- Background: Heat stress (HS) is a major stress event in the life of an animal, with detrimental upshots in production and health. - 0.05) were identified in the liver and adrenal glands of the Control and H120 groups, respectively. - Furthermore and 73 target differentially-expressed genes (DEGs) in the liver were predicted to interact with DElncRNAs based on trans. - Similarly, 437, 73 and 41 target DEGs in the adrenal glands were mostly significantly enriched in the cell cycle ( trans -prediction) and lysosome pathways ( cis -prediction). - The DElncRNAs interacting with DEGs that encode heat shock proteins (HSPs) may play an important role in HS response, which include Hsf4 , Dnaja1 , Dnajb4 , Hsph1 and Hspb1 in the liver, and Dnajb13 and Hspb8 in the adrenal glands. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. - Escalating global warming, combined with the global increase in the number of production animals and the intensification of agriculture [4, 5], has resulted in HS becoming a difficult challenge for live- stock and poultry production. - The current trends in the increase of global temperature [9, 10] indicate that it is necessary and urgent to comprehensively investigate the genetic and biological mechanisms of HS, as well as develop long-lasting, cumulative, and significant strategies for preventing HS.. - Comprehensive identification of lncRNAs in liver and adrenal glands. - A total of ~ 29.9 and 28.3 million raw reads in the liver and adrenal glands were obtained (Add- itional file 2: Table S2), in which 29.8 and 28.1 million clean reads were aligned to the reference gen- ome (Ensemble release version Rnor 6.0.91). - The average mapping rate of clean reads in the liver and adrenal glands was 95.71 and 92.99%, respectively.. - Secondly, the transcripts that might encode conserved protein do- mains were further filtered out by comparing them to two protein databases including (National Center for Biotechnology Information) NCBI non-redundant (NR) protein database and Universal Protein Resource (Uni- Prot) database and, as a result, 12,840 and 20,850 tran- scripts in the liver and adrenal glands were retained.. - Based on these features, a third filter was applied, and transcripts in the liver and transcripts in the adrenal glands were removed.. - Finally, the coding-non-coding index (CNCI), the coding potential assessment tool (CPAT), and the predictor of lncRNAs and mRNAs based on the k-mer scheme (PLEK) were used to evaluate the protein-coding poten- tial, and 4498 and 7627 transcripts in the liver and adrenal gland tissues were retained (Fig. - Finally, 4498 and 7627 transcripts in the liver and adrenal gland tissues were considered as putative lncRNAs (Fig. - Classification and characterization of lncRNAs in liver and adrenal glands. - According to the location relative to the nearest protein- coding gene (PCG), lncRNAs in the liver and adrenal glands were further classified into four types, including intergenic, intronic, sense, and antisense (Fig. - About 45.75% of lncRNAs in the liver (Fig. - 3a_left panel) and 57.31% of lncRNAs in the adrenal glands (Fig. - In addition, 19.45% of lncRNAs in the liver were antisense of PCGs, which were more frequent than those lncRNAs that overlapped with genes (11.72. - Figure 3b shows that almost 70.8% of lncRNAs in the liver ranged in size from 200 to 1000 nucleotides, with only 29.20% >. - In the ad- renal glands, similar characteristics of lncRNAs and protein-coding transcripts were observed with 55.79% of lncRNAs having >. - 0.05) in the liver and adrenal glands were obtained and further divided into six categories according to fold change (FC) values (Table 1 and Additional file 3: Table S3). - The top 20 DElncRNAs in the liver (12 up-regulated and 8 down- regulated) and adrenal glands (11 up-regulated and 9. - Additionally, 13 DElncRNAs were shared be- tween the liver and adrenal glands (Fig. - 4b), 469 and 258 DElncRNAs were identified in the liver and adrenal glands, respectively, as having tissue-specific expression.. - Among which, most lncRNAs (63.54%) were down- regulated in the liver, and over half (54.6%) of lncRNAs were down regulated in the adrenal glands. - 0.05) were identified in rat liver and adrenal glands in a previous study [22].. - The co-expression network between DElncRNAs and DEGs in the liver and adrenal gland tissues was created (Fig. - 1,935,712 connections between DElncRNAs and DEGs in the liver were identified, in which 44.46% were positive connections, and 55.54% were negative connec- tions (Fig. - In the adrenal glands links were identified between DElncRNAs and DEGs. - Moreover, most PCCs between DElncRNAs and DEGs in the adrenal glands (15.41%) ranged from − 0.8 to − 0.6, followed by 12.14% PCCs between − 0.6 and. - Three thousand seven hundred twenty-five connections including 317 DElncRNAs and 1274 DEGs, and 1969 connections in- cluding 139 DElncRNAs and 437 DEGs in the liver and adrenal glands were retained (Additional file 4: Table S4). - All connections between DElncRNAs and DEGs were then divided into 6 or 7 categories in the liver and adrenal glands, respectively (Fig. - The largest number of connections between DElncRNAs and DEGs in the liver was identified in the cluster of one DElncRNAs interacting with 11 ~ 20 DEGs, which includes 81 unique DElncRNAs and 648 DEGs. - Four hundred eighty-two connec- tions in the adrenal glands were clustered in the classifi- cation of one DElncRNA interacting with 21 ~ 30 DEGs, which includes 20 unique DElncRNAs and 207 unique DEGs. - The functions of 1274 and 437 DEGs interacting with 317 and 139 DElncRNAs in the liver and adrenal glands. - In the liver, 1274 DEGs were significantly enriched ( P <. - 3 The classification and characterization of lncRNAs identified in liver and adrenal glands. - 0.05) by 437 DEGs in the adrenal glands (Additional file 5: Table S5), with three of them shared with liver, i.e. - 0.05) were detected (Additional file 6: Figure S1A_right panel), but none of them were shared in the liver.. - A total of 512 and 545 genes were predicted in the liver and adrenal glands, with 121 and 191 DEGs (Additional file 7: Table S6). - In the liver, 121 DEGs were significantly enriched ( P <. - All DEGs in the liver were enriched in five pathways, and only one pathway, acute myeloid leukemia (rno05221), was significantly enriched ( P <. - In the adrenal glands, 33 BPs (Additional file 9: Table S8), as well as four pathways [e.g., lysosome (rno04142), peroxisome (rno04146), gap junction (rno04540) and NF-kappa B signaling pathway (rno04064. - Liver Adrenal glands. - Overall, 17,251 poten- tial RNA-mRNA interactions in the liver were detected between 1180 DElncRNAs and 364 genes, and 9917 potential RNA-mRNA interactions between 1985 DElncRNAs and 171 genes were identified in the adrenal glands (Additional file 10: Table S9). - In the liver, functional enrichment analysis of the 364 genes revealed. - Furthermore, 26 BPs were identified in the adrenal glands ( P <. - a The Pheatmap of the top20 DElncRNAs in liver and adrenal glands. - b The Pheatmap of commonly identified DElncRNAs in liver and adrenal glands. - Twenty significantly regulated pathways were detected in the adrenal glands (Additional file 6: Figure S1C_right panel), 15 of them are directly engaged in different types of cancer, suggesting that innate immunity and inflammation-related pathways in the adrenal glands could be mobilized to respond to HS. - By combining the DEGs identified in the current study, 73 (48 up-regulated and 25 down-regulated) and 41 (12 up-regulated and 29 down-regulated) target genes. - in the liver and adrenal glands were differentially expressed. - Seventy-three DEGs in the liver were significantly enriched ( P <. - 0.05) in the process of muscle development, such as striated muscle contraction (GO myosin filament as- sembly (GO muscle contraction (GO:. - 0.05) in the pathways of glucagon signaling and tight junction. - Functional annotation for the 41 DEGs ob- tained in the adrenal glands revealed that the positive regulation of axon regeneration (GO which showed the highest fold enrichment score of 106.27, was significantly enriched ( P <. - a Pearson correlation coefficient (PCC) analyses between DElncRNAs and DEGs in liver and adrenal glands. - 0070062) with 11 genes in the adrenal glands being part of the extracellular exosome, of which four genes were up-regulated and seven genes were down-regulated (Additional file 12: Table S11). - No pathway was signifi- cantly enriched in the adrenal glands.. - From a previous study, 30 and 33 genes of the HSP family genes in the liver and adrenal glands were differentially expressed, with fold change ranging from 0.19 to 28.03 and from 0.11 to . - All of these 30 HSP encoding genes in the liver were sig- nificantly enriched ( P <. - The 33 genes in the adrenal glands were significantly enriched ( P <. - The predictive analysis of target genes for the lncRNAs also displayed 19 and 6 HSP encoding genes in the liver and adrenal glands, respectively (Fig. - Among which, 15 and 5 DEGs in the liver and adrenal gland tissues were regulated by DElncRNAs (Fig. - In the present study, a well- established HS-rat model was used to explore the ex- pression profile and potential functions of lncRNAs in- volved in the HS response process in rat liver and adrenal glands by strand-specific RNA-seq. - A total of 4498 and 7627 transcripts were identified in the liver and adrenal glands, which were considered as putative lncRNAs (Figs. - The majority of lncRNAs in the liver and adrenal glands is located in intergenic regions, which is consistent with previous studies performed in other mammalian [49, 50], plant [51, 52] and fungal [53, 54] species. - Out of them, 13 DElncRNAs were shared in the liver and adrenal gland tissues (Fig. - Therefore, in order to further demonstrate the potential function of lncRNAs in the HS process, the putative tran- and cis- regulatory, as well as sequencing similarity regulatory module, were analysed. - Furthermore, all the 3909 and 4953 DEGs in the liver and adrenal glands were used as targets for DElncRNAs and performed functional annotation for the DEGs that met various rules of function prediction (Additional file 6: Figure S1 and Additional file 5: Table S5, Additional file 8: Table S7, Additional file 9: Table S8, Additional file 11: Table S10, Additional file 12: Table S11). - Furthermore, the shared pathways produced from target DEGs in the liver and adrenal glands might contribute to the understanding the poten- tial crosstalk mechanisms between two tissues under HS treatment [61].. - Furthermore, previous studies have discovered the crucial role of several lncRNAs in the regulation of. - When HS occurs, HSF1 is released and binds to heat shock elements in the HSP encoding gene promoter, thereby inducing its transacti- vation [64]. - In the present study, the DEGs that encode HSPs were functionally annotated (Fig. - Two HSF genes, Hsf4 and Hsf2 , in the liver were found to interact with one (TCONS_. - In addition, among all the DEGs encoding HSPs with a fold change greater than 5, the Dnaja1 , Dnajb4, Hsph1 , Hspb1 genes in the liver, and Dnajb13 and Hspb8 genes in the adrenal glands are all known to play diverse roles in HS regulation . - Many lncRNAs involved in the HS response in rat liver and adrenal gland tissues were discovered and character- ized, and their potential cis. - Moreover, the experi- ment was performed in the floor-standing artificial climate incubator (BIO250, BOXUN Medicine Instru- ment Co, Shanghai, China). - Rats in the Control group were never introduced to the incubator and were placed at room temperature. - In the PCR experiment, the Universal PCR primers, Index (X) Primer and Phu- sion High-Fidelity DNA polymerase were added in the reaction system. - In a previous research [22], the mRNA profiles in the liver ( n = 5) and adrenal glands ( n = 5), including the same samples of liver and adrenal glands sequenced by strand-specific transcriptome sequencing in the current study, were analyzed using the RNA-seq technique.. - The identification of DElncRNAs in the liver and adrenal glands between H120 and Control was carried out using Ballgown package of R version 3.5.3 (TUNA Team, Tsinghua University, Beijing, China). - All DEGs encoding HSPs were searched in the DEGs list and annotated by the ClueGO software [92]. - Summary of the DElncRNAs and DEGs identified in liver and adrenal gland tissues.. - Pearson Correlation Coefficient (PCC) analysis of DElncRNAs and DEGs identified in liver and adrenal gland tissues.. - The top 20 pathways from the enrichment analysis of the target DEGs in liver and adrenal glands under heat stress (H120). - The strand-specific RNA sequencing datasets generated during the current study are available in the Sequence Read Archive (SRA) database at the Na- tional Center for Biotechnology Information (NCBI) with the BioProject ID PRJNA624751.. - The Institutional Animal Care and Use Committee approved all the experimental procedures, which complied with the China Physiological Society ’ s guiding principles for research involving animals and adhered to the high standard (best practice) of veterinary care as stipulated in the Guide for Care and Use of Laboratory Animals.. - Heat stress- responsive transcriptome analysis in the liver tissue of Hu sheep. - The long noncoding RNA NEAT1 and nuclear paraspeckles are up- regulated by the transcription factor HSF1 in the heat shock response. - A long noncoding RNA acts as a post- transcriptional regulator of heat shock protein (HSP70) synthesis in the cold hardy Diamesa tonsa under heat shock. - Identification of long non-coding RNAs in the immature and mature rat anterior pituitary. - Genome-wide identification and functional prediction of long non-coding RNAs involved in the heat stress response in Metarhizium robertsii. - Characteristics of long non-coding RNAs in the Brown Norway rat and alterations in the Dahl salt-sensitive rat. - Non-coding RNAs turn up the heat: an emerging layer of novel regulators in the mammalian heat shock response. - Immobilization of proteins in the nucleolus by ribosomal intergenic spacer noncoding RNA. - Cardiovascular function in the heat-stressed human
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