Lower Expression of SLC27A1 Enhances Intramuscular Fat Deposition in Chicken Via Down-Regulated Fatty Acid Oxidation Mediated by CPT1A
ABSTRACT: Purpose: The goals of this study are to investigate the differentially expressed genes between High IMF chickens (WC) and Low IMF chickens (WRR) breast muscles by Illumina deep sequencing, to reveal the mechanism underlying chicken IMF deposition. Methods: Both WC chickens and WRR chickens were raised up to 120 d of age (D120) or 180 d of age (D180), two female birds of similar weight from each breed per age were subjected to RNA-sequencing by Illumina Hiseq 2000. So eight muscle samples in total were subjected to RNA-seq analysis, four WC chicken samples including WC.D120.B-1, WC.D120.B-3, WC.D180.B-2 and WC.D180.B-3, and four WRR chicken samples including WRR.D120.B-4, WRR.D120.B-6, WRR.D180.B-2 and WRR.D180.B-5. Results: The clean reads of each sample were over 20 million, the expressed genes ranged from 16202 to 17838, and a little higher in WRR samples than in WC samples. Differentially expresse analysis showed that there were 525, 161, 23, 87 DEGs detected in the comparisons of WRR.D120.B-VS-WC.D120.B, WRR.D180.B-VS-WC.D180.B, WC.D120.B-VS-WC.D180.B and WRR.D120.B-VS-WRR.D180.B, respectively. Many genes related to lipid catabolism were down-regulated in WC chickens. Conclusions: Our present study suggest that lower lipid catabolism exists in WC chickens but not in WRR chickens, and lower expression of SLC27A1 is through down-regulating fatty acid oxidation mediated by CPT1A to facilitate IMF deposition. Moreover, these findings indicate that reduced lipid catabolism, rather than increased lipid anabolism, contributes to chicken IMF deposition. Overall design: Two female birds from WC and WRR chickens at 120 d of age (D120) and 180 d of age (D180) respectively were subjected to RNA-sequencing by Illumina Hiseq 2000.
Project description:Muscle development and lipid deposition are complex processes regulated by a coordinated expression profile of genes. Pekin ducks displayed a significant difference from Cherry Valley duck in muscle fiber development and IMF contents. Genetic comparisons between these two breeds would contribute to the exploration of mechanisms underlying the phenotypic differences. In the present study, breast tissues of Pekin (BD) and Cherry Valley (CD) ducks were used for RNA-seq in two different time points (3 and 6-week) to investigate the transcriptome basis. A total of 16705 genes from duck breast muscle were detected as positively expressed genes (RPKM>0.1) and 2273 genes were regarded as novel genes. Differentially expressed genes (DEGs) in BD3 VS CD3 were regarded as muscle development-related genes as CD3 grown faster than BD3 in muscle fibers. DEGs in BD6 VS CD6 were regarded as lipid-related genes as a much higher IMF contents in BD6 than CD6 while no differences observed in 3-week. DEGs obtained from BD3 VS BD6 and CD3 VS CD6 were also analyzed as relative genes here. In all, 9 genes (MAT1A, KAZALD1, SHROOM3, KLHL6, MYH13, ALDOA, TNNT2, PDLIM3 and PFKM) were validated as muscle development correlated candidate genes, and another 11 genes (DHCR24, CNTFR, ANGPTL4, BCL6, HIP1, TRIB1, ADORA1, C1QTNF2, CD36, PRKAG2 and ACSL1) were regarded as lipid correlated genes in duck. What’s more, functional analysis confirmed that the immune reaction, ECM and energy metabolism also correlated with muscle development and lipid deposition closely. The present study not only enlarged the duck genetic information pool but also provided a dozen of candidate genes related to muscle development and lipid deposition, which laid a firm foundation for the further studies on molecular mechanisms in duck. Overall design: RNA-deep sequencing of breast muscle in 3-week and 6-week age native Pekin duck and Cherry Valley Pekin duck under Hi-seq 2000
Project description:The process of commercial catching, transport and slaughter (CTS) is known to be an acute stressful event in broiler chickens. Corticosteroid concentrations increase, impacting measures of IGF-1, growth hormone and metabolites of the immune system from blood plasma samples. We used ARK-Genomics chicken 20K oligo array, a two channel DNA microarray, to investigate the significantly differentially expressed genes in the livers of chickens during CTS. Overall design: We investigate the differences of gene expression profiles in hepatic tissues between control birds (n=10) and birds experiencing CTS (n=10) using an ARK-Genomics chicken 20K oligo array, a two channel DNA array (http://www.ark-genomics.orgmicroarray) with full dye swap.
Project description:The process of commercial catching, transport and slaughter (CTS) is known to be an acute stressful event in broiler chickens. Corticosteroid concentrations increase, impacting measures of IGF-1, growth hormone and metabolites of the immune system from blood plasma samples. We used ARK-Genomics chicken 20K oligo array, a two channel DNA microarray, to investigate the significantly differentially expressed genes in the livers of chickens during CTS. We investigate the differences of gene expression profiles in hepatic tissues between control birds (n=10) and birds experiencing CTS (n=10) using an ARK-Genomics chicken 20K oligo array, a two channel DNA array (http://www.ark-genomics.orgmicroarray) with full dye swap.
Project description:Salmonella causes inflammation in infected hosts. Inflammation is a well-characterized defensive mechanism of innate immunity. The recognition and engagement of lipopolysaccharide (LPS) endotoxins in the outer membranes of Salmonella to Toll-like receptor 4 of immune cells (macrophages and dendritic cells) trigger inflammatory responses characterized by secretion of pro-inflammatory cytokines, including TNF-beta, IL-1 and IL-6. These cytokines cause fever, anorexia, bodyweight losses, and catabolism of skeletal muscles and adipose tissues. However, molecular events underlying innate immune responses and metabolic activities during the later stage of inflammation are poorly understood. Additionally, the effects of prebiotics and antibiotics on innate immunity and nutrient metabolism are not yet reported. The objective of this study is to investigate the effects of a mannanoligosaccharide (MOS) prebiotic and virginiamycin (VIRG) sub-therapeutic antibiotic on innate immunity and glucose metabolism during late inflammation. We induced Salmonella LPS-systemic inflammation in a chicken model. Differentially regulated gene expressions were measured using 2 colour focussed oligonucleotide chicken-specific microarrays. Microarray analysis was performed on liver, intestinal and skeletal muscle tissues. We found that late inflammation was principally modulated by interleukin 3 (IL 3) and that glucose was mobilized from gluconeogenesis occurring in the intestines only. MOS and VIRG modulated innate immunity and metabolic genes differently. In contrast to VIRG, MOS terminated inflammatory responses earlier. Our results indicate IL 3 gene up-regulation in VIRG-fed chickens. To meet the higher energy requirements of VIRG chickens, genes for intestinal gluconeogenesis and liver glycolysis were respectively induced. Our study reveals the potential mechanisms by which prebiotic and antibiotic modulated innate immunity and glucose metabolism during late inflammation. 14-day old chickens were injected i.p. with saline or LPS. For each tissue and experimental conditions (saline or LPS challenge), a total of 12 microarrays (6 MOS birds + 6 VIRG birds) were used in a 2 x 2 factorial design and complete interwoven loop arrangement. We compared gene expression from prebiotic-fed birds with antibiotic-fed birds without including reference RNA. LPS challenge, antibiotic or prebiotic, innate immunity, glucose metabolism
Project description:Avibacterium paragallinarum is the causative agent of Infectious Coryza, an acute upper respiratory tract disease in chickens. The occurrence of outbreaks has emphasized that the disease can be significant in broiler as well as layer chickens. In developing countries, infectious coryza is commonly complicated by a range of other infections, resulting in severe disease and significant economic losses. There are vaccines on the market but with limited efficiency, due to the serological differences amongst the different serogroups of A. paragallinarum. Recent advances in genomics have led to whole genome sequencing of the chicken, creating an opportunity for the use of high-throughput technology such as microarrays. The objectives of this study was to screen for gene expression patterns across clinical scores associated with the immune response in chickens infected with A. paragallinarum serovar C3, as well as to establish which biological pathways are stumulated when infected with A. paragallinarum. A total of 15 birds (male, leghorn) were obtained at 10 weeks of age. The birds were kept in separate layer cages up until 21 weeks, this is the susceptible age for infectious coryza. Twelve (12) birds were challenged via the infra-orbital eye area with 0.1ml challenge bacterium (A.paragallinarum serovar C3), Three were left unchallenged, which served as the control. As symptoms developed birds were scored, with score1 representing mild symptoms, score2, moderate and score3 representing severe symptoms. Each score is represented by two biological replicates. Thus a total of 8 samples were hybridized, two representing control.
Project description:Divergently selected chickens for either high growth (HG genotype) or low growth (LG genotype) developed at SRA-INRA, France were used to profile hepatic gene expression during juvenile development (1 to 11 weeks of age) and to identify differentially expressed genes associated with genotype and age. The HG and LG chickens are different in various phenotypic and metabolic measurements, including growth rate, abdominal fat, plasma glycemia, insulinemia, T4, T3, triglyceride and NEFA. The HG and LG chickens are valuable as a model for biomedical and agricultural traits. The Del-Mar 14K Chicken Integrated Systems microarrays were used for a transcriptional scan in liver during juvenile development using a balanced block hybridization design. Log2-transformed fluorescence intensities were analyzed with a two-stage mixed model. A total number of 531 differentially expressed genes were identified. The greatest number of genes was detected at 7 weeks of age where 178 genes were up-regulated in the HG and 162 genes up-regulated in the LG. The differentially expressed genes include metabolic enzymes, acute phase proteins, immune factors and transcription factors involved in various pathways (i.e., fatty acid and amino acid metabolism, glycolysis, oxidative phosphorylation, growth factor signaling and immune defense). Several of these functional genes are also identified as positional candidate genes within QTLs in an F2 population established from an intercross between the HG and LG lines. Keywords: divergently selected chickens, growth, transcriptional profiling, differentially expressed genes Overall design: A balance block design was used for microarray hybridizations, where half of the birds of each genotype and age were labeled with Alexa Flour 647 (red) and the other half with Alexa Flour 555 (green). Four biological replicates were used for each genotype (HG or LG) at six different ages (1, 3, 5, 7, 9 and 11 wk). An additional hybridization of eight replicates for each age and genotype was performed to verify the small number of differentially expressed genes detected at 1 and 3 weeks in the first hybridization. The second hybridization included four technical replicates (same birds that were originally used for the first hybridization) and four additional biological replicates with different birds from each genotype at 1 and 3 weeks of age.
Project description:Infectious laryngotracheitis (ILT) is an acute, contagious, upper respiratory disease, which is caused by gallid herpesvirus 1 (GaHV-1). Due to the mortality rates up to 70% depending on the virulence of the virus, it is of economic importance of the disease to explore the etiology of the ILT in the poultry industry. In this study, 15-day-old SPF white leghorn chickens were used to transcriptome analysis in chicken trachea immunized with infectious laryngotracheitis virus vaccine. In conclusion, chicken embryo origin (CEO) vaccine activation of the MHC-I and MHC-II pathways provides insight into the molecular mechanism of immune response in chickens, and holds potential for evaluation and design of new ILT vaccines in a manner adapted to the host immune response to the virus. Ten vaccine inoculated birds were randomly divided in two groups. Each group represents one replication of five pooled tissues, for inoculated birds. Control group consists of five birds that received sterile vaccine diluent.
Project description:Relative expression levels of mRNAs in chicken cecal epithelia experimentally infected with Eimeria tenella were measured at 4.5 days post-infection. Two weeks old chickens were uninfected (negative control) or were orally inoculated with sporulated oocysts of Eimeria tenella. Cecal epithelia samples were collected from >12 birds in infected or uninfected group at 4.5 d following infections, in which samples from 4 birds were pooled together to form a total 3 biological replicates in each group. Parasite merozoites were also collected from four infected chickens at 5 d after infections. Uninfected control samples, merozoites and infection group samples were selected for RNA extraction and hybridization on Affymetrix microarrays. We used Affymetrix GeneChip chicken genome arrays to detail the chicken cecal epithelia gene expression in the control and E. tenella-infected birds. Infected, uninfected chicken cecal epithelia and merozoites were selected for RNA extraction and hybridization with Affymetrix microarrays. Our goal was to analyze global transcriptome changes in chicken cecal mucous membranes in response to E. tenella infection in vivo. We used infected (T1,T2,T3; three biological replicates) and uninfected (Neg1, Neg2, Neg3; three biological replicates) samples to identify genes that were differentially expressed. Meanwhile, RNA and probes were also prepared from parasite merozoites (Mzt) from infected samples (Mzt) and used as an additional control in microarray hybridization.
Project description:8 weeks old Chickens (White leghorn (LSL), 4 per group), were i.v. injected every three hours with 1x10^7 Units recombinant chicken interferon alpha to obtain a plasma concentration similar to the amount of type I IFN produced during natural infection. Three (1 IFN injection), six (2 injections) and nine (three injections) hours after the first injection spleen and lung of the birds were sampled and subjected to microarray analysis using Agilent 4x44k chicken arrays customized with a multitude of immune genes (e.g. chemokines and chemokine receptors, cytokines and cytokine receptors). Birds receiving buffer only served as control.
Project description:A deletion mutation in the growth hormone receptor (GHR) gene results in the inhibition of skeletal muscle growth and fat deposition in dwarf chickens. In this study, microarray techniques were used to detect the miRNA and mRNA expression profiles of 14-day-old embryo and 7-week-old chicken skeletal muscle of deletion-type dwarf chickens and normal-type chickens. Skeletal muscle tissues of Dwarf recessive White Rock chickens and normal recessive White Rock chickens were used to make the microarray assay. Results show the expression of miR-1623 and miR-181b in 14-day-old embryos and of let-7b and miR-128 in 7-week-old chickens. let-7b was the only miRNA found to be completely complementary to its target in the 3'UTR of GHR and inhibited GHR gene expression. KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathway analysis and RT-PCR verified that there were three main signalling pathways regulating the skeletal muscle growth and fat deposition of chickens influenced by the let-7b-regulated GHR gene. The suppression of the cytokine signalling 3 (SOCS3) gene was found to be involved in the signalling pathway of adipocytokines. We found that let-7b is the critical miRNA involved in the regulation of the GHR gene. SOCS3 plays a critical role in the network regulating skeletal muscle growth and fat deposition via let-7b-mediated GHR gene expression. Two groups were analyzed in the array assay: one group consisted of normal recessive White Rock 7-week-old chicken leg muscle tissues, and the other group consisted of dwarf recessive White Rock 7-week-old chicken leg muscle tissues. The control samples were labeled as A1b, A2b, A3b, and the dwarf chicken samples were labeled as B1b, B2b, and B3b. 9 total chickens per breed, 3 chickens used per breed for each sample. 523 mature miRNA sequences were assembled and integrated into the LC miRNA microarray design, and different expression miRNAs were measured on the 7000HT Fast Real-Time PCR system. REPLACE This submission represents the miRNA profiling component of the study.