Comprehensive analysis of the transcription of starch synthesis genes and the transcription factor RSR1 in wheat (Triticum aestivum) endosperm

Genome ◽  
2013 ◽  
Vol 56 (2) ◽  
pp. 115-122 ◽  
Author(s):  
Guo-Zhang Kang ◽  
Wei Xu ◽  
Guo-Qin Liu ◽  
Xiao-Qi Peng ◽  
Tian-Cai Guo
Keyword(s):  
Triticum Aestivum ◽  
Transcription Factor ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Starch Synthesis ◽  
Grain Development ◽  
Wheat Endosperm ◽  
Group 2 ◽  
Endosperm Starch ◽  
Late Stages

The cDNA sequences of 26 starch synthesis genes were identified in common wheat (Triticum aestivum L.), and their transcript levels were measured using quantitative real-time RT–PCR to assess the function of individual genes and the regulatory mechanism in wheat endosperm. The expression patterns of 26 genes in wheat endosperm were classified into three groups. The genes in group 1 were richly expressed in the early stage of grain development and may be involved in the construction of fundamental cell machinery, synthesis of glucan primers, and initiation of starch granules. The genes in group 2 were highly expressed during the middle and late stages of grain development, and their expression profiles were similar to the accumulation rate of endosperm starch; these genes are presumed to play a crucial role in starch production. The genes in group 3 were scantily expressed throughout the grain development period and might be associated with transitory starch synthesis. Transcripts of the negative transcription factor TaRSR1 were high at the early and late stages of grain development but low during the middle stage. The expression pattern of TaRSR1 was almost opposite to those of the group 2 starch synthesis genes, indicating that TaRSR1 might negatively regulate the expression of many endosperm starch synthesis genes during grain development.

scholarly journals Transcriptomic Analysis of Starch Biosynthesis in the Developing Grain of Hexaploid Wheat

2009 ◽  
Vol 2009 ◽  
pp. 1-23 ◽  
Author(s):  
Boryana S. Stamova ◽  
Debbie Laudencia-Chingcuanco ◽  
Diane M. Beckles
Keyword(s):  
Gene Expression ◽  
Dna Microarrays ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Soluble Sugars ◽  
Starch Synthesis ◽  
Gene Families ◽  
Starch Accumulation ◽  
Protein Accumulation ◽  
High Accumulation

The expression of genes involved in starch synthesis in wheat was analyzed together with the accumulation profiles of soluble sugars, starch, protein, and starch granule distribution in developing caryopses obtained from the same biological materials used for profiling of gene expression using DNA microarrays. Multiple expression patterns were detected for the different starch biosynthetic gene isoforms, suggesting their relative importance through caryopsis development. Members of the ADP-glucose pyrophosphorylase, starch synthase, starch branching enzyme, and sucrose synthase gene families showed different expression profiles; expression of some members of these gene families coincided with a period of high accumulation of starch while others did not. A biphasic pattern was observed in the rates of starch and protein accumulation which paralleled changes in global gene expression. Metabolic and regulatory genes that show a pattern of expression similar to starch accumulation and granule size distribution were identified, suggesting their coinvolvement in these biological processes.

scholarly journals Gene co-expression networks identify novel candidate genes for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis)

2021 ◽  
Author(s):  
Zhaoran Zhou ◽  
Christiane Eichner ◽  
Frank Nilsen ◽  
Inge Jonassen ◽  
Michael Dondrup
Keyword(s):  
Transcription Factor ◽  
Rna Interference ◽  
Atlantic Salmon ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Transcriptional Level ◽  
Lepeophtheirus Salmonis ◽  
Salmon Louse ◽  
Transcription Factor Genes ◽  
Regulatory Impact

Background: The salmon louse (Lepeophtheirus salmonis) is an obligate ectoparasitic copepod, living on Atlantic salmon and other salmonids in the marine environment. Salmon lice cause a number of environmental problems and lead to large economical losses in aquaculture every year. In order to develop novel parasite control strategies, a better understanding of the mechanisms of moulting and development of the salmon louse at the transcriptional level is required. Methods: Three weighted gene co-expression networks were constructed based on the pairwise correlations of salmon louse gene expression profiles at different life stages. Network-based approaches and gene annotation information were applied to identify genes that might be important for the moulting and development of the salmon louse. RNA interference was performed for validation. Regulatory impact factors were calculated for all the transcription factor genes by examining the changes in co-expression patterns between transcription factor genes and deferentially expressed genes in middle stages and moulting stages. Results: Eight gene modules were predicted as important, and 10 genes from six of the eight modules have been found to show observable phenotypes in RNA interference experiments. We knocked down five hub genes from three modules and observed phenotypic consequences in all experiments. In the infection trial, no copepodids with the RAB1A-like gene knocked down were found on fish, while control samples developed to chalimus-1 larvae. Also, a FOXO-like gene obtained highest scores in the regulatory impact factor calculation. Conclusions: We propose a gene co-expression network-based approach to identify genes playing an important role in the moulting and development of salmon louse. The RNA interference experiments confirmed the effectiveness of our approach and demonstrated the indispensable role of RAB1A-like gene in the development of salmon louse. In addition to salmon louse, this approach could be generalized to identify important genes associated with a phenotype of interest in other organisms.

scholarly journals Genome-Wide Identification and Expression Profile of OSCA Gene Family Members in Triticum aestivum L.

2021 ◽  
Vol 23 (1) ◽  
pp. 469
Author(s):  
Kai Tong ◽  
Xinyang Wu ◽  
Long He ◽  
Shiyou Qiu ◽  
Shuang Liu ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Gene Family ◽  
Expression Profiles ◽  
Stomatal Closure ◽  
Expression Patterns ◽  
Family Members ◽  
Triticum Aestivum L ◽  
Free Calcium ◽  
Cis Acting ◽  
Gene Structures

Hyperosmolality and various other stimuli can trigger an increase in cytoplasmic-free calcium concentration ([Ca2+]cyt). Members of the Arabidopsis thaliana (L.) reduced hyperosmolality-gated calcium-permeable channels (OSCA) gene family are reported to be involved in sensing extracellular changes to trigger hyperosmolality-induced [Ca2+]cyt increases and controlling stomatal closure during immune signaling. Wheat (Triticum aestivum L.) is a very important food crop, but there are few studies of its OSCA gene family members. In this study, 42 OSCA members were identified in the wheat genome, and phylogenetic analysis can divide them into four clades. The members of each clade have similar gene structures, conserved motifs, and domains. TaOSCA genes were predicted to be regulated by cis-acting elements such as STRE, MBS, DRE1, ABRE, etc. Quantitative PCR results showed that they have different expression patterns in different tissues. The expression profiles of 15 selected TaOSCAs were examined after PEG (polyethylene glycol), NaCl, and ABA (abscisic acid) treatment. All 15 TaOSCA members responded to PEG treatment, while TaOSCA12/-39 responded simultaneously to PEG and ABA. This study informs research into the biological function and evolution of TaOSCA and lays the foundation for the breeding and genetic improvement of wheat.

scholarly journals A transcriptional landscape of 28 porcine tissues obtained by Super deepSAGE sequencing

2020 ◽  
Author(s):  
Tinghua Huang ◽  
Min Yang ◽  
Kaihui Dong ◽  
Mingjiang Xu ◽  
Jinhui Liu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Cell Signaling ◽  
B Cell ◽  
Bacterial Infections ◽  
Mononuclear Cells ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Farm Animals ◽  
B Cell Signaling

Abstract Background: Gene expression regulators identified in transcriptome profiling experiments may serve as ideal targets for genetic manipulations in farm animals. Results: In this study, we developed a gene expression profile of 76,000+ unique transcripts for 224 porcine samples from 28 tissues collected from 32 animals using Super deepSAGE technology. Excellent sequencing depth was achieved for each multiplexed library, and replicated samples from the same tissues clustered together, demonstrating the high quality of Super deepSAGE data. Comparison with previous research indicated that our results not only have good reproducibility but also have greatly extended the coverage of the sample types as well as the number of genes. Clustering analysis revealed ten groups of genes showing distinct expression patterns among these samples. Our analysis of over-represented binding motifs identified 41 regulators, and we demonstrated a potential application of this dataset in infectious diseases and immune biology research by identifying an LPS-dependent transcription factor, runt-related transcription factor 1 (RUNX1), in peripheral blood mononuclear cells (PBMCs). The selected genes are specifically responsible for the transcription of toll-like receptor 2 (TLR2), lymphocyte-specific protein tyrosine kinase (LCK), and vav1 oncogene (VAV1), which belong to the T and B cell signaling pathways.Conclusions: The Super deepSAGE technology and tissue-differential expression profiles are valuable resources for investigating the porcine gene expression regulation. The identified RUNX1 target genes belong to the T and B cell signaling pathways, making them novel potential targets for the diagnosis and therapy of bacterial infections and other immune disorders.

The NAC transcription factor NAC019-A1 is a negative regulator of starch synthesis in wheat developing endosperm

2020 ◽  
Vol 71 (19) ◽  
pp. 5794-5807
Author(s):  
Yunchuan Liu ◽  
Jian Hou ◽  
Xiaolu Wang ◽  
Tian Li ◽  
Uzma Majeed ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Oryza Sativa L ◽  
Starch Content ◽  
Wheat Yield ◽  
Starch Synthesis ◽  
Kernel Weight ◽  
Nac Transcription Factor ◽  
Negative Regulator ◽  
Starch Granules ◽  
Wheat Endosperm

Abstract Starch is a major component of wheat (Triticum aestivum L.) endosperm and is an important part of the human diet. The functions of many starch synthesis genes have been elucidated. However, little is known about their regulatory mechanisms in wheat. Here, we identified a novel NAC transcription factor, TaNAC019-A1 (TraesCS3A02G077900), that negatively regulates starch synthesis in wheat and rice (Oryza sativa L.) endosperms. TaNAC019-A1 was highly expressed in the endosperm of developing grains and encoded a nucleus-localized transcriptional repressor. Overexpression of TaNAC019-A1 in rice and wheat led to significantly reduced starch content, kernel weight, and kernel width. The TaNAC019-A1-overexpression wheat lines had smaller A-type starch granules and fewer B-type starch granules than wild-type. Moreover, TaNAC019-A1 could directly bind to the ‘ACGCAG’ motif in the promoter regions of ADP-glucose pyrophosphorylase small subunit 1 (TaAGPS1-A1, TraesCS7A02G287400) and TaAGPS1-B1 (TraesCS7B02G183300) and repress their expression, thereby inhibiting starch synthesis in wheat endosperm. One haplotype of TaNAC019-B1 (TaNAC019-B1-Hap2, TraesCS3B02G092800) was positively associated with thousand-kernel weight and underwent positive selection during the Chinese wheat breeding process. Our data demonstrate that TaNAC019-A1 is a negative regulator of starch synthesis in wheat endosperm and provide novel insight into wheat yield improvement.

scholarly journals DNA Methylation and Expression Profiles of Whole Blood in Parkinson’s Disease

2021 ◽  
Vol 12 ◽  
Author(s):  
Adrienne R. Henderson ◽  
Qi Wang ◽  
Bessie Meechoovet ◽  
Ashley L. Siniard ◽  
Marcus Naymik ◽  
...  
Keyword(s):  
Gene Expression ◽  
Parkinson’S Disease ◽  
Dna Methylation ◽  
Parkinson's Disease ◽  
Transcription Factor ◽  
Whole Blood ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Motor Deficits ◽  
Age Related

Parkinson’s disease (PD) is the second most common age-related neurodegenerative disease. It is presently only accurately diagnosed at an advanced stage by a series of motor deficits, which are predated by a litany of non-motor symptoms manifesting over years or decades. Aberrant epigenetic modifications exist across a range of diseases and are non-invasively detectable in blood as potential markers of disease. We performed comparative analyses of the methylome and transcriptome in blood from PD patients and matched controls. Our aim was to characterize DNA methylation and gene expression patterns in whole blood from PD patients as a foundational step toward the future goal of identifying molecular markers that could predict, accurately diagnose, or track the progression of PD. We found that differentially expressed genes (DEGs) were involved in the processes of transcription and mitochondrial function and that PD methylation profiles were readily distinguishable from healthy controls, even in whole-blood DNA samples. Differentially methylated regions (DMRs) were functionally varied, including near transcription factor nuclear transcription factor Y subunit alpha (NFYA), receptor tyrosine kinase DDR1, RING finger ubiquitin ligase (RNF5), acetyltransferase AGPAT1, and vault RNA VTRNA2-1. Expression quantitative trait methylation sites were found at long non-coding RNA PAX8-AS1 and transcription regulator ZFP57 among others. Functional epigenetic modules were highlighted by IL18R1, PTPRC, and ITGB2. We identified patterns of altered disease-specific DNA methylation and associated gene expression in whole blood. Our combined analyses extended what we learned from the DEG or DMR results alone. These studies provide a foundation to support the characterization of larger sample cohorts, with the goal of building a thorough, accurate, and non-invasive molecular PD biomarker.

scholarly journals A novel approach to co-expression network analysis identifies modules and genes relevant for moulting and development in the Atlantic salmon louse (Lepeophtheirus salmonis)

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Zhaoran Zhou ◽  
Christiane Eichner ◽  
Frank Nilsen ◽  
Inge Jonassen ◽  
Michael Dondrup
Keyword(s):  
Transcription Factor ◽  
Rna Interference ◽  
Atlantic Salmon ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Transcriptional Level ◽  
Lepeophtheirus Salmonis ◽  
Salmon Louse ◽  
Transcription Factor Genes ◽  
Regulatory Impact

Abstract Background The salmon louse (Lepeophtheirus salmonis) is an obligate ectoparasitic copepod living on Atlantic salmon and other salmonids in the marine environment. Salmon lice cause a number of environmental problems and lead to large economical losses in aquaculture every year. In order to develop novel parasite control strategies, a better understanding of the mechanisms of moulting and development of the salmon louse at the transcriptional level is required. Methods Three weighted gene co-expression networks were constructed based on the pairwise correlations of salmon louse gene expression profiles at different life stages. Network-based approaches and gene annotation information were applied to identify genes that might be important for the moulting and development of the salmon louse. RNA interference was performed for validation. Regulatory impact factors were calculated for all the transcription factor genes by examining the changes in co-expression patterns between transcription factor genes and deferentially expressed genes in middle stages and moulting stages. Results Eight gene modules were predicted as important, and 10 genes from six of the eight modules have been found to show observable phenotypes in RNA interference experiments. We knocked down five hub genes from three modules and observed phenotypic consequences in all experiments. In the infection trial, no copepodids with a RAB1A-like gene knocked down were found on fish, while control samples developed to chalimus-1 larvae. Also, a FOXO-like transcription factor obtained highest scores in the regulatory impact factor calculation. Conclusions We propose a gene co-expression network-based approach to identify genes playing an important role in the moulting and development of salmon louse. The RNA interference experiments confirm the effectiveness of our approach and demonstrated the indispensable role of a RAB1A-like gene in the development of the salmon louse. We propose that our approach could be generalized to identify important genes associated with a phenotype of interest in other organisms.

scholarly journals Clustered, information-dense transcription factor binding sites identify genes with similar tissue-wide expression profiles

2018 ◽  
Author(s):  
Ruipeng Lu ◽  
Peter K. Rogan
Keyword(s):  
Gene Expression ◽  
Machine Learning ◽  
Transcription Factor ◽  
Binding Site ◽  
Target Gene ◽  
Target Genes ◽  
Gene Prediction ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Factor Binding

ABSTRACTBackgroundThe distribution and composition ofcis-regulatory modules (e.g. transcription factor binding site (TFBS) clusters) in promoters substantially determine gene expression patterns and TF targets, whose expression levels are significantly regulated by TF binding. TF knockdown experiments have revealed correlations between TF binding profiles and gene expression levels. We present a general framework capable of predicting genes with similar tissue-wide expression patterns from activated or repressed TF targets using machine learning to combine TF binding and epigenetic features.MethodsGenes with correlated expression patterns across 53 tissues were identified according to their Bray-Curtis similarity. DNase I HyperSensitive region (DHS) -accessible promoter intervals of direct TF target genes were scanned with previously derived information theory-based position weight matrices (iPWMs) of 82 TFs. Features from information density-based TFBS clusters were used to predict target genes with machine learning classifiers. The accuracy, specificity and sensitivity of the classifiers were determined for different feature sets. Mutations in TFBSs were also introduced to examine their impact on cluster densities and the regulatory states of predicted target genes.ResultsWe initially chose the glucocorticoid receptor gene (NR3C1), whose regulation has been extensively studied, to test this approach.SLC25A32andTANKwere found to exhibit the most similar expression patterns to this gene across 53 tissues. Prediction of other genes with similar expression profiles was significantly improved by eliminating inaccessible promoter intervals based on DHSs. A Random Forest classifier exhibited the best performance in detecting such coordinately regulated genes (accuracy was 0.972 for training, 0.976 for testing). Target gene prediction was confirmed using CRISPR knockdown data of TFs, which was more accurate than siRNA inactivation. Mutation analyses of TFBSs also revealed that one or more information-dense TFBS clusters in promoters are required for accurate target gene prediction.ConclusionsMachine learning based on TFBS information density, organization, and chromatin accessibility accurately identifies gene targets with comparable tissue-wide expression patterns. Multiple, information-dense TFBS clusters in promoters appear to protect promoters from the effects of deleterious binding site mutations in a single TFBS that would effectively alter the expression state of these genes.

TubZIP28 , a novel bZIP family transcription factor from Triticum urartu , and TabZIP28 , its homologue from Triticum aestivum , enhance starch synthesis in wheat

2020 ◽  
Vol 226 (5) ◽  
pp. 1384-1398 ◽  
Author(s):  
Yanhong Song ◽  
Guangbin Luo ◽  
Lisha Shen ◽  
Kang Yu ◽  
Wenlong Yang ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Transcription Factor ◽  
Starch Synthesis ◽  
Triticum Urartu ◽  
Bzip Family

scholarly journals Genome-wide identification, characterization, and expression patterns analysis of the SBP-box gene family in wheat (Triticum aestivum L.)

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Ying Li ◽  
Qilu Song ◽  
Yamin Zhang ◽  
Zheng Li ◽  
Jialin Guo ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Abiotic Stress ◽  
Stress Responses ◽  
Tandem Duplication ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Triticum Aestivum L ◽  
Genome Wide ◽  
Related Development ◽  
Gene Structures

Abstract SQUAMOSA promoter-binding protein (SBP)-box genes encode a family of plant-specific transcription factors that play roles in plant growth and development. The characteristics of SBP-box genes in rice (Oryza sativa) and Arabidopsis have been reported, but their potential roles in wheat (Triticum aestivum) are not fully understood. In this study, 48 SBP-box genes (TaSBPs) were identified; they were located in all wheat chromosomes except for 4B and 4D. Six TaSBPs were identified as tandem duplication genes that formed three tandem duplication pairs, while 22 were segmentally duplicated genes that formed 16 segmental duplication pairs. Subcellular localization prediction showed TaSBPs were located in nucleus. Among the 48 TaSBPs, 24 were predicted to be putative targets of TamiR156. Phylogenetic analysis showed that TaSBPs, AtSBPs, and OsSBPs that shared similar functions were clustered into the same subgroups. The phylogenetic relationships between the TaSBPs were supported by the identification of highly conserved motifs and gene structures. Four types of cis-elements––transcription-related, development-related, hormone-related, and abiotic stress-related elements––were found in the TaSBP promoters. Expression profiles indicated most TaSBPs participate in flower development and abiotic stress responses. This study establishes a foundation for further investigation of TaSBP genes and provides novel insights into their biological functions.

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