Unknown,Transcriptomics,Genomics,Proteomics

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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.

ORGANISM(S): Gallus gallus

SUBMITTER: OuYang Hongjia

PROVIDER: E-GEOD-62971 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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: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.

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Deep Sequencing Analysis of miRNAs Expression in Breast Muscle of Fast-Growing and Slow-Growing Broilers

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