Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice
MYB transcription factor (TF) is one of the largest TF families and regulates defense responses to various stresses, hormone signaling as well as many metabolic and developmental processes in plants. Understanding these regulatory hierarchies of gene expression networks in response to developmental...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2015-12-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2015.01157/full |
| _version_ | 1818344235091361792 |
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| author | Shuchi eSmita Shuchi eSmita AMIT eKATIYAR AMIT eKATIYAR Dev Mani ePandey Viswanathan eChinnusamy Kailash C BansaL |
| author_facet | Shuchi eSmita Shuchi eSmita AMIT eKATIYAR AMIT eKATIYAR Dev Mani ePandey Viswanathan eChinnusamy Kailash C BansaL |
| author_sort | Shuchi eSmita |
| collection | DOAJ |
| description | MYB transcription factor (TF) is one of the largest TF families and regulates defense responses to various stresses, hormone signaling as well as many metabolic and developmental processes in plants. Understanding these regulatory hierarchies of gene expression networks in response to developmental and environmental cues is a major challenge due to the complex interactions between the genetic elements. Correlation analyses are useful to unravel co-regulated gene pairs governing biological process as well as identification of new candidate hub genes in response to these complex processes. High throughput expression profiling data are highly useful for construction of co-expression networks. In the present study, we utilized transcriptome data for comprehensive regulatory network studies of MYB TFs by top down and guide gene approaches. More than 50% of OsMYBs were strongly correlated under fifty experimental conditions with 51 hub genes via top down approach. Further, clusters were identified using Markov Clustering (MCL). To maximize the clustering performance, parameter evaluation of the MCL inflation score (I) was performed in terms of enriched GO categories by measuring F-score. Comparison of co-expressed cluster and clads analyzed from phylogenetic analysis signifies their evolutionarily conserved co-regulatory role. We utilized compendium of known interaction and biological role with Gene Ontology enrichment analysis to hypothesize function of coexpressed OsMYBs. In the other part, the transcriptional regulatory network analysis by guide gene approach revealed 40 putative targets of 26 OsMYB TF hubs with high correlation value utilizing 815 microarray data. The putative targets with MYB-binding cis-elements enrichment in their promoter region, functional co-occurrence as well as nuclear localization supports our finding. Specially, enrichment of MYB binding regions involved in drought-inducibility implying their regulatory role in drought response in rice. Thus, the co-regulatory network analysis facilitated the identification of complex OsMYB regulatory networks, and candidate target regulon genes of selected guide MYB genes. The results contribute to the candidate gene screening, and experimentally testable hypotheses for potential regulatory MYB TFs, and their targets under stress conditions. |
| first_indexed | 2024-12-13T16:43:15Z |
| format | Article |
| id | doaj.art-88a8598df9454e129b570ba5afe735e7 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-13T16:43:15Z |
| publishDate | 2015-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-88a8598df9454e129b570ba5afe735e72022-12-21T23:38:14ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2015-12-01610.3389/fpls.2015.01157170915Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in RiceShuchi eSmita0Shuchi eSmita1AMIT eKATIYAR2AMIT eKATIYAR3Dev Mani ePandey4Viswanathan eChinnusamy5Kailash C BansaL6 Indian Agricultural Research Institute CampusDepartment of Biotechnology Indian Agricultural Research Institute CampusDepartment of BiotechnologyDepartment of Biotechnology Indian Agricultural Research Institute Indian Agricultural Research Institute CampusMYB transcription factor (TF) is one of the largest TF families and regulates defense responses to various stresses, hormone signaling as well as many metabolic and developmental processes in plants. Understanding these regulatory hierarchies of gene expression networks in response to developmental and environmental cues is a major challenge due to the complex interactions between the genetic elements. Correlation analyses are useful to unravel co-regulated gene pairs governing biological process as well as identification of new candidate hub genes in response to these complex processes. High throughput expression profiling data are highly useful for construction of co-expression networks. In the present study, we utilized transcriptome data for comprehensive regulatory network studies of MYB TFs by top down and guide gene approaches. More than 50% of OsMYBs were strongly correlated under fifty experimental conditions with 51 hub genes via top down approach. Further, clusters were identified using Markov Clustering (MCL). To maximize the clustering performance, parameter evaluation of the MCL inflation score (I) was performed in terms of enriched GO categories by measuring F-score. Comparison of co-expressed cluster and clads analyzed from phylogenetic analysis signifies their evolutionarily conserved co-regulatory role. We utilized compendium of known interaction and biological role with Gene Ontology enrichment analysis to hypothesize function of coexpressed OsMYBs. In the other part, the transcriptional regulatory network analysis by guide gene approach revealed 40 putative targets of 26 OsMYB TF hubs with high correlation value utilizing 815 microarray data. The putative targets with MYB-binding cis-elements enrichment in their promoter region, functional co-occurrence as well as nuclear localization supports our finding. Specially, enrichment of MYB binding regions involved in drought-inducibility implying their regulatory role in drought response in rice. Thus, the co-regulatory network analysis facilitated the identification of complex OsMYB regulatory networks, and candidate target regulon genes of selected guide MYB genes. The results contribute to the candidate gene screening, and experimentally testable hypotheses for potential regulatory MYB TFs, and their targets under stress conditions.http://journal.frontiersin.org/Journal/10.3389/fpls.2015.01157/fullNetwork analysisco-expressionriceabiotic stressMYB TFco-regulatory |
| spellingShingle | Shuchi eSmita Shuchi eSmita AMIT eKATIYAR AMIT eKATIYAR Dev Mani ePandey Viswanathan eChinnusamy Kailash C BansaL Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice Frontiers in Plant Science Network analysis co-expression rice abiotic stress MYB TF co-regulatory |
| title | Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice |
| title_full | Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice |
| title_fullStr | Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice |
| title_full_unstemmed | Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice |
| title_short | Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice |
| title_sort | transcriptional regulatory network analysis of myb transcription factor family genes in rice |
| topic | Network analysis co-expression rice abiotic stress MYB TF co-regulatory |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2015.01157/full |
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