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Transcriptional regulatory network of WOX11 is involved in the control of crown root development, cytokinin signals, and redox in rice.

ABSTRACT: The rice root system is mainly composed of post-embryonic shoot-borne roots called crown roots. WOX11, encoding a WUSCHEL-related homeobox domain transcription factor, is a key regulator of crown root growth and development in rice (Oryza sativa. L). In addition to specifically activating crown root development, WOX11 is also involved in lateral root initiation, root hair formation, and abiotic stresses. However, the gene regulatory network downstream of WOX11 remains largely unknown. Here, we studied the transcriptome of wox11 root tips by RNA-Seq and determined direct WOX11-binding targets by bioinformatic and biochemical analysis. The transcriptomic analysis revealed 664 differentially expressed genes, which covered a wide range of functions related to root development, cytokinin homeostasis/signaling, stress response, and redox metabolic processes. Bioinformatic analysis also revealed that the WOX11-binding motif was distributed over 41% (273/664) of the differentially expressed genes, and was mostly enriched in the promoter and intron regions. We used qRT-PCR and/or in situ hybridization to confirm co-expression of some of the WOX11-regulated genes in crown root development. We also used electrophoretic mobility shift assay and chromatin immunoprecipitation with anti-WOX11 antibody to validate direct regulation of these genes by WOX11. The analysis identified several genes that acted downstream of WOX11 in controlling crown root formation, cytokinin signaling, stress response, and redox metabolism. This work built a hierarchical regulatory model of WOX11 in rice crown root development.

SUBMITTER: Jiang W

PROVIDER: S-EPMC5853245 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature

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Transcriptional regulatory network of WOX11 is involved in the control of crown root development, cytokinin signals, and redox in rice.

Jiang Wei W Zhou Shaoli S Zhang Qian Q Song Huazhi H Zhou Dao-Xiu DX Zhao Yu Y

Journal of experimental botany 20170501 11

The rice root system is mainly composed of post-embryonic shoot-borne roots called crown roots. WOX11, encoding a WUSCHEL-related homeobox domain transcription factor, is a key regulator of crown root growth and development in rice (Oryza sativa. L). In addition to specifically activating crown root development, WOX11 is also involved in lateral root initiation, root hair formation, and abiotic stresses. However, the gene regulatory network downstream of WOX11 remains largely unknown. Here, we s ...[more]

PMID: 28830102

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Project 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 50 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.

Dataset Information

Transcriptional regulatory network of WOX11 is involved in the control of crown root development, cytokinin signals, and redox in rice.

Publications

Transcriptional regulatory network of WOX11 is involved in the control of crown root development, cytokinin signals, and redox in rice.

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