scholarly journals Applying cis-regulatory codes to predict conserved and variable heat and cold stress response in maize

2021 ◽  
Author(s):  
Peng Zhou ◽  
Tara A. Enders ◽  
Zachary A. Myers ◽  
Erika Magnusson ◽  
Peter A Crisp ◽  
...  
Keyword(s):  
Gene Expression ◽  
Abiotic Stress ◽  
Cold Stress ◽  
Transcriptome Profiling ◽  
Transcript Abundance ◽  
Regulatory Elements ◽  
Variable Response ◽  
Heat And Cold Stress ◽  
Expression Response ◽  
Predict Gene Expression

AbstractChanges in gene expression are important for response to abiotic stress. Transcriptome profiling performed on maize inbred and hybrid genotypes subjected to heat or cold stress identifies many transcript abundance changes in response to these environmental conditions. Motifs that are enriched near differentially expressed genes were used to develop machine learning models to predict gene expression responses to heat or cold. The best performing models utilize the sequences both upstream and downstream of the transcription start site. Prediction accuracies could be improved using models developed for specific co-expression clusters compared to using all up- or down-regulated genes or by only using motifs within unmethylated regions. Comparisons of expression responses in multiple genotypes were used to identify genes with variable response and to identify cis- or trans-regulatory variation. Models trained on B73 data have lower performance when applied to Mo17 or W22, this could be improved by using models trained on data from all genotypes. However, the models have low accuracy for correctly predicting genes with variable responses to abiotic stress. This study provides insights into cis-regulatory motifs for heat- and cold-responsive gene expression and provides a framework for developing models to predict expression response to abiotic stress across multiple genotypes.One sentence summaryTranscriptome profiling of maize inbred and hybrid seedlings subjected to heat or cold stress was used to identify key cis-regulatory elements and develop models to predict gene expression responses.

scholarly journals RETRACTED ARTICLE: The specific MYB binding sites bound by TaMYB in the GAPCp2/3 promoters are involved in the drought stress response in wheat

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Lin Zhang ◽  
Zhiqiang Song ◽  
Fangfang Li ◽  
Xixi Li ◽  
Haikun Ji ◽  
...  
Keyword(s):  
Gene Expression ◽  
Abiotic Stress ◽  
Drought Stress ◽  
Reporter Gene ◽  
Binding Sites ◽  
Promoter Sequence ◽  
Regulatory Elements ◽  
Cis Elements ◽  
Gus Reporter ◽  
Almost All

Abstract Background Drought stress is one of the major abiotic stresses that affects plant growth and productivity. The GAPCp genes play important roles in drought stress tolerance in multiple species. The aim of this experiment was to identify the core cis-regulatory elements that may respond to drought stress in the GAPCp2 and GAPCp3 promoter sequences. Results In this study, the promoters of GAPCp2 and GAPCp3 were cloned. The promoter activities were significantly improved under abiotic stress via regulation of Rluc reporter gene expression, while promoter sequence analysis indicated that these fragments were not almost identical. In transgenic Arabidopsis with the expression of the GUS reporter gene under the control of one of these promoters, the activities of GUS were strong in almost all tissues except the seeds, and the activities were induced after abiotic stress. The yeast one-hybrid system and EMSA demonstrated that TaMYB bound TaGAPCp2P/3P. By analyzing different 5′ deletion mutants of these promoters, it was determined that TaGAPCp2P (− 1312~ − 528) and TaGAPCp3P (− 2049~ − 610), including the MYB binding site, contained enhancer elements that increased gene expression levels under drought stress. We used an effector and a reporter to co-transform tobacco and found that TaMYB interacted with the specific MYB binding sites of TaGAPCp2P (− 1197~ − 635) and TaGAPCp3P (− 1456~ − 1144 and − 718~ − 610) in plant cells. Then, the Y1H system and EMSA assay demonstrated that these MYB binding sites in TaGAPCp2P (− 1135 and − 985) and TaGAPCp3P (− 1414 and − 665) were the target cis-elements of TaMYB. The deletion of the specific MYB binding sites in the promoter fragments significantly restrained the drought response, and these results confirmed that these MYB binding sites (AACTAAA/C) play vital roles in improving the transcription levels under drought stress. The results of qRT-PCR in wheat protoplasts transiently overexpressing TaMYB indicated that the expression of TaGAPCp2/3 induced by abiotic stress was upregulated by TaMYB. Conclusion The MYB binding sites (AACTAAA/C) in TaGAPCp2P/3P were identified as the key cis-elements for responding to drought stress and were bound by the transcription factor TaMYB.

Transcriptome profiling of wheat under heat and cold stress treatments

2012 ◽  
Vol 29 ◽  
pp. S130
Author(s):  
Mehmet Cengiz Baloglu ◽  
M. Tufan Oz ◽  
Huseyin Avni Oktem ◽  
Meral Yucel
Keyword(s):  
Cold Stress ◽  
Transcriptome Profiling ◽  
Heat And Cold Stress

Phloem fibres as motors of gravitropic behaviour of flax plants: level of transcriptome

2018 ◽  
Vol 45 (2) ◽  
pp. 203 ◽  
Author(s):  
Oleg Gorshkov ◽  
Natalia Mokshina ◽  
Nadezda Ibragimova ◽  
Marina Ageeva ◽  
Natalia Gogoleva ◽  
...  
Keyword(s):  
Cell Wall ◽  
Large Scale ◽  
Turgor Pressure ◽  
Control Plant ◽  
Transcriptome Profiling ◽  
Transcript Abundance ◽  
Regulatory Elements ◽  
Wall Structure ◽  
Vertical Position ◽  
Genes Encoding

Restoration of stem vertical position after plant inclination is a widely spread version of plant orientation in accordance with gravity vector direction. Gravitropic behaviour of flax plants involves the formation of curvature in stem region that has ceased elongation long in advance of stem inclination. The important participants of such behaviour are phloem fibres with constitutively formed tertiary cell wall (G-layer). We performed the large-scale transcriptome profiling of phloem fibres isolated from pulling and opposite sides of gravitropic curvature and compared with control plant fibres. Significant changes in transcript abundance take place for genes encoding proteins of several ion channels, transcription factors and other regulating elements. The largest number of upregulated genes belonged to the cell wall category; many of those were specifically upregulated in fibres of pulling stem side. The obtained data permit to suggest the mechanism of fibre participation in gravitropic reaction that involves the increase of turgor pressure and the rearrangements of cell wall structure in order to improve contractile properties, and to identify the regulatory elements that operate specifically in the fibres of the pulling stem side making gelatinous phloem fibres an important element of gravitropic response in herbaceous plants.

scholarly journals Molecular Cloning, Expression and Insilco Analysis of Drought Stress Inducible MYB Transcription Factor Encoding Gene From C4 Plant Eleusine Coracana

2021 ◽  
Author(s):  
MEGHA BHATT
Keyword(s):  
Gene Expression ◽  
Abiotic Stress ◽  
Drought Stress ◽  
Molecular Cloning ◽  
Stress Responses ◽  
Promoter Region ◽  
Regulatory Elements ◽  
Full Length ◽  
Growth And Yield ◽  
Yield Potential

Abstract Drought is one of the key abiotic stresses that critically influences the crops by restraining their growth and yield potential. Being sessile, plant tackle the detrimental effects of drought stress via modulating the cellular state by changing the gene expression. Such alteration of gene expression is essentially driven by the transcriptional syndicate. Transcription factors (TF) are the key regulatory protein that controls the expression of their target gene by binding to the cis-regulatory elements present in the promoter region. Myb-TF subiquitously present in all eukaryotes belong to one of the largest TF family, and play wide array of biological functions in plants including anthocyanin biosynthesis, vasculature system, cell signaling, seed maturation and abiotc stress responses. In the present study, isolation, and molecular cloning of full length Myb TF from Eleusine corocana has been performed. The isolated full-length coding sequence has 1053 bp and 350 aa was submitted to NCBI (Accession number MT312253). The transcript level of EcMYB increases under different abiotic stress treatment including dehydration, salinity, and high temperature stress. The promoter region of EcMyb1 was found to be enriched in stress-responsive cis-regulatory elements such as DRE, HSE, ABRE etc. In phylogenetic analysis, EcMyb1 appeared to have high homology with its monocot orthologs particularly Sateria italica, Hordeum vulgare, Saccharum barberi and Oryza sativa. The three-dimension protein structure was generated based on homology modeling and structural aspects were discussed. Further, Insilco analysis was conducted to explore the physiological properties, subcellular localization, potential post-translational modification sites (phosphorylation and glycosylation sites), and molecular and biological function of full-length protein. Overall, the expression profiling and Insilco analysis of EcMyb1 strongly indicated its potential role in abiotic stress response in Eleusine corocana.

scholarly journals TRAP-based allelic translation efficiency imbalance analysis to identify genetic regulation of ribosome occupancy in specific cell types in vivo

2020 ◽  
Author(s):  
Yating Liu ◽  
Anthony D. Fischer ◽  
Celine L. St. Pierre ◽  
Juan F. Macias-Velasco ◽  
Heather A. Lawson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Genetic Regulation ◽  
Transcript Abundance ◽  
Cell Types ◽  
Regulatory Elements ◽  
Model Organisms ◽  
Specific Cell ◽  
Translation Efficiency ◽  
Mrna Levels

AbstractThe alteration of gene expression due to variations in the sequences of transcriptional regulatory elements has been a focus of substantial inquiry in humans and model organisms. However, less is known about the extent to which natural variation contributes to post-transcriptional regulation. Allelic Expression Imbalance (AEI) is a classical approach for studying the association of specific haplotypes with relative changes in transcript abundance. Here, we piloted a new TRAP based approach to associate genetic variation with transcript occupancy on ribosomes in specific cell types, to determine if it will allow examination of Allelic Translation Imbalance (ATI), and Allelic Translation Efficiency Imbalance, using as a test case mouse astrocytes in vivo. We show that most changes of the mRNA levels on ribosomes were reflected in transcript abundance, though ∼1.5% of transcripts have variants that clearly alter loading onto ribosomes orthogonally to transcript levels. These variants were often in conserved residues and altered sequences known to regulate translation such as upstream ORFs, PolyA sites, and predicted miRNA binding sites. Such variants were also common in transcripts showing altered abundance, suggesting some genetic regulation of gene expression may function through post-transcriptional mechanisms. Overall, our work shows that naturally occurring genetic variants can impact ribosome occupancy in astrocytes in vivo and suggests that mechanisms may also play a role in genetic contributions to disease.

scholarly journals Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network

2019 ◽  
Author(s):  
Wanwen Zeng ◽  
Yong Wang ◽  
Rui Jiang
Keyword(s):  
Neural Network ◽  
Gene Expression ◽  
Convolutional Neural Network ◽  
Driving Forces ◽  
Wide Spectrum ◽  
Regulatory Elements ◽  
Proximal Promoter ◽  
Supplementary Information ◽  
Promoter Sequences ◽  
Predict Gene Expression

Abstract Motivation Interactions among cis-regulatory elements such as enhancers and promoters are main driving forces shaping context-specific chromatin structure and gene expression. Although there have been computational methods for predicting gene expression from genomic and epigenomic information, most of them neglect long-range enhancer–promoter interactions, due to the difficulty in precisely linking regulatory enhancers to target genes. Recently, HiChIP, a novel high-throughput experimental approach, has generated comprehensive data on high-resolution interactions between promoters and distal enhancers. Moreover, plenty of studies suggest that deep learning achieves state-of-the-art performance in epigenomic signal prediction, and thus promoting the understanding of regulatory elements. In consideration of these two factors, we integrate proximal promoter sequences and HiChIP distal enhancer–promoter interactions to accurately predict gene expression. Results We propose DeepExpression, a densely connected convolutional neural network, to predict gene expression using both promoter sequences and enhancer–promoter interactions. We demonstrate that our model consistently outperforms baseline methods, not only in the classification of binary gene expression status but also in regression of continuous gene expression levels, in both cross-validation experiments and cross-cell line predictions. We show that the sequential promoter information is more informative than the experimental enhancer information; meanwhile, the enhancer–promoter interactions within ±100 kbp around the TSS of a gene are most beneficial. We finally visualize motifs in both promoter and enhancer regions and show the match of identified sequence signatures with known motifs. We expect to see a wide spectrum of applications using HiChIP data in deciphering the mechanism of gene regulation. Availability and implementation DeepExpression is freely available at https://github.com/wanwenzeng/DeepExpression. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Integrating distal and proximal information to predict gene expression via a densely connected convolutional neural network

2018 ◽  
Author(s):  
Wanwen Zeng ◽  
Yong Wang ◽  
Rui Jiang
Keyword(s):  
Neural Network ◽  
Gene Expression ◽  
Convolutional Neural Network ◽  
Driving Forces ◽  
Wide Spectrum ◽  
Regulatory Elements ◽  
Proximal Promoter ◽  
Supplementary Information ◽  
Promoter Sequences ◽  
Predict Gene Expression

AbstractMotivationInteractions among such cis-regulatory elements as enhancers and promoters are main driving forces shaping context-specific chromatin structure and gene expression. Although there have been computational methods for predicting gene expression from genomic and epigenomic information, most of them overlook long-range enhancer-promoter interactions, due to the difficulty in precisely linking regulatory enhancers to target genes. Recently, a novel high-throughput experimental approach named HiChIP has been developed and generating comprehensive data on high-resolution interactions between promoters and distal enhancers. On the other hand, plenty of studies have suggested that deep learning achieves state-of-the-art performance in epigenomic signal prediction, and thus promoting the understanding of regulatory elements. In consideration of these two factors, we integrate proximal promoter sequences and HiChIP distal enhancer-promoter interactions to accurately model gene expression.ResultsWe propose DeepExpression, a densely connected convolutional neural network to predict gene expression using both promoter sequences and enhancer-promoter interactions. We demonstrate that our model consistently outperforms baseline methods not only in the classification of binary gene expression status but also in the regression of continuous gene expression levels, in both cross-validation experiments and cross-cell lines predictions. We show that sequential promoter information is more informative than experimental enhancer information while enhancer-promoter interactions are most beneficial from those within ±100 kbp around the TSS of a gene. We finally visualize motifs in both promoter and enhancer regions and show the match of identified sequence signatures and known motifs. We expect to see a wide spectrum of applications using HiChIP data in deciphering the mechanism of gene regulation.AvailabilityDeepExpression is freely available at https://github.com/wanwenzeng/[email protected], [email protected] informationSupplementary data are available at Bioinformatics online.

scholarly journals Abiotic stress responsive cis-regulatory elements (CREs) in rice (Oryza sativa L.) and other plants

2019 ◽  
Author(s):  
Sangram Lenka ◽  
Kailash C Bansal
Keyword(s):  
Gene Expression ◽  
Abiotic Stress ◽  
Large Scale ◽  
Sequence Data ◽  
Oryza Sativa L ◽  
Crop Improvement ◽  
Regulatory Elements ◽  
Plant Genome ◽  
Agricultural Crop ◽  
Cis Acting

Capability of crop plants to adjust to the adverse environmental conditions in a spatiotemporalfashion is critical for their survival and maintaining agricultural productivity.Genetic engineering efforts for improving tolerance to diverse abiotic stresses in crop plantsusing well characterised stress-inducible promoter elements have proven to be advantageous.Combinatorial interactions of cis-acting DNA elements in the promoters with trans-actingprotein factors are key processes governing spatio-temporal gene expression. It is becomingincreasingly evident that targeted modification of molecular genetic network is feasible, forexploiting the potential of specific abiotic stress responsive element and its correspondingmaster regulatory genes via plant genetic engineering.The importance of inducible promotersin agricultural crop improvement is enormous; hence it is very crucial to characteriseinducible promoters from plant genome sequence data bases on a large scale. We will brieflydiscuss here abiotic stress responsive cis-acting elements and their role in abiotic stressregulated gene expression.

Invited Review: Effects of heat and cold stress on mammalian gene expression

2002 ◽  
Vol 92 (4) ◽  
pp. 1725-1742 ◽  
Author(s):  
Larry A. Sonna ◽  
Jun Fujita ◽  
Stephen L. Gaffin ◽  
Craig M. Lilly
Keyword(s):  
Gene Expression ◽  
Cold Stress ◽  
Cellular Responses ◽  
Cell Stress ◽  
Expression Of Genes ◽  
Heat And Cold Stress ◽  
Similarities And Differences ◽  
Cell Stress Response ◽  
Shock Proteins ◽  
Mammalian Gene Expression

This review examines the effects of thermal stress on gene expression, with special emphasis on changes in the expression of genes other than heat shock proteins (HSPs). There are ∼50 genes not traditionally considered to be HSPs that have been shown, by conventional techniques, to change expression as a result of heat stress, and there are <20 genes (including HSPs) that have been shown to be affected by cold. These numbers will likely become much larger as gene chip array and proteomic technologies are applied to the study of the cell stress response. Several mechanisms have been identified by which gene expression may be altered by heat and cold stress. The similarities and differences between the cellular responses to heat and cold may yield key insights into how cells, and by extension tissues and organisms, survive and adapt to stress.

scholarly journals Analysis of PYL Genes and Their Potential Relevance to Stress Tolerance and Berry Ripening in Grape

2020 ◽  
Vol 145 (5) ◽  
pp. 308-317
Author(s):  
Yanxia Zhao ◽  
Guimei Qi ◽  
Fengshan Ren ◽  
Yongmei Wang ◽  
Pengfei Wang ◽  
...  
Keyword(s):  
Abiotic Stress ◽  
Cold Stress ◽  
Stress Responses ◽  
Gene Families ◽  
Regulatory Elements ◽  
Genome Database ◽  
Genome Wide ◽  
Berry Ripening ◽  
Relationship Of

Abscisic acid (ABA) is an essential phytohormone that regulates plant growth and development, particularly in response to abiotic stress. The ABA receptor PYR/PYL/RCAR (PYL) family has been identified from some plant species. However, knowledge about the PYL family (VvPYLs) in grape (Vitis vinifera) is limited. This study aims to conduct genome-wide analyses of VvPYLs. We successfully identified eight PYL genes from the newest grape genome database. These VvPYLs could be divided into three subfamilies. Exon-intron structures were closely related to the phylogenetic relationship of the genes, and PYL genes that clustered in the same subfamily had a similar number of exons. VvPYL1, VvPYL2, VvPYL4, VvPYL7, and VvPYL8 were relatively highly expressed in roots. VvPYL1, VvPYL3, VvPYL7, and VvPYL8 were expressed in response to cold, salt, or polyethylene glycol stress. VvPYL6 was up-regulated by cold stress for 4 hours, and the expression of VvPYL2 was 1.74-fold greater than that of the control under cold stress. VvPYL8 was up-regulated 1.64-, 1.83-, and 1.90-fold compared with the control when treated with salt, PEG, or cold stress after 4 hours, respectively. Additionally, abiotic stress-inducible elements exist in VvPYL2, VvPYL3, VvPYL7, and VvPYL8, indicating that in these four genes, the response to abiotic stress may be regulated by cis-regulatory elements. The transcriptional levels of VvPYL1 and VvPYL8 significantly increased from fruit set to the ripening stage and decreased in the berry when treated by exogenous ABA. The eight VvPYL genes have diverse roles in grape stress responses, berry ripening, or development. This work provides insight into the role of VvPYL gene families in response to abiotic stress and berry ripening in grape.

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