The Promoter Signatures in Rice LEA Genes Can Be Used to Build a Co-expressing LEA Gene Network

Meier, Stuart; Gehring, Chris; MacPherson, Cameron Ross; Kaur, Mandeep; Maqungo, Monique; Reuben, Sheela; Muyanga, Samson; Shih, Ming Der; Wei, Fu‐Jin; Wanchana, Samart; Mauleon, Ramil; Radovanović, Aleksandar; Bruskiewich, Richard; Tanaka, Tsuyoshi; Mohanty, Bijayalaxmi; Itoh, Takeshi; Wing, Rod A.; Gojobori, Takashi; Sasaki, Takuji; Swarup, Sanjay; Hsing, Y. I.; Bajic, Vladimir B.

doi:10.1007/s12284-008-9017-4

Cited by 15 publications

(16 citation statements)

References 35 publications

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“…Circadian element, which is involved in circadian control, was abundantly found in the promoter region of chickpea and soybean Aux/IAA genes (Supplementary Table S6 ), potentially indicating that they may have a distinct diurnal expression pattern. In Arabidopsis and rice, a class of element defined by the core motif ‘(a/g)CCGAC’ named as dehydration responsive element/C-repeat (DRE/CRT) was reported for drought, low temperature, and salt inducible expression ( Yamaguchi-Shinozaki and Shinozaki, 1994 ; Meier et al, 2008 ). Interestingly, we also found this motif in many of the CaIAA and GmIAA gene promoters (Supplementary Table S6 ), indicating their role under abiotic stress conditions.…”

Section: Resultsmentioning

confidence: 99%

Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean

Singh

Jain

2015

Front. Plant Sci.

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Auxin plays a central role in many aspects of plant growth and development. Auxin/Indole-3-Acetic Acid (Aux/IAA) genes cooperate with several other components in the perception and signaling of plant hormone auxin. An investigation of chickpea and soybean genomes revealed 22 and 63 putative Aux/IAA genes, respectively. These genes were classified into six subfamilies on the basis of phylogenetic analysis. Among 63 soybean Aux/IAA genes, 57 (90.5%) were found to be duplicated via whole genome duplication (WGD)/segmental events. Transposed duplication played a significant role in tandem arrangements between the members of different subfamilies. Analysis of Ka/Ks ratio of duplicated Aux/IAA genes revealed purifying selection pressure with restricted functional divergence. Promoter sequence analysis revealed several cis-regulatory elements related to auxin, abscisic acid, desiccation, salt, seed, and endosperm, indicating their role in development and stress responses. Expression analysis of chickpea and soybean Aux/IAA genes in various tissues and stages of development demonstrated tissue/stage specific differential expression. In soybean, at least 16 paralog pairs, duplicated via WGD/segmental events, showed almost indistinguishable expression pattern, but eight pairs exhibited significantly diverse expression patterns. Under abiotic stress conditions, such as desiccation, salinity and/or cold, many Aux/IAA genes of chickpea and soybean revealed differential expression. qRT-PCR analysis confirmed the differential expression patterns of selected Aux/IAA genes in chickpea. The analyses presented here provide insights on putative roles of chickpea and soybean Aux/IAA genes and will facilitate elucidation of their precise functions during development and abiotic stress responses.

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Section: Resultsmentioning

confidence: 99%

Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean

Singh

Jain

2015

Front. Plant Sci.

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“…As many LEA genes share similar expression characteristics (Tunnacliffe and Wise, 2007; Meier et al. , 2008), we analyzed the expression patterns of other LEA genes.…”

Section: Resultsmentioning

confidence: 99%

The rice transcription factor IDEF1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes

et al. 2009

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SUMMARYHigher plants maintain iron homeostasis by regulating the expression of iron (Fe)-related genes in accordance with Fe availability. The transcription factor IDEF1 regulates the response to Fe deficiency in Oryza sativa (rice) by recognizing CATGC sequences within the Fe deficiency-responsive cis-acting element IDE1. To investigate the function of IDEF1 in detail, we analyzed the response to Fe deficiency in transgenic rice plants exhibiting induced or repressed IDEF1 expression. Fe-deficiency treatment in hydroponic culture revealed that IDEF1 knock-down plants are susceptible to early-stage Fe deficiency, in contrast to IDEF1-induced plants. Timecourse expression analyses using quantitative reverse-transcriptase PCR revealed that the IDEF1 expression level was positively correlated with the level of induction of the Fe utilization-related genes OsIRO2, OsYSL15, OsIRT1, OsYSL2, OsNAS1, OsNAS2, OsNAS3 and OsDMAS1, just after the onset of Fe starvation. However, this overall transactivation mediated by IDEF1 became less evident in subsequent stages. Microarray and in-silico analyses revealed that genes positively regulated by IDEF1, especially at the early stage, exhibit overrepresentation of CATGC and IDE1-like elements within the proximal promoter regions. These results indicate the existence of early and subsequent responses to Fe deficiency, with the former requiring IDEF1 more specifically. Proximal regions of IDEF1-regulated gene promoters also showed enrichment of RY elements (CATGCA), which regulate gene expression during seed maturation. The expression of several genes encoding late embryogenesis abundant proteins, including Osem, was induced in Fe-deficient roots and/or leaves in an IDEF1-dependent manner, suggesting a possible function of seed maturation-related genes in Fe-deficient vegetative organs.

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“…Advances in high throughput omics technologies complemented with comprehensive system biology approaches offers many ways to identify gene networks that operate in a given time or a biological processes. Several TF families have been explored for regulatory network study (Meier et al, 2008 ; Berri et al, 2009 ; Lim et al, 2010 ; Ouyang et al, 2012 ), while the MYB family network has not been explored in spite of its important roles in several biological processes. In the present study, we applied co-expression network based analysis, to dissect MYB transcriptional regulatory networks and their correlated links in rice.…”

Section: Introductionmentioning

confidence: 99%

Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice

et al. 2015

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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.

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The Promoter Signatures in Rice LEA Genes Can Be Used to Build a Co-expressing LEA Gene Network

Cited by 15 publications

References 35 publications

Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean

Genome-wide survey and comprehensive expression profiling of Aux/IAA gene family in chickpea and soybean

The rice transcription factor IDEF1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes

Transcriptional Regulatory Network Analysis of MYB Transcription Factor Family Genes in Rice

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