Integrating miRNA and mRNA expression profiles in plasma of laying hens associated with heat stress

Whole genome discovery of regulatory genes responsible for the response of chicken to heat stress

Long noncoding RNAs (lncRNAs) are functional bridges connecting the genome with phenotypes by interacting with DNA, mRNA, and proteins. Using publically available acute heat stress (AHS)-related RNA-seq data, we discovered novel lncRNAs and tested their association with AHS along with ~ 8800 known lncRNAs and ~ 28,000 mRNA transcripts. Our pipeline discovered a total of 145 potentially novel-lncRNAs. One of them (Fishcomb_p-value = 0.06) along with another novel transcript (annotated as protein-coding; Fishcomb_p-value = 0.03) were identified as significantly associated with AHS. We found five known-lncRNAs and 134 mRNAs transcripts that were significantly associated with AHS. Four novel lncRNAs interact cis-regulated with 12 mRNA transcripts and are targeted by 11 miRNAs. Also six meta-lncRNAs associate with 134 meta-mRNAs through trans-acting co-expression, each targeted by 15 and 216 miRNAs, respectively. Three of the known-lncRNAs significantly co-expressed with almost 97 of the significant mRNAs (Pearson correlation p-value < 0.05). We report the mentioned three known-lncRNAs (ENSGALT00000099876, ENSGALT00000107573, and ENSGALT00000106323) as the most, significantly regulatory elements of AHS in chicken. It can be concluded that in order to alleviate the adverse effects of AHS on chicken, the manipulation of the three regulatory lncRNAs could lead to a more desirable result than the manipulation of the most significant mRNAs.

miRNA profiling of chicken follicles during follicular development

MicroRNAs (miRNAs) play a crucial role as transcription regulators in various aspects of follicular development, including steroidogenesis, ovulation, apoptosis, and gene regulation in poultry. However, there is a paucity of studies examining the specific impact of miRNAs on ovarian granulosa cells (GCs) across multiple grades in laying hens. Consequently, this study aims to investigate the roles of miRNAs in chicken GCs. By constructing miRNA expression profiles of GCs at 10 different time points, encompassing 4 pre-hierarchical, 5 preovulatory, and 1 postovulatory follicles stage, we identified highly expressed miRNAs involved in GC differentiation (miR-148a-3p, miR-143-3p), apoptosis (let7 family, miR-363-3p, miR-30c-5p, etc.), and autophagy (miR-128-3p, miR-21-5p). Furthermore, we discovered 48 developmentally dynamic miRNAs (DDMs) that target 295 dynamic differentially expressed genes (DDGs) associated with follicular development and selection (such as oocyte meiosis, progesterone-mediated oocyte maturation, Wnt signaling pathway, TGF-β signaling pathway) as well as follicular regression (including autophagy and cellular senescence). These findings contribute to a more comprehensive understanding of the intricate mechanisms underlying follicle recruitment, selection, and degeneration, aiming to enhance poultry's reproductive capacity.

Egg Quality, Yolk Fatty Acid Profiles from Laying Hens Housed in Conventional Cage and Cage-Free Production Systems in the Andean Tropics

Egg consumers worldwide have increased their concerns about laying hens' welfare and its impact on final egg product quality. This study compared the egg quality parameters under the conventional cage (CC) and cage-free (CF) egg production systems in the tropics. The study was conducted on a commercial farm in Colombia using Hy-Line Brown pullets, reared under the same conditions for the first 15 wks. At 16 wks, the hens were distributed into two housing systems, CC and CF, on the same farm. The hens were fed the same diet for each phase in both systems and feed intake varied slightly. Egg samples were collected every six wks, from 22 to 82 wks of age. A total of 3960 eggs were analyzed at 11 sampling times. Parameters such as albumen height, egg weight, yolk color, eggshell thickness, eggshell strength, and Haugh units were determined using a DET-6000 machine. At 22 and 82 wks, screening for Salmonella spp. status was conducted using environmental and egg samples. Additionally, at 34, 64, and 82 wks, yolk samples were obtained for fatty acid profiles and crude protein (CP) analysis. The data were analyzed in a completely randomized block design with repeated measures (11 times): mean separation by Student's t-test yolk pigmentation, Haugh Units, and albumen height (p < 0.001) were higher in the CF compared with the CC between 38 and 69 wks of age, and eggs at 63 and 82 wks (p < 0.05) were heavier in the CF compared to the CC. Likewise, eggs from the CC had better eggshell strength from 57 to 82 wks. In the egg yolk fatty acid profile at the 34th wk, the pentadecanoic, palmitic, and heptadecanoic acids had higher concentrations in the CF systems than the CC. At the 64th wk, the egg yolk fatty acids-lauric, myristic, and heptadecanoic-had higher concentrations in the CF; likewise, at the 82nd wk, egg yolks from the CC had higher concentrations of lauric, heptadecanoic, and nervonic fatty acids than the CF. The eggs and environmental samples were negative for Salmonella spp. throughout the whole production phase. These results indicated that the production system might impact internal and external egg quality measures, potentially due to various stressors, including environmental factors or behavior restrictions.

The network regulation mechanism of the effects of heat stress on the production performance and egg quality of Jinding duck was analyzed by miRNA‒mRNA

To explore the differential regulation mechanism of heat stress on the egg production performance and egg quality of Jinding ducks, 200 Jinding ducks (360-day-old) in good health and with similar body weights and a normal appetite were selected and randomly divided into a control (normal temperature [NT]) group (20°C-25°C) and a heat stress (HS) group (32°C-36°C), with 4 replicates in each group and 25 ducks in each replicate. The pretrial period was 1 wk, and the formal trial period was 4 wk. At the end of the 4th wk, 12 duck eggs were collected from each replicate to determine egg quality. Pituitary and ovarian tissues of Jinding ducks were collected, transcriptome sequencing was performed to screen differentially expressed miRNAs and mRNAs related to high temperature and heat stress, and a competitive endogenous RNA regulatory network was constructed. The sequencing data were verified by qRT‒PCR method. The following results were obtained: (1) Compared with the NT group, the HS group had a significantly lower laying rate, total egg weight, average egg weight, total feed intake, and feed intake per duck (P < 0.01), an extremely significantly higher feed-to-egg ratio (P < 0.01), and a higher mortality rate. (2) Compared with the NT group, the HS group had an extremely significantly lower egg weight, egg yolk weight, eggshell weight, and eggshell strength (P < 0.01) and an extremely significantly lower yolk ratio and eggshell thickness (P < 0.01, P < 0.05); however, there was no significant difference in the egg shape index, Haugh unit or protein height (P > 0.05). (3) A total of 1,974 and 1,202 genes were identified in the pituitary and ovary, respectively, and there were 5 significantly differentially expressed miRNAs. The differentially expressed genes were involved in the arginine and proline metabolism pathways, ether lipid metabolism pathway, and drug metabolism-cytochrome P450 pathway, which are speculated to be related to the egg production performance of Jingding ducks under high-temperature heat stress. (4) Novel_221 may target the PRPS1 gene to participate in egg production performance; novel_168 and novel_289 may target PIGW; novel_289 may target Q3MUY2; and novel_289 and novel_208 may target PIGN or genes that may be related to high-temperature heat stress. (5) In pituitary tissue, upregulated novel_141 (center of the network) formed a regulatory network with HSPB1 and HSP30A, and downregulated novel_366 (center of the network) formed a regulatory network with the JIP1 gene. In ovarian tissue, downregulated novel_289 (center of the network) formed a regulatory network with the ZSWM7, ABI3, and K1C23 genes, novel_221 formed a regulatory network with the IGF1, BCL7B, SMC6, APOA4, and FARP2 genes, and upregulated novel_40 formed a regulatory network with the HA1FF10 gene. In summary, heat stress affects the production performance and egg quality of Jinding ducks by regulating the secretion of endocrine-related hormones and the release of neurotransmitters as well as the expression of miRNAs and mRNAs in pituitary and ovarian tissues. The miRNA‒mRNA regulatory network provides a theoretical basis for the molecular mechanism that regulates the stress response in pituitary and ovarian tissues, egg quality, and production performance under heat stress.

The miR-216/miR-217 Cluster Regulates Lipid Metabolism in Laying Hens With Fatty Liver Syndrome via PPAR/SREBP Signaling Pathway

Fatty liver syndrome (FLS), a common metabolic disease in laying hens, caused by excessive hepatic fat deposition is a bottleneck in the poultry industry. However, no specific therapeutic methods have been developed. Evidence suggests that microRNAs (miRNAs) are essential for liver lipid metabolism and homeostasis, providing strong evidence for targeting miRNAs as a potential treatment option for liver diseases. However, the roles of miRNAs in the pathogenesis of FLS remain unclear. In present study, RNA-sequencing was performed to discern the expression patterns of miRNAs in normal and fatty livers of laying hens. In total, 12 dysregulated miRNAs (2 down-regulated and 10 up-regulated) were detected between the normal and fatty livers. Functional enrichment analysis showed the potential impacts of the dysregulated miRNAs on lipid metabolism. Notably, miR-216a/b and miR-217-5p, which belong to the miR-216/miR-217 cluster, were up-regulated in the sera and livers of FLS chickens, as well as free fatty acid (FFA)-induced LMH cells. Oil-red O staining revealed that up-regulation of the miR-216/miR-217 cluster induced lipid accumulation in FFA-induced LMH cells. Furthermore, the dual luciferase gene reporter assay and RT-qPCR analysis demonstrated that 3-hydroxyacyl-CoA dehydratase 2, F-box protein 8, and transmembrane 9 superfamily member 3 (TM9SF3) were directly targeted by miR-216a/b and miR-217-5p, respectively, and suppressed in the fatty livers of laying hens. Moreover, overexpression of the miR-216/miR-217 cluster or reduction in TM9SF3 levels led to activation of the proliferator-activated receptor/sterol regulatory-element binding protein (PPAR/SREBP) pathway. Overall, these results demonstrate that the miR-216/miR-217 cluster regulates lipid metabolism in laying hens with FLS, which should prove helpful in the development of new interventional strategies.

Dietary Chitosan Supplementation Improved Egg Production and Antioxidative Function in Laying Breeders

Simple Summary

Chitosan is a natural, non-toxic and biodegradable compound, which has antibacterial, antioxidant and anti-tumor properties. Several studies have shown that chitosan also improve the antioxidant capacity of poultry. Recent research showed that chitosan decreased oxidative damage by activating the nuclear factor erythroid-2 related factor 2 pathway, then elevated the meat quality of broilers. Egg breeders are susceptible to oxidative stress during peak egg production, which increase their susceptibility to diseases and lead performance decline. In addition, previous reports on the effect of chitosan on poultry production performance were inconsistent. Based on above reports, this study explored whether chitosan could promote the production performance, and antioxidant defense of laying hens by affecting the nuclear factor erythroid-2 related factor 2 pathway. The results showed that addition chitosan to layer hen diet could increase egg production and feed conversion ratio, and the effect was better at the level of 250~500 mg/kg; as well as, chitosan promoted the antioxidant status in serum, liver and duodenum tissues and the effect was better at the level of 500 mg/kg. Chitosan was likely to increase antioxidant enzyme activities by enhancing the expression of nuclear factor erythroid-2 related factor 2, thereby improving the antioxidant capacity of laying breeders.

Abstract

This study was conducted to explore the dietary effect of chitosan on the production performance, and antioxidative enzyme activities and corresponding gene expression in the liver and duodenum of laying breeders. A total of 450 laying breeders (92.44% ± 0.030% of hen-day egg production) were randomly assigned to five dietary treatments fed 8 weeks: maize-soybean meal as the basal control diet and the basal diet containing 250, 500, 1000 and 2000 mg/kg of chitosan, respectively. Each treatment was randomly divided into 6 equal replicates, with 15 laying breeders in each replicate. The results showed that dietary chitosan could increase hen-day egg production and feed conversion ratio, especially at the level of 250~500 mg/kg; however, chitosan had no prominent effect on feed intake and average egg weight. Dietary chitosan could dose-dependently promote the antioxidant status in serum, liver and duodenum of layer breeders. It has a better promotion effect at the level of 500 mg/kg; however, the effect was weakened at the level of 2000 mg/kg. Chitosan was likely to enhance the gene expression and activities of Nrf2-mediated phase II detoxification enzyme by up-regulating the expression of Nrf2, thereby improving the antioxidant capacity of laying breeder hens.

Analysis of Genomic Alternative Splicing Patterns in Rat under Heat Stress Based on RNA-Seq Data

Heat stress is one of the most severe challenges faced in livestock production in summer. Alternative splicing as an important post-transcriptional regulation is rarely studied in heat-stressed animals. Here, we performed and analyzed RNA-sequencing assays on the liver of Sprague-Dawley rats in control (22 °C, n = 5) and heat stress (4 °C for 120 min, H120; n = 5) groups, resulting in the identification of 636 differentially expressed genes. Identification analysis of the alternative splicing events revealed that heat stress-induced alternative splicing events increased by 20.18%. Compared with other types of alternative splicing events, the alternative start increased the most (43.40%) after heat stress. Twenty-eight genes were differentially alternatively spliced (DAS) between the control and H120 groups, among which Acly, Hnrnpd and mir3064 were also differentially expressed. For DAS genes, Srebf1, Shc1, Srsf5 and Ensa were associated with insulin, while Cast, Srebf1, Tmem33, Tor1aip2, Slc39a7 and Sqstm1 were enriched in the composition of the endoplasmic reticulum. In summary, our study conducts a comprehensive profile of alternative splicing in heat-stressed rats, indicating that alternative splicing is one of the molecular mechanisms of heat stress response in mammals and providing reference data for research on heat tolerance in mammalian livestock.

Differential expression of miRNAs and related mRNAs during heat stress in buffalo heifers

The present experiment was aimed to study differential expression of miRNAs and related mRNAs during heat stress (HS) in buffalo heifers. Twelve Murrah buffalo heifers aged between 1.5 and 2.0 years, weighting between 250 and 300 Kg were randomly assigned into two equal groups. The animals were kept in the psychrometric chamber under Thermo-neutral (TN; THI = 72) and HS (THI = 87-90) conditions for 6 h every day between 1000 and 1600 h for 21 days. The blood sampling was done at 1500 h on 15th day of the experiment and physiological parameters viz. pulse rate (PR), respiratory rate (RR) and rectal temperature (RT) were recorded at 1500 h on day -5, -3, -1, 0, +1, +3, +5 with respect to blood sampling. PBMCs were used for extraction of miRNAs and total RNA; and first strand cDNA was synthesized. qPCR was performed for relative gene expression studies. Physiological, hematological (erythrocytic indices), biochemical (triglycerides, urea, ALT, AST, LDH), redox (SOD, ROS) and endocrine parameters (T₄) altered significantly (P < 0.05) during HS as compared to TN. Out of eight targeted miRNAs only four were expressed in buffalo heifers. The relative expression of bta-mir-142, bta-mir-1248 and bta-mir-2332 was significantly (P < 0.05) up-regulated whereas expression of bta-mir-2478 was significantly (P < 0.05) down-regulated during HS as compared to TN. The relative expression of the predicted target genes i.e. HSF1, HSP60, HSP70, HSPA8 and HSP90 were significantly (P < 0.05) up-regulated whereas HSF4 expression was significantly (P < 0.05) down-regulated during HS as compared to TN. It can be concluded that a THI of 87-90 could lead to a moderate HS in buffalo heifers. Differential expression studies of miRNAs and related mRNAs in present study deciphers the role of miRNAs in the heat tolerance in buffalo heifers.

Potential role of specific microRNAs in the regulation of thermal stress response in livestock

Thermal stress is known to have harmful effects on livestock productivity and can cause livestock enterprises considerable financial loss. These effects may be aggravated by climate change. Stress responses to nonspecific systemic actions lead to perturbation of molecular pathways in the organism. The molecular response is regulated in a dynamic and synchronized manner that assurances robustness and flexibility for the restoration of functional and structural homeostasis in stressed cells and tissues. MicroRNAs (miRNAs) are micro molecules of small non-coding RNA that control gene expression at the post-transcriptional level. Recently, various studies have discovered precise types of miRNA that regulate cellular machinery and homeostasis under various types of stress, suggesting a significant role of miRNA in thermal stress responses in animals. The miRNAs revealed in this paper could serve as promising candidates and biomarkers for heat stress and could be used as potential pharmacological targets for mitigating the consequences of thermal stress. Stress miRNA pathways may be associated with thermal stress, which offers some potential approaches to combat the negative impacts of thermal stress in livestock. The review provides new data that can assist the elucidation of the miRNA mechanisms that mediate animals' responses to thermal stress.

MicroRNAs as Biomarkers for Animal Health and Welfare in Livestock

MicroRNAs (miRNAs) are small and highly conserved non-coding RNA molecules that orchestrate a wide range of biological processes through the post-transcriptional regulation of gene expression. An intriguing aspect in identifying these molecules as biomarkers is derived from their role in cell-to-cell communication, their active secretion from cells into the extracellular environment, their high stability in body fluids, and their ease of collection. All these features confer on miRNAs the potential to become a non-invasive tool to score animal welfare. There is growing interest in the importance of miRNAs as biomarkers for assessing the welfare of livestock during metabolic, environmental, and management stress, particularly in ruminants, pigs, and poultry. This review provides an overview of the current knowledge regarding the potential use of tissue and/or circulating miRNAs as biomarkers for the assessment of the health and welfare status in these livestock species.

The Mediation of miR-34a/miR-449c for Immune Cytokines in Acute Cold/Heat-Stressed Broiler Chicken

Simple Summary

In the intensive and scale poultry industry, the level of heat stress (HS) directly affects the growth, development, and production performance of poultry. To alleviate the adverse effects of stress in broilers, microRNA (miRNA) was regarded as a potential regulator of immune cytokines. In this study, through the sequencing analysis of spleens after cold/heat stress, we found that 33 and 37 miRNA were differentially expressed in the heat stress group compared with the normal (NS) group and cold stress (CS) group, respectively. The differential miRNA were mainly involved in biological processes such as the cytokine–cytokine receptor interaction. To further understand the miRNA-mediated effect of heat stress on the immune level of chickens, we selected miR-34a and miR-449c as the research objects, predicted and verified that interleukin 2 (IL-2) and interleukin 12α (IL-12α) were the target genes of miR-34a and miR-449c. Coupled with the analysis of the expression of other cytokines, we found that miRNA could change the expression of immune cytokines directly or indirectly. This discovery provides a new insight into the mediation of miRNA for immune cytokines in acute cold/heat stressed broiler chicken.

Abstract

An increasing amount of evidence has revealed that microRNAs (miRNAs) participated in immune regulation and reaction to acute cold and heat stresses. As a new type of post-transcriptional regulatory factor, miRNA has received widespread attention; However, the specific mechanism used for this regulation still needs to be determined. In this study, thirty broilers at the same growth period were divided into three groups and treated with different temperature and humidity of CS (10–15 °C and 90% Relative Humidity (RH)), HS (39 °C and 90% RH), and NS (26 °C and 50–60% RH) respectively. After 6 h, splenic tissues were collected from all study groups. miRNA sequencing was performed to identify the differentially expressed miRNAs (DEMs) between HS, CS, and NS. We found 33, 37, and 7 DEMs in the HS-NS, HS-CS, CS-NS group. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis showed that DEMs were significantly enriched in cytokine–cytokine receptor interaction and functioned as the cellular responders to stress. We chose two miRNA, miR-34a and miR-449c, from the same family and differential expressed in HS-CS and HS-NS group, as the research objects to predict and verify the target genes. The dual-luciferase reporter assay and quantitative real-time PCR (qRT-PCR) confirmed that two cytokines, IL-2 and IL-12α, were the direct target genes of miR-34a and miR-449c. To further understand the mediation mechanism of miRNAs in acute cold/heat-stressed broiler chicken, a splenic cytokines profile was constructed. The results showed that IL-1β was strongly related to acute heat stress in broiler chicken, and from this we predicted that the increased expression of IL-1β might promote the expression of miR-34a, inducing the upregulation of interferon-γ (INF-γ) and IL-17. Our finds have laid a theoretical foundation for the breeding of poultry resistance and alleviation of the adverse effects of stress.

Gga-miR-3525 Targets PDLIM3 through the MAPK Signaling Pathway to Regulate the Proliferation and Differentiation of Skeletal Muscle Satellite Cells

MicroRNAs (miRNAs) are evolutionarily conserved, small noncoding RNAs that post-transcriptionally regulate expression of their target genes. Emerging evidence demonstrates that miRNAs are important regulators in the development of skeletal muscle satellite cells (SMSCs). Our previous research showed that gga-miR-3525 is differentially expressed in breast muscle of broilers (high growth rate) and layers (low growth rate). In this study, we report a new role for gga-miR-3525 as a myogenic miRNA that regulates skeletal muscle development in chickens. Exogenous increases in the expression of gga-miR-3525 significantly inhibited proliferation and differentiation of SMSCs, whereas the opposite effects were observed in gga-miR-3525 knockdown SMSCs. We confirmed that PDLIM3 (PDZ and LIM domain 3) is a target gene of gga-miR-3525 that can promote proliferation and differentiation of SMSCs. We found that PDLIM3 overexpression elevated the abundance of phosphorylated (p-)p38 protein but that the gga-miR-3525 mimic and p38-MAPK inhibitor (SB203580) weakened the activation of p-p38. Furthermore, treatment with SB203580 reduced the promoting effect of PDLIM3 on SMSC proliferation and differentiation. Overall, our results indicate that gga-miR-3525 regulates the proliferation and differentiation of SMSCs by targeting PDLIM3 via the p38/MAPK signaling pathway in chickens.