Dataset Information

Integrated analysis of transcriptome and miRNAome reveals the heat stress response of Pinellia ternata seedlings

ABSTRACT: Pinellia ternata (Thunb.) Briet., a valuable herb native to China, is susceptible to the "sprout tumble" phenomenon due to high temperatures, resulting in a significant reduction in yield. The molecular regulatory mechanisms underlying the response of P. ternata to heat stress are not well understood. In this study, we integrated transcriptome and miRNAome sequencing to identify heat response genes, microRNAs (miRNAs), and key miRNA-target pairs in P. ternata under heat stress and room temperature conditions. Transcriptome analysis revealed extensive reprogramming of 4,960 genes across various categories, predominantly associated with cellular and metabolic processes, responses to stimuli, biological regulation, cell parts, organelles, membranes, catalytic and binding activity. miRNAome sequencing identified 1,597 known/conserved miRNAs that were differentially expressed in two test conditions. According to the analysis, genes and miRNAs associated with regulation of transcription, DNA-templated, transcription factor activity and sequence-specific DNA binding pathway, may play a major role in the resistance to heat stress in P. ternata. Integration of expression data of transcriptome and miRNAome determined high confidence 41 miRNA-mRNA pairs forming 25 modules. MYB-like protein and calcium-responsive transcription coactivator may play an integral role in the resistance to heat stress in P. ternata. In addition, the candidate genes and miRNAs were subjected to quantitative real-time PCR to evaluate their expression patterns. These results offer a foundation for future studies exploring the mechanism and critical genes of resistance to heat stress in P. ternata.

ORGANISM(S): Pinellia ternata

PROVIDER: GSE243965 | GEO | 2023/09/28

REPOSITORIES: GEO

ACCESS DATA

Similar Datasets

Project description:Schmitz2014 - RNA triplex formation The model is parameterized using the parameters for gene CCDC3 from Supplementary Table S1. The two miRNAs which form the triplex together with CCDC3 are miR-551b and miR-138. This model is described in the article: Cooperative gene regulation by microRNA pairs and their identification using a computational workflow. Schmitz U, Lai X, Winter F, Wolkenhauer O, Vera J, Gupta SK. Nucleic Acids Res. 2014 Jul; 42(12): 7539-7552 Abstract: MicroRNAs (miRNAs) are an integral part of gene regulation at the post-transcriptional level. Recently, it has been shown that pairs of miRNAs can repress the translation of a target mRNA in a cooperative manner, which leads to an enhanced effectiveness and specificity in target repression. However, it remains unclear which miRNA pairs can synergize and which genes are target of cooperative miRNA regulation. In this paper, we present a computational workflow for the prediction and analysis of cooperating miRNAs and their mutual target genes, which we refer to as RNA triplexes. The workflow integrates methods of miRNA target prediction; triplex structure analysis; molecular dynamics simulations and mathematical modeling for a reliable prediction of functional RNA triplexes and target repression efficiency. In a case study we analyzed the human genome and identified several thousand targets of cooperative gene regulation. Our results suggest that miRNA cooperativity is a frequent mechanism for an enhanced target repression by pairs of miRNAs facilitating distinctive and fine-tuned target gene expression patterns. Human RNA triplexes predicted and characterized in this study are organized in a web resource at www.sbi.uni-rostock.de/triplexrna/. This model is hosted on BioModels Database and identified by: BIOMD0000000530. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information.

Project description:Korean peninsular weather is rapidly becoming subtropical due to global warming. In summer 2018, South Korea experienced the highest temperatures since the meteorological observations recorded in 1907. Heat stress has a negative effect on Holstein cows, the most popular breed of dairy cattle in South Korea, which is susceptible to heat. To examine physiological changes in dairy cows under heat stress conditions, we analyzed the profiles circulating microRNAs isolated from whole blood samples collected under heat stress and non-heat stress conditions using small RNA sequencing. We compared the expression profiles in lactating cows under heat stress and non-heat stress conditions to understand the regulation of biological processes in heat-stressed cows. Moreover, we measured several heat stress indicators, such as rectal temperature, milk yield, average daily gain, and progesterone concentration. All these assessments showed that pregnant cows were more susceptible to heat stress than non-pregnant cows. Particularly, progesterone concentrations known to have maternal warming effects were at similar levels in non-pregnant cows but significantly increased in pregnant cows under heat stress conditions. The differentially expressed miRNAs and their putative target genes were analyzed in pregnant cows. Interestingly, we found that differentially expressed miRNAs (bta-miR-146b, bta-miR-20b, bta-miR-29d-3p, bta-miR-1246) specifically targeted progesterone biosynthesis (StAR) and the function of corpus luteum-related genes (CCL11, XCL), suggesting that pregnant cows with elevated progesterone concentrations are more susceptible to heat stress. In addition, we found the differential expression of 11 miRNAs (bta-miR-19a, bta-miR-19b, bta-miR-30a-5p, and several from the bta-miR-2284 family) in both pregnant and non-pregnant cows under heat stress conditions. In target gene prediction and gene set enrichment analysis, these miRNAs were found to be associated with the cytoskeleton, cell junction, vasculogenesis, cell proliferation, ATP synthesis, oxidative stress, and immune responses involved in heat response. These miRNAs can be used as potential biomarkers for heat stress.

Dataset Information

Integrated analysis of transcriptome and miRNAome reveals the heat stress response of Pinellia ternata seedlings

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure