Mapping and Developmental Expression Analysis of the WD-Repeat Gene Preb

The inositol phospholipid signaling system mediates plant growth, development, and responses to adverse conditions. Diacylglycerol kinase (DGK) is one of the key enzymes in the phosphoinositide-cycle (PI-cycle), which catalyzes the phosphorylation of diacylglycerol (DAG) to form phosphatidic acid (PA). To date, comprehensive genomic and functional analyses of DGKs have not been reported in wheat. In this study, 24 DGK gene family members from the wheat genome (TaDGKs) were identified and analyzed. Each putative protein was found to consist of a DGK catalytic domain and an accessory domain. The analyses of phylogenetic and gene structure analyses revealed that each TaDGK gene could be grouped into clusters I, II, or III. In each phylogenetic subgroup, the TaDGKs demonstrated high conservation of functional domains, for example, of gene structure and amino acid sequences. Four coding sequences were then cloned from Chinese Spring wheat. Expression analysis of these four genes revealed that each had a unique spatial and developmental expression pattern, indicating their functional diversification across wheat growth and development processes. Additionally, TaDGKs were also prominently up-regulated under salt and drought stresses, suggesting their possible roles in dealing with adverse environmental conditions. Further cis-regulatory elements analysis elucidated transcriptional regulation and potential biological functions. These results provide valuable information for understanding the putative functions of DGKs in wheat and support deeper functional analysis of this pivotal gene family. The 24 TaDGKs identified and analyzed in this study provide a strong foundation for further exploration of the biological function and regulatory mechanisms of TaDGKs in response to environmental stimuli.

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Genomic profiling and expression analysis of the diacylglycerol kinase gene family in heterologous hexaploid wheat

10.21203/rs.3.rs-49275/v1 ◽

2020 ◽

Author(s):

Xiaowei Jia ◽

Xuyang Si ◽

Yangyang Jia ◽

Hongyan Zhang ◽

Shijun Tian ◽

...

Keyword(s):

Gene Family ◽

Expression Analysis ◽

Gene Structure ◽

Hexaploid Wheat ◽

Catalytic Domain ◽

Diacylglycerol Kinase ◽

Regulatory Elements ◽

Amino Acid Sequences ◽

Developmental Expression ◽

Chinese Spring Wheat

Abstract Background The inositol phospholipid signaling system, which is based on the metabolism of phosphoinositide (PI), mediates plant growth, development, and responses to adversity. Diacylglycerol kinase (DGK) is one of the key enzymes in the PI-cycle, which catalyzes the phosphorylation of diacylglycerol (DAG) to form phosphatidic acid (PA). To date, comprehensive genomic and functional analyses of DGK genes have not been reported in wheat. Results In this study, 20 DGK gene family members from the heterologous hexaploid wheat genome (TaDGKs) were identified and analyzed. Each putative protein was found to consist of a DGK catalytic domain and a accessory domain. The analyses of phylogenetic and gene structure revealed that each TaDGK gene could be grouped to clusters I, II, or III. In each phylogenetic subgroup, the TaDGKs demonstrated high conservation in functional domains, for example gene structure and amino acid sequences. By cloning, four coding sequences were ascertained from Chinese spring wheat. Expression analysis of these four genes revealed that each had a unique spatial and developmental expression pattern, indicating their functional diversification in wheat growth and development processes. Additionally, TaDGKs were also prominently up-regulated express under salt and drought stresses, suggesting their possible roles in dealing with adversity environment. Further cis-regulatory elements analysis elucidated transcriptional regulation and potential biological functions. Conclusions These results provide valuable information for understanding the putative functions of DGK genes in wheat, and conduce to ulterior functional analysis of this pivotal gene family. The 20 TaDGKs identified and analyzed in this study provide a strong foundation for further exploration of the biological function and regulatory mechanisms of TaDGKs in response to environmental stimuli.

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The Drosophila melanogaster gene for the NADH:ubiquinone oxidoreductase acyl carrier protein: developmental expression analysis and evidence for alternatively spliced forms

MGG Molecular & General Genetics ◽

10.1007/s004380050012 ◽

1999 ◽

Vol 261 (4-5) ◽

pp. 690-697 ◽

Cited By ~ 13

Author(s):

G. Ragone ◽

R. Caizzi ◽

R. Moschetti ◽

P. Barsanti ◽

V. De Pinto ◽

...

Keyword(s):

Drosophila Melanogaster ◽

Expression Analysis ◽

Acyl Carrier Protein ◽

Developmental Expression ◽

Nadh:Ubiquinone Oxidoreductase ◽

Carrier Protein ◽

Alternatively Spliced

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Developmental expression analysis of murine autotaxin (ATX)

Mechanisms of Development ◽

10.1016/s0925-4773(99)00048-9 ◽

1999 ◽

Vol 84 (1-2) ◽

pp. 121-125 ◽

Cited By ~ 58

Author(s):

Dietmar Bächner ◽

Marion Ahrens ◽

Nicole Betat ◽

Dietmar Schröder ◽

Gerhard Gross

Keyword(s):

Expression Analysis ◽

Developmental Expression

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Cloning and developmental expression analysis of prokineticin 2 and its receptor PKR2 in the Syrian hamster surpachiasmatic nucleus

Brain Research ◽

10.1016/j.brainres.2009.03.021 ◽

2009 ◽

Vol 1271 ◽

pp. 18-26 ◽

Cited By ~ 5

Author(s):

Yaoting Ji ◽

Xiaodong Li

Keyword(s):

Expression Analysis ◽

Syrian Hamster ◽

Developmental Expression ◽

Prokineticin 2

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Association of CDH11 with Autism Spectrum Disorder Revealed by Matched-gene Co-expression Analysis and Mouse Behavioral Studies

Neuroscience Bulletin ◽

10.1007/s12264-021-00770-0 ◽

2021 ◽

Author(s):

Nan Wu ◽

Yue Wang ◽

Jing-Yan Jia ◽

Yi-Hsuan Pan ◽

Xiao-Bing Yuan

Keyword(s):

Autism Spectrum Disorder ◽

Expression Analysis ◽

Gene Prediction ◽

Expression Profiles ◽

Autism Spectrum ◽

Spectrum Disorder ◽

Developmental Expression ◽

Behavioral Alterations ◽

Risk Genes ◽

Behavioral Studies

AbstractA large number of putative risk genes for autism spectrum disorder (ASD) have been reported. The functions of most of these susceptibility genes in developing brains remain unknown, and causal relationships between their variation and autism traits have not been established. The aim of this study was to predict putative risk genes at the whole-genome level based on the analysis of gene co-expression with a group of high-confidence ASD risk genes (hcASDs). The results showed that three gene features – gene size, mRNA abundance, and guanine-cytosine content – affect the genome-wide co-expression profiles of hcASDs. To circumvent the interference of these features in gene co-expression analysis, we developed a method to determine whether a gene is significantly co-expressed with hcASDs by statistically comparing the co-expression profile of this gene with hcASDs to that of this gene with permuted gene sets of feature-matched genes. This method is referred to as "matched-gene co-expression analysis" (MGCA). With MGCA, we demonstrated the convergence in developmental expression profiles of hcASDs and improved the efficacy of risk gene prediction. The results of analysis of two recently-reported ASD candidate genes, CDH11 and CDH9, suggested the involvement of CDH11, but not CDH9, in ASD. Consistent with this prediction, behavioral studies showed that Cdh11-null mice, but not Cdh9-null mice, have multiple autism-like behavioral alterations. This study highlights the power of MGCA in revealing ASD-associated genes and the potential role of CDH11 in ASD.

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