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A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing (small RNA)

ABSTRACT: Pig is the important animal model for human obesity and diseases. However, the complexity of the porcine transcriptome is not yet fully elucidated. Here we have used massively parallel high-throughput sequencing of cDNA (RNA-seq) to generate a high-resolution map of the porcine miRNA in liver (LI), longissimus dorsi (LD) and abdominal fat (AF) from a F2 female full-sib pair with extreme phenotypes on growth and fat deposit. Through small RNA sequencing and on the basis of miRbase15.0, we detected a total of 184 mature miRNAs and 164 unique porcine novel miRNAs. Some conserved miRNAs, such as miR-122, miR-1, miR-206 and let-7 family showed high expression level in this study. Finally, we identified 10, 20 and 63 differentially expressed miRNAs, respectively, in LI, LD and AF. This high resolution and comprehensive transcriptome analysis significantly enhances the current genome annotation of pigs.

ORGANISM(S): Sus scrofa

PROVIDER: GSE25923 | GEO | 2010/12/20

SECONDARY ACCESSION(S): PRJNA142489

REPOSITORIES: GEO

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A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing (small RNA)

Project description:Pig is the important animal model for human obesity and diseases. However, the complexity of the porcine transcriptome is not yet fully elucidated. Here we have used massively parallel high-throughput sequencing of cDNA (RNA-seq) to generate a high-resolution map of the porcine miRNA in liver (LI), longissimus dorsi (LD) and abdominal fat (AF) from a F2 female full-sib pair with extreme phenotypes on growth and fat deposit. Through small RNA sequencing and on the basis of miRbase15.0, we detected a total of 184 mature miRNAs and 164 unique porcine novel miRNAs. Some conserved miRNAs, such as miR-122, miR-1, miR-206 and let-7 family showed high expression level in this study. Finally, we identified 10, 20 and 63 differentially expressed miRNAs, respectively, in LI, LD and AF. This high resolution and comprehensive transcriptome analysis significantly enhances the current genome annotation of pigs. examining the complexity of pig transcriptome in three organs from a female full-sib pair

2010-12-20 | E-GEOD-25923 | biostudies-arrayexpress

A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing (mRNA)

Project description:Pig is an important animal model for human obesity and diseases. However, the complexity of the porcine transcriptome is not yet fully elucidated. Here we have used massively parallel high-throughput sequencing of cDNA (RNA-Seq) to generate a high-resolution map of the porcine transcriptome and miRNA in liver (LI), longissimus dorsi (LD) and abdominal fat (AF) from an F2 female full-sib pair with extreme phenotypes in growth and fat deposit. On the basis of the porcine annotated genes against the UCSC database, we identified 21,414 annotated genes in our RNA-Seq analysis and 48,045-122,931 novel transcript fragments, which could be clustered into 17,085-29,499 novel transcriptional active regions (nTARs). We found that ~18.8% of the detected known genes showed alternative splicing patterns, and alternative 3’ splicing was the most common type of alternative splicing events in pigs. We also detected that more than 22.7% of the known genes identified here were extended at their 5’ and/or 3’ end. We identified 2,796, 1,551 and 835 differentially expressed genes (DEGs), respectively, in AF, LI and LD between the two individuals.

2011-01-12 | GSE26382 | GEO

A global view of the complexity of the porcine transcriptome using a full-sib pair with extreme phenotypes in growth and fat deposit by deep RNA sequencing (mRNA)

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MicroRNAome comparison between intramuscular and subcutaneous vascular stem cell adipogenesis

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Project description:Cattle plays an important role in providing essential nutrients through meat production. Thus, we focused on epigenetic factors associated with meat yield. To investigating circulating miRNAs that are involved with meat yield and connect biofluids and longissimus dorsi (LD) muscle in Korean cattle, we performed analyses of the carcass characteristics, miRNA array, qPCR, and bioinformatics. Carcass characteristics relative to the yield grade (YG) showed that the yield index and rib eye area were the highest, whereas the backfat thickness was the lowest for YG A (equal to high yield grade) cattle among the three YGs. miRNA array sorted the circulating miRNAs that connect biofluids and LD muscle. miRNA qPCR showed that miR-15a (r = 0.84), miR-26b (r = 0.91), and miR-29c (r = 0.92) had positive relationships with biofluids and LD muscle. In YG A cattle, miR-26b was considered to be a circulating miRNA connecting biofluids and LD muscle because the target genes of miR-26b was more involved with myogenesis. Then, miR-26b targeted genes, DIAPH3 and YOD1 were downregulated in YG A cattle. Our results suggest that miR-15a, miR-26b, and miR-29c are upregulated in biofluids and LD muscle whereas, downregulation of DIAPH3 and YOD1 in the LD muscle of finishing cattle steers.

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Identification of a circulating miRNA that is involved in meat yield and connects exosomes and longissimus dorsi muscle in Korean cattle steers

Project description:MicroRNAs (miRNAs) regulate gene expression. The aim of this study was to identify circulating miRNAs that are involved with meat yield and connect exosomes and longissimus dorsi (LD) muscle in Korean cattle steer. Thus, we performed analyses of the carcass characteristics, exosome extraction, bovine miRNA array, mature miRNA qPCR, bioinformatics, and qPCR. Our analysis of the carcass characteristics relative to the yield grade (YG) showed that the yield index (YI) and rib eye area were the highest, whereas the backfat thickness was the lowest for YG A cattle among the three YGs. We performed a miRNA microarray and a Venn diagram analysis to sort the circulating miRNAs that connect exosomes and LD muscle. Mature miRNA qPCR showed that miR-15a (r = 0.84), miR-26b (r = 0.91), and miR-29c (r = 0.92) had positive relationships with exosomes and LD muscle. In YG A cattle, miR-26b was considered to be a circulating miRNA connecting exosomes and LD muscle because the expression pattern of miR-26b was similar in the microarray and miRNA qPCR for miR-26b-targeted genes, where the expression levels of DIAPH3 and YOD1 were lower than those in YG C cattle. Our results suggest that circulating miR-26b may participate in cell maintenance by regulating DIAPH3 and YOD1 in the LD muscle of Korean cattle. 29 or 30 month Korean cattle steers were classified by yield grade(YG) A, B, and C. miRNA expression patterns for exosome and LD muscle were compared among YGs.

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The miRNA-targeted transcriptome of porcine alveolar macrophages upon infection with Porcine Reproductive and Respiratory Syndrome Virus (total RNA)

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