Deep Sequencing Analysis of miRNAs Expression in Breast Muscle of Fast-Growing and Slow-Growing Broilers
ABSTRACT: To investigate the function of miRNAs in chicken growth, breast muscle tissues of the two-tail samples (highest and lowest body weight) from Recessive White Rock (WRR) and Xinghua Chickens (XH) were performed on high throughput small RNA deep sequencing. In this study, a total of 921 miRNAs were identified, including 733 known mature miRNAs and 188 novel miRNAs. There were 200, 279, 257 and 297 differentially expressed miRNAs in the contrasts of WRRh Vs. WRRl, WRRh Vs. XHh, WRRl Vs. XHl, and XHh Vs. XHl group, respectively. A total of 22 serious differentially expressed miRNAs (fold change > 2 or < 0.5; P-value < 0.05; q-value < 0.01) which also have abundant expression (read counts > 1,000) were found in our contrasts. As far as two contrasts (WRRh Vs. WRRl, and XHh Vs. XHl) are concerned, we found 80 common differentially expressed miRNAs, meanwhile 110 miRNAs were found in WRRh Vs. XHh and WRRl Vs. XHl. Furthermore, only 26 common miRNAs were identified among all of four contrasts. Examination of miRNA profiles in two-tail samples of WRR and XH strains.
Project description:The objective of this study was to identify candidate genes associated with chicken growth and investigate their potential mechanisms. We used RNA-Seq to study the breast muscle transcriptome in high and low tails of Recessive White Rock (WRRh, WRRl) and Xinghua chickens (XHh, XHl). A total of 60, 23, 153 and 359 differentially expressed genes were detected in WRRh vs. WRRl, XHh vs. XHl, WRRh vs. XHh and WRRl vs. XHl, respectively. GO, KEGG pathway and gene network analyses showed that CEBPB, FBXO32, FOXO3 and MYOD1 played key roles in growth. The functions of FBXO32 and FOXO3 were validated. Examination of mRNA profiles in two-tail samples of WRR and XH strains.
Project description:Chicken growth traits are important in poultry production, however, little is known for its regulatory mechanism at epigenetic level. Therefore, this study aims to compare DNA methylation profiles between fast- and slow-growing broilers in order to identify candidate genes underlying chicken growth. Methylated DNA immunoprecipitation-sequencing (MeDIP-seq) was used to investigate the genome-wide DNA methylation pattern in high and low tails of Recessive White Rock (WRRh, WRRl) and that of Xinhua Chickens (XHh, XHl). The results showed that the average of methylation density was the lowest in CGIs followed by promoters. Within the gene body, the methylation density of introns was higher than UTRs and exons. Moreover, different methylation levels were observed in different repeat types with the highest in LINE/CR1. Methylated CGIs were prominently distributed in the intergenic regions and were enriched in the size range of 200-300 bp. In total 13,294 methylated genes were found in four samples, including 4,085 differentially methylated genes between WRRh and WRRl, 5,599 between XHh and XHl, 4,204 between WRRh and XHh, as well as 7,301 between WRRl and XHl. Moreover, 132 differentially methylated genes related to growth and metabolism were observed in both inner contrasts (WRRh Vs. WRRl and XHh Vs. XHl), whereas 129 differentially methylated genes related to growth and metabolism were found in both across-breed contrasts (WRRh Vs. XHh and WRRl Vs. XHl). Further analysis showed that overall 75 genes exhibited altered DNA methylation in all four contrasts, which included some well-known growth factors of IGF1R, FGF12, FGF14, FGF18, FGFR2, and FGFR3. In addition, we further validate the MeDIP-seq results by bisulfite sequencing in some regions. 12 Breast muscle samples were collected from two breeds of different growth rate, Recessive White Rock (WRR) and Xinhua Chickens (XH). Each breed included low and high-weight groups and 3 samples from each group were pooled equally for methylated DNA immunoprecipitation-sequencing (MeDIP-seq).
Project description:Long non-coding RNAs (lncRNAs) can have potential roles in development of tissues and organs. We selected breast muscle of fast-growing White Recessive Rock chicken (WRR) and slow-growing Xing Hua chicken (XH) to identify lncRNA transcripts by LncRNA-Seq. This study identified 21,993 novel lncRNAs. Among 7,339 differentially expressed lncRNAs, 723 up-regulated and 6,616 down-regulated lncRNAs were found in WRR compared with XH. Of them, five novel lncRNA were antisense transcripts for growth-related genes CACNA1D (unigene 14689_all), IL4I1 (unigene 15355_all), LEF-1 (unigene 19525_all) and FABP1 (unigenes 17536_all and 17537_all) respectively. Meanwhile, 12 other novel lncRNAs were found in the intron or downstream of some known growth-related genes (IGF1, IGF2BP2, IGF2BP3, CACNA1D, IL4I1, LEF-1 and FABP1). In addition, 4,043 SSRs and 200,049 SNPs were identified. Our data revealed the global lncRNA expression pattern in muscle tissue, and contributed a useful genomic resource towards studying the effects of lncRNAs in regulating chicken growth. Two RNA pool for WRR and XH strains
Project description:Purpose: The goals of this study are to investigate the differentially expressed miRNAs between ALV-J infected (WRR+) and uninfected (WRR-)chickens spleens by Illumina deep sequencing. Methods: 140-day-old female chickens of White Recessive Rock (WRR) were confirmed as J subgroup avian leukosis virus (ALV-J) infection. Total RNA from three ALV-J-infected spleens (designated: WRR1+, WRR2+, WRR3+) and three uninfected normal spleen samples (designated: WRR1-, WRR2-, WRR3-) was isolated by TRIzol following the manufacturer’s instruction (Invitrogen, CA, USA). RNA samples of three individuals within each group were pooled with equal amounts, and then were subjected to Illumina deep sequencing by Illumina Hiseq 2500. Results: After raw data filtered, 12,150,275 and 15,227,930 reads of 18-32 bp, representing 569,847 and 543,062 unique sequences, were obtained for WRR- and WRR+ libraries, respectively. Through blasting with the chicken reference genome, 360,180 WRR- sequences and 327,391 WRR+ sequences, which accounted for more than 60% of the unique sequences, were perfectly matched.To analyze the miRNA detection efficiency of Illimuna deep sequencing, all the clean reads were blasted with the Rfam data base 10.1, annotated and then removed rRNA, tRNA, snoRNA and other snRNAs. The annotation results revealed that miRNAs accounted for more than 68% of all clean reads in the WRR− and WRR+ libraries. In this study, a total of 476 miRNAs were identified after compared the unique sequences against the chicken miRNAs precursors in miRBase 18.0. Base on unique sequences matched counts, 167 differential expression miRNAs were identified by DEGseq package using Benjamini-q-value of 0.001 as a cut-off. In ALV-J infected spleens, 83 miRNAs showed up-regulated expression and 84 were down-regulated when compared to uninfected samples. Conclusions: Our study represents the first time to analysis of miRNA Expression in Spleen of J Subgroup Avian Leukosis Virus (ALV-J) Infected (WRR+) and Uninfected (WRR-) Broilers. A total of 167 miRNAs were found to be differentially expressed in ALV-J infected spleens when compared to uninfected chickens. These miRNAs can be considered as candidates for further study ALV-J invasion. Overall design: Spleen miRNA profiles of 140-day-old ALV-J infected (WRR+) and uninfected (WRR-) female chickens of White Recessive Rock were generated by deep sequencing, using Illumina Hiseq 2500.
Project description: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:Whole lung RNA-seq of 8 mice with experimental Schistosoma-induced pulmonary hypertension, compared to 8 control mice. All mice on a C57Bl6/J background. 3 schisto-PH and 3 control mice (#s 1-3 in each group) were also processed by Affy microarray and separately submitted. 3 of the mice in each group (labeled 1D11) were also treated with the pan-TGF-beta neutralizing antibody 1D11. Illumina HiSeq 2000 used. Data published in: Protective Role of IL6 in Vascular Remodeling in Schistosoma-Pulmonary Hypertension. Graham BB, Chabon J, Kumar R, Kolosionek E, Gebreab L, Debella E, Edwards M, Diener K, Shade T, Bifeng G, Bandeira A, Butrous G, Jones K, Geraci M, Tuder RM. Am J Respir Cell Mol Biol. 2013 Jul 1. [Epub ahead of print] PMID: 23815102 Whole lung transcriptome of 8 mice with experimental Schistosoma-induced pulmonary hypertension, compared to 8 control mice. All mice on a C57Bl6/J background.
Project description:In the present study, goal was to scan the potential biomarker for acute kidney injury induced by aristolochic acid I (AAI).We utilized the microarry analysis to investigate the microRNA (miRNA) expression profile in kidneys from rat treated by 40mg/kg AA I for 2-6 days. miRNAs with significantly different expression of global miRNA expression profile were validated by qRT-PCR. For miRNAs still significantly disregulation, we further examined the expression in plasma of rats treated with AAI dosed at 10, 20 and 40mg/kg AAI for 2-6 days by qRT-PCR. miRNAs with significantly dysregulation in plasma, their expression in brain, liver and heart was examined for kicking out the non-specific disregulation in AAI induced acute kidney injury, so that the significant dysregulation miRNAs with specificity in kidney and plasma was found as potential biomarkers for AAI induced acute kidney injury. Five control and 15 kidneys treated with 40mg/kg AAI on day 2, 4 and 6 was examined by microarray.
Project description:Rationale: Schistosomiasis is one of the most common causes of pulmonary arterial hypertension worldwide, but the pathogenic mechanism by which the host inflammatory response contributes to vascular remodeling is unknown. We sought to identify signaling pathways that play protective or pathogenic roles in experimental Schistosoma-induced pulmonary vascular disease by whole-lung transcriptome analysis. Methods: Wildtype mice were experimentally exposed to S. mansoni ova by intraperitoneal sensitization followed by tail vein augmentation, and the phenotype assessed by right ventricular catheterization and tissue histology, RNA and protein analysis. Whole-lung transcriptome analysis by microarray and RNA sequencing was performed, the latter analyzed using 2 bioinformatic methods. Functional testing of the candidate IL-6 pathway was determined using IL6-knockout mice and the STAT3 inhibitor STI-201. Results: Wild-type mice exposed to S. mansoni had increased right ventricular systolic pressure and thickness of the pulmonary vascular media. Whole lung transcriptome analysis identified the IL6-STAT3-NFATc2 pathway as being upregulated, which was confirmed by PCR and immunostaining of lung tissue from S. mansoni-exposed mice and patients who died of the disease. Mice lacking IL6 or treated with STI-201 developed pulmonary hypertension associated with significant intima remodeling after exposure to S. mansoni. Conclusions: Whole lung transcriptome analysis identified upregulation of the IL6-STAT3-NFATc2 pathway, and IL6 signaling was found to be protective against Schistosoma-induced intimal remodeling. Affy Mouse ST1.0 chip used. Whole lung transcriptome of 3 mice with experimental Schistosoma-induced pulmonary hypertension, compared to 3 control mice. All mice on a C57Bl6/J background.
Project description:We used Affymetrix microarrays to investigate gene expression changes in PBMNCs isolated from female and male pigs to determine significant modulatory effects that may have been induced by the intake of GE and (or) RES during 4 months in animals fed an atherogenic diet (AD) . The aim of this work was to determine whether the intake of low doses of a Grape Extract (GE; 1 g/70 Kg animal body weight) and (or) Resveratrol (RES; 18 mg/70 Kg animal body weight) exerted any modulatory effects, at the level of gene expression, in PBMNCs isolated from female and male pigs exposed to an atherogenic diet (AD) for 4 months. We isolated PBMNCs, and the corresponding total RNA, from 2 female and 2 male pigs for each group. Pure RNA was extracted from the PBMNCs for microarrays analyses (Affymetrix) and gene differential expression determined between the AD fed animals and control (CT) animals (to determine the effects of a high-fat consumption) and between the AD fed animals supplemented with GE and (or) RES and the animals fed the AD diet alone (to determine the effects of GE and (or) RES on the fat consumption). In addition, the effects of the consumption of GE and RES against a standard control diet (CT) were also determined. Differential gene expression: 1) AD vs CT (response to exposure to a high-fat diet); 2) AD-GE vs AD (modulatory effects of the intake of a grape extract on high-fat fed animals); 3) AD-GE-RES vs AD (modulatory effects of the intake of a resveratrol-enriched grape extract on high-fat fed animals); 4) AD-RES vs AD (modulatory effects of the intake of resveratrol on high-fat fed animals); 5) CT-GE-RES vs CT (modulatory effects of the intake of a resveratrol-enriched grape extract on animals fes a standard pig chow).