plant and animal biology, particularly OMICS-es including:
Coverage extends to the most corners of plant and animal biology, including molecular biology, genetics, functional and non-functional molecular breeding and physiology, developmental biology, and new technologies such as vaccines. This journal also covers the combination of many areas of molecular plant and animal biology. Plant Omics is also exteremely interested in molecular aspects of stress biology in plants and animals, including molecular physiology.