scholarly journals Transcriptional regulation of photosynthesis under heat stress in poplar

2019 ◽  
Author(s):  
Yiyang Zhao ◽  
Jianbo Xie ◽  
Weijie Xu ◽  
Sisi Chen ◽  
Yousry A. El-Kassaby ◽  
...  
Keyword(s):  
Heat Stress ◽  
Regulatory Network ◽  
Functional Role ◽  
Time Course ◽  
Expression Trait ◽  
Regulatory Pathway ◽  
Trait Association ◽  
Motif Enrichment ◽  
Photosynthetic Genes ◽  
Key Genes

Abstract Background Photosynthesis has been recognized as a complicated process that is modulated through the intricate regulating network at transcriptional level. However, its underlying mechanism at molecular level under heat stress remains to be understood. Analysis of the adaptive response and regulatory networks of trees to heat stress will expand our understanding of thermostability in perennial plants. In this study, we used a multi-gene network to investigate the regulatory pathway under heat stress, as constructed by a multifaceted approach of combining time-course RNA-seq, regulatory motif enrichment, and expression-trait association analysis. Results By analyzing changes in the transcriptome under heat stress, we identified 77 key photosynthetic genes, of which 97.4% (75 genes) were down-regulated, and these results conformed to the decreased photosynthesis measured values. According to analysis of regulating motif enrichment, these 77 differentially expressed genes (DEGs) had common vital light-responsive elements involved in photosynthesis. When integrating all the differential expressed genes, 5 co-expressed gene modules (1,548 genes) were identified to be significantly correlated with 4 photosynthesis-related traits. Thus, based on this, a three-layered gene regulatory network (GRN) was established, which had included 77 photosynthetic genes (in the bottom layer), 40 TFs/miRNAs (in the second layer), as well as 20 TFs/miRNAs (in the top layer), using a backward elimination random forest (BWERF) algorithm. Importantly, 6 miRNAs and 4 TFs were found to be key regulators in this regulatory pathway, emphasizing the significant roles of TFs/miRNAs in affecting photosynthetic traits. The results imply a functional role for these key genes in mediating photosynthesis under heat stress, demonstrating the potential of combining time-course transcriptome-based regulatory pathway construction, cis-elements enrichment analysis, and expression-trait association approaches to dissect complex genetic networks. Conclusions The heat-responsive pathway in regulating photosynthesis is a multi-layered complex network which is co-controlled by TFs and miRNAs. Our work not only imply a functional role for these key genes in mediating photosynthesis responding to abiotic stress in poplar, but demonstrate time-course transcriptome-based regulatory network construction will facilitate further the genetic network and key nodes examining in plants.

scholarly journals Differential regulatory network-based quantification and prioritization of key genes underlying cancer drug resistance based on time-course RNA-seq data

2019 ◽  
Vol 15 (11) ◽  
pp. e1007435 ◽  
Author(s):  
Jiajun Zhang ◽  
Wenbo Zhu ◽  
Qianliang Wang ◽  
Jiayu Gu ◽  
L. Frank Huang ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Regulatory Network ◽  
Time Course ◽  
Cancer Drug ◽  
Rna Seq ◽  
Cancer Drug Resistance ◽  
Key Genes

scholarly journals Comparative Analysis of Proanthocyanidin Metabolism and Genes Regulatory Network in Fresh Leaves of Two Different Ecotypes of Tetrastigma hemsleyanum

Plants ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 211
Author(s):  
Erkui Yue ◽  
Yuqing Huang ◽  
Lihua Qian ◽  
Qiujun Lu ◽  
Xianbo Wang ◽  
...  
Keyword(s):  
Comparative Analysis ◽  
Anticancer Agents ◽  
Regulatory Network ◽  
Land Plants ◽  
Regulatory Pathway ◽  
Targeted Metabolomics ◽  
Structural Units ◽  
Regulatory Relationship ◽  
Tetrastigma Hemsleyanum ◽  
Key Genes

Tetrastigma hemsleyanum Diels et Gilg is a rare and wild medicinal resource. Metabolites, especially secondary metabolites, have an important influence on T. hemsleyanum adaptability and its medicinal quality. The metabolite proanthocyanidin (PA) is a polyphenol compound widely distributed in land plants, which can be used as antioxidants and anticancer agents. Here, we discovered that three types of PA accumulated in large amounts in purple leaves (PL), but not in green leaves (RG), based on widely non-targeted metabolomics. In addition, we further found that catechins and their derivatives, which are the structural units of PA, are also enriched in PL. Afterwards, we screened and obtained five key genes, DNR1/2, ANS, ANR and LAR closely related to PA biosynthesis through transcriptome analysis and found they were all highly expressed in PL compared to RG. Therefore, observed the regulatory relationship between the main compounds and genes network, and the PA metabolism regulatory pathway was complicated, which may be different to other species.

Identification of heat-responsive miRNAs to reveal the miRNA-mediated regulatory network of heat stress response in Betula luminifera

Trees ◽  
2017 ◽  
Vol 31 (5) ◽  
pp. 1635-1652 ◽  
Author(s):  
Ying Pan ◽  
Mingyue Niu ◽  
Junsheng Liang ◽  
Erpei Lin ◽  
Zaikang Tong ◽  
...  
Keyword(s):  
Heat Stress ◽  
Stress Response ◽  
Regulatory Network ◽  
Heat Stress Response ◽  
Betula Luminifera

scholarly journals Identification of Key Genes in ‘Luang Pratahn’, Thai Salt-Tolerant Rice, Based on Time-Course Data and Weighted Co-expression Networks

2021 ◽  
Vol 12 ◽  
Author(s):  
Pajaree Sonsungsan ◽  
Pheerawat Chantanakool ◽  
Apichat Suratanee ◽  
Teerapong Buaboocha ◽  
Luca Comai ◽  
...  
Keyword(s):  
Salt Stress ◽  
Salt Tolerance ◽  
Stress Responses ◽  
Time Course ◽  
Rice Variety ◽  
Enrichment Analysis ◽  
Normal Growth ◽  
Growth Conditions ◽  
Pathway Enrichment Analysis ◽  
Key Genes

Salinity is an important environmental factor causing a negative effect on rice production. To prevent salinity effects on rice yields, genetic diversity concerning salt tolerance must be evaluated. In this study, we investigated the salinity responses of rice (Oryza sativa) to determine the critical genes. The transcriptomes of ‘Luang Pratahn’ rice, a local Thai rice variety with high salt tolerance, were used as a model for analyzing and identifying the key genes responsible for salt-stress tolerance. Based on 3' Tag-Seq data from the time course of salt-stress treatment, weighted gene co-expression network analysis was used to identify key genes in gene modules. We obtained 1,386 significantly differentially expressed genes in eight modules. Among them, six modules indicated a significant correlation within 6, 12, or 48h after salt stress. Functional and pathway enrichment analysis was performed on the co-expressed genes of interesting modules to reveal which genes were mainly enriched within important functions for salt-stress responses. To identify the key genes in salt-stress responses, we considered the two-state co-expression networks, normal growth conditions, and salt stress to investigate which genes were less important in a normal situation but gained more impact under stress. We identified key genes for the response to biotic and abiotic stimuli and tolerance to salt stress. Thus, these novel genes may play important roles in salinity tolerance and serve as potential biomarkers to improve salt tolerance cultivars.

Identification of key genes and construction of regulatory network for the progression of cervical cancer

Gene Reports ◽  
2020 ◽  
Vol 21 ◽  
pp. 100965
Author(s):  
Monika Rajput ◽  
Mukesh Kumar ◽  
Mayuri Kumari ◽  
Atanu Bhattacharjee ◽  
Aanchal Anant Awasthi
Keyword(s):  
Cervical Cancer ◽  
Regulatory Network ◽  
Key Genes

STABILITY OF REGULATORY PROTEIN GRADIENTS INDUCED BY MORPHOGEN DPP IN DROSOPHILA WING DISC

2013 ◽  
Vol 23 (08) ◽  
pp. 1350138 ◽  
Author(s):  
HONGWEI YIN ◽  
XIAOYONG XIAO ◽  
XIAOQING WEN ◽  
TIANSHOU ZHOU
Keyword(s):  
Regulatory Network ◽  
Regulatory Protein ◽  
Reaction Rates ◽  
Wing Disc ◽  
Drosophila Wing ◽  
Major Reaction ◽  
Key Genes ◽  
Pattern Information ◽  
Protein Gradients ◽  
And Control

In the development of Drosophila wing disc, morphogen Dpp, which is a signaling molecule from a local region and disperses into anterior and posterior compartments, builds up a gradient with precise pattern information. Experiments have demonstrated that the key genes (brk, dad, omb and sal) and phosphorylated protein (pMad), which are activated by Dpp signaling molecules and form the gradients of the corresponding proteins of these genes, direct and control the spatial pattern of the wing disc. However, the regulatory network of these genes are in complex and nonlinear interaction with upstream regulators and downstream targets. In this paper, the mathematical model is built according to the regulatory relationships of these key genes. The stabilities of the gradients of these corresponding proteins are investigated. Furthermore, numerical simulations show that these gradients are robust with respect to some major reaction rates in this regulatory network.

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