Comprehensive RNA-Seq Profiling Reveals Temporal and Tissue-Specific Changes in Gene Expression in Sprague–Dawley Rats as Response to Heat Stress Challenges

Understanding heat stress physiology and identifying reliable biomarkers are paramount for developing effective management and mitigation strategies. However, little is known about the molecular mechanisms underlying thermal tolerance in animals. In an experimental model of Sprague–Dawley rats subjected to temperatures of 22 ± 1°C (control group; CT) and 42°C for 30 min (H30), 60 min (H60), and 120 min (H120), RNA-sequencing (RNA-Seq) assays were performed for blood (CT and H120), liver (CT, H30, H60, and H120), and adrenal glands (CT, H30, H60, and H120). A total of 53, 1,310, and 1,501 differentially expressed genes (DEGs) were significantly identified in the blood (P < 0.05 and |fold change (FC)| >2), liver (P < 0.01, false discovery rate (FDR)–adjusted P = 0.05 and |FC| >2) and adrenal glands (P < 0.01, FDR-adjusted P = 0.05 and |FC| >2), respectively. Of these, four DEGs, namely Junb, P4ha1, Chordc1, and RT1-Bb, were shared among the three tissues in CT vs. H120 comparison. Functional enrichment analyses of the DEGs identified in the blood (CT vs. H120) revealed 12 biological processes (BPs) and 25 metabolic pathways significantly enriched (FDR = 0.05). In the liver, 133 BPs and three metabolic pathways were significantly detected by comparing CT vs. H30, H60, and H120. Furthermore, 237 BPs were significantly (FDR = 0.05) enriched in the adrenal glands, and no shared metabolic pathways were detected among the different heat-stressed groups of rats. Five and four expression patterns (P < 0.05) were uncovered by 73 and 91 shared DEGs in the liver and adrenal glands, respectively, over the different comparisons. Among these, 69 and 73 genes, respectively, were proposed as candidates for regulating heat stress response in rats. Finally, together with genome-wide association study (GWAS) results in cattle and phenome-wide association studies (PheWAS) analysis in humans, five genes (Slco1b2, Clu, Arntl, Fads1, and Npas2) were considered as being associated with heat stress response across mammal species. The datasets and findings of this study will contribute to a better understanding of heat stress response in mammals and to the development of effective approaches to mitigate heat stress response in livestock through breeding.

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RNA-Seq-mediated transcriptomic analysis of heat stress response in a polar Chlorella sp. (Trebouxiophyceae, Chlorophyta)

Journal of Applied Phycology ◽

10.1007/s10811-018-1455-9 ◽

2018 ◽

Vol 30 (6) ◽

pp. 3103-3119 ◽

Cited By ~ 2

Author(s):

Sze-Wan Poong ◽

Kok-Keong Lee ◽

Phaik-Eem Lim ◽

Tun-Wen Pai ◽

Chiew-Yen Wong ◽

...

Keyword(s):

Heat Stress ◽

Stress Response ◽

Transcriptomic Analysis ◽

Rna Seq ◽

Heat Stress Response ◽

Chlorella Sp

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Comparative transcriptomic analysis of the heat stress response in the filamentous fungus Metarhizium anisopliae using RNA-Seq

Applied Microbiology and Biotechnology ◽

10.1007/s00253-014-5763-y ◽

2014 ◽

Vol 98 (12) ◽

pp. 5589-5597 ◽

Cited By ~ 35

Author(s):

Zhang-Xun Wang ◽

Xia-Zhi Zhou ◽

Hui-Min Meng ◽

Yu-Jun Liu ◽

Quan Zhou ◽

...

Keyword(s):

Heat Stress ◽

Stress Response ◽

Filamentous Fungus ◽

Metarhizium Anisopliae ◽

Transcriptomic Analysis ◽

Rna Seq ◽

Heat Stress Response ◽

Comparative Transcriptomic Analysis

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Comparative transcriptome profiling of heat stress response of the mangrove crab Scylla serrata across different sites

10.21203/rs.3.rs-124588/v1 ◽

2020 ◽

Author(s):

Anish M.S. Shrestha ◽

Crissa Ann I. Lilagan ◽

Joyce Emlyn B. Guiao ◽

Maria Rowena R. Romana-Eguia ◽

Ma. Carmen Ablan Lagman

Keyword(s):

Heat Stress ◽

Stress Response ◽

The Philippines ◽

Differentially Expressed ◽

Scylla Serrata ◽

Rna Seq ◽

Heat Stress Response ◽

Site Analysis ◽

Mangrove Crab ◽

Heat Response

Abstract Background: The fishery and aquaculture of the widely distributed mangrove crab Scylla serrata is a steadily growing, high-value, global industry. Climate change poses a risk to this industry as temperature elevations are expected to threaten the mangrove crab habitat and the supply of mangrove crab seeds from the wild. It is therefore important to understand the genomic and molecular basis of how mangrove crab populations from sites with different climate profiles respond to heat stress. Towards this, we performed RNA-seq on the gill tissue of S. serrata individuals sampled from 3 sites (Cagayan, Bicol, and Bataan) in the Philippines, under normal and heat-stressed conditions. To compare the transcriptome expression profiles, we designed a 2-factor generalized linear model containing interaction terms, which allowed us to simultaneously analyze within-site response to heat-stress and across-site differences in the response.Results: We present the first ever transcriptome assembly of S. serrata obtained from a massive data set containing ~66 Gbases of cleaned RNA-seq reads. With lowly-expressed and short contigs excluded, the assembly contains roughly 17,000 genes with an N50 length of 2,366 bp. Based on sequence comparison to the fruitfly and shrimp proteomes, our assembly contains several thousands of almost full-length transcripts. Differential expression analysis found population-specific differences in heat-stress response. Within-site analysis of heat response showed 177, 755, and 221 differentially expressed (DE) genes in the Cagayan, Bataan, and Bicol group, respectively. Across-site analysis of difference in heat response showed that between Cagayan and Bataan, there were 389 differently differentially expressed (DDE) genes associated with 48 signalling and stress-response pathways; and between Cagayan and Bicol, there were 101 DDE genes affecting 8 pathways.Conclusion: In light of previous work on climate profiling and on population genetics of marine species in the Philippines, our findings suggest that the variation in thermal response among populations might be derived from acclimatory plasticity due to pre-exposure to extreme temperature variations or from population structure shaped by connectivity which leads to adaptive genetic differences among populations.

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Comparative transcriptome profiling of heat stress response of the mangrove crab Scylla serrata across sites of varying climate profiles

BMC Genomics ◽

10.1186/s12864-021-07891-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Anish M.S. Shrestha ◽

Crissa Ann I. Lilagan ◽

Joyce Emlyn B. Guiao ◽

Maria Rowena R. Romana-Eguia ◽

Ma. Carmen Ablan Lagman

Keyword(s):

Heat Stress ◽

Stress Response ◽

Transcriptome Assembly ◽

The Philippines ◽

Scylla Serrata ◽

Rna Seq ◽

Data Set ◽

Heat Stress Response ◽

Site Analysis ◽

Mangrove Crab

Abstract Background The fishery and aquaculture of the widely distributed mangrove crab Scylla serrata is a steadily growing, high-value, global industry. Climate change poses a risk to this industry as temperature elevations are expected to threaten the mangrove crab habitat and the supply of mangrove crab juveniles from the wild. It is therefore important to understand the genomic and molecular basis of how mangrove crab populations from sites with different climate profiles respond to heat stress. Towards this, we performed RNA-seq on the gill tissue of S. serrata individuals sampled from 3 sites (Cagayan, Bicol, and Bataan) in the Philippines, under normal and heat-stressed conditions. To compare the transcriptome expression profiles, we designed a 2-factor generalized linear model containing interaction terms, which allowed us to simultaneously analyze within-site response to heat-stress and across-site differences in the response. Results We present the first ever transcriptome assembly of S. serrata obtained from a data set containing 66 Gbases of cleaned RNA-seq reads. With lowly-expressed and short contigs excluded, the assembly contains roughly 17,000 genes with an N50 length of 2,366 bp. Our assembly contains many almost full-length transcripts – 5229 shrimp and 3049 fruit fly proteins have alignments that cover >80% of their sequence lengths to a contig. Differential expression analysis found population-specific differences in heat-stress response. Within-site analysis of heat-stress response showed 177, 755, and 221 differentially expressed (DE) genes in the Cagayan, Bataan, and Bicol group, respectively. Across-site analysis showed that between Cagayan and Bataan, there were 389 genes associated with 48 signaling and stress-response pathways, for which there was an effect of site in the response to heat; and between Cagayan and Bicol, there were 101 such genes affecting 8 pathways. Conclusion In light of previous work on climate profiling and on population genetics of marine species in the Philippines, our findings suggest that the variation in thermal response among populations might be derived from acclimatory plasticity due to pre-exposure to extreme temperature variations or from population structure shaped by connectivity which leads to adaptive genetic differences among populations.

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Arabidopsis bZIP18 and bZIP52 Accumulate in Nuclei Following Heat Stress where They Regulate the Expression of a Similar Set of Genes

International Journal of Molecular Sciences ◽

10.3390/ijms22020530 ◽

2021 ◽

Vol 22 (2) ◽

pp. 530

Author(s):

Anna J. Wiese ◽

Lenka Steinbachová ◽

Ljudmilla Timofejeva ◽

Vojtěch Čermák ◽

Božena Klodová ◽

...

Keyword(s):

Gene Expression ◽

Heat Stress ◽

Metabolic Pathways ◽

Elevated Temperatures ◽

Crop Yields ◽

Nuclear Accumulation ◽

Rna Seq ◽

Regulate Gene Expression ◽

Heat Stress Response ◽

Group I

Heat stress (HS) is a major abiotic stress that negatively impacts crop yields across the globe. Plants respond to elevated temperatures by changing gene expression, mediated by transcription factors (TFs) functioning to enhance HS tolerance. The involvement of Group I bZIP TFs in the heat stress response (HSR) is not known. In this study, bZIP18 and bZIP52 were investigated for their possible role in the HSR. Localization experiments revealed their nuclear accumulation following heat stress, which was found to be triggered by dephosphorylation. Both TFs were found to possess two motifs containing serine residues that are candidates for phosphorylation. These motifs are recognized by 14–3–3 proteins, and bZIP18 and bZIP52 were found to bind 14–3–3 ε, the interaction of which sequesters them to the cytoplasm. Mutation of both residues abolished 14–3–3 ε interaction and led to a strict nuclear localization for both TFs. RNA-seq analysis revealed coordinated downregulation of several metabolic pathways including energy metabolism and translation, and upregulation of numerous lncRNAs in particular. These results support the idea that bZIP18 and bZIP52 are sequestered to the cytoplasm under control conditions, and that heat stress leads to their re-localization to nuclei, where they jointly regulate gene expression.

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A Novel Noncoding RNA dsr11 Involved in Heat Stress Tolerance in Deinococcus radiodurans

Biomolecules ◽

10.3390/biom10010022 ◽

2019 ◽

Vol 10 (1) ◽

pp. 22 ◽

Cited By ~ 1

Author(s):

Dong Xue ◽

Yun Chen ◽

Jiang Li ◽

Jiahui Han ◽

Zhengfu Zhou ◽

...

Keyword(s):

Heat Stress ◽

Stress Response ◽

Environmental Stress ◽

Noncoding Rna ◽

Deinococcus Radiodurans ◽

Pcr Analysis ◽

Resistant Bacteria ◽

Rna Seq ◽

Environmental Stress Response ◽

Heat Stress Response

Deinococcus radiodurans is an extremely resistant bacteria that has evolved masterful strategies to enable survival under various environmental stress conditions. Heat stress is a major environmental stress factor that can cause denaturation of proteins, membrane disruption, and oxidative stress. Previous studies have examined the mechanisms of the heat stress response by analyzing changes in protein levels; however, little is known about the role of small noncoding RNAs (ncRNAs), which are known to play important regulatory functions in bacteria during various environmental stress response. The ncRNA dsr11 of D. radiodurans was previously identified by RNA-seq and Northern blot. In this study, we showed that the transcription level of dsr11 was up-regulated 4.2-fold under heat stress by qRT-PCR analysis. Heat tolerance assay showed that deleting dsr11 significantly inhibited the viability under high temperature conditions. To assess the influence of dsr11 on the D. radiodurans transcriptome, 157 genes were found differentially expressed in the knock-out mutant by RNA-seq experiment. Combining RNA-seq and in silico analysis, we found that trmE (tRNA modification GTPase) and dr_0651 (arginase) were likely to be the direct targets of dsr11. Further microscale thermophoresis results demonstrated that dsr11 can directly bind to the mRNA of trmE and dr_0651. Our results indicated that dsr11 can enhance the tolerance to heat stress of D. radiodurans by binding to trmE and dr_0651 mRNA. Overall, these results extend our understanding of ncRNA regulation and provide new insights into the heat stress response in D. radiodurans.

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PSX-39 Late-Breaking Abstract: Characterization of epigenetic and transcriptional landscape in heat stressed rats using ATAC-seq and RNA-seq

Journal of Animal Science ◽

10.1093/jas/skaa278.621 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 353-354

Author(s):

Jinhuan Dou ◽

Flavio Schenkel ◽

Ying Yu ◽

Yachun Wang

Keyword(s):

Heat Stress ◽

Management Strategies ◽

Open Chromatin ◽

Rna Seq ◽

Sprague Dawley ◽

Physiological Regulation ◽

Animal Physiology ◽

Sprague Dawley Rats ◽

Differential Expression Genes ◽

Transcriptional Start Sites

Abstract Understanding animal physiology and identifying reliable biomarkers may help to establish effective management strategies for the prevention of heat stress (HS). However, little is known about the molecular mechanism of mammal tolerance to high temperatures. In a previous study with Sprague-Dawley rats, we performed RNA-seq assays on the liver of rats in control (CT; 22 ℃, n = 5) and heat stress (HS120; 42 ℃ for 120 min, n = 5) groups. A total of 3,909 differential expression genes (DEGs, Q < 0.05) were observed. This study was conducted to further examine the epigenetic landscape in the liver of rats under HS and identify transcription factors (TFs), as well as their regulated genes. Three liver tissues were selected from the RNA-seq samples and performed an Assay for Transpose Accessible Chromatin (ATAC-seq). Peaks meeting criteria of P< 0.05 and |Fold Change| >1.5 were considered as differential peaks. All ATAC-seq libraries generated an expected distribution of the insert fragment lengths, with the majority of fragments being small, which characterize inter-nucleosomal open chromatin, and progressively fewer fragments of larger size, which are spanning nucleosomes. The accessibility of transcriptional start sites (TSS) was significantly enriched. After merging data, 2,356 differential peaks showed CT having more accessible TSS than H120 and only 230 differential peaks showed H120 group having more accessible TSS than CT. Thirty-six and 22 TF motifs were predicted by up- and down-regulated differential peaks in H120 vs. CT. Together with the previous DEG results, we proposed candidate TFs annotated to Cebpa, Foxa4, and Sp3 DEGs, which are involved in the regulation of oxidative stress. In summary, we showed that nuclear chromatin in the liver of heat stressed rats was less open than that of control rats. We suggest that the TFs (Cebpa, Foxa4, and Sp3) may be involved in the physiological regulation of HS.

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