Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of lamb muscle from animals with maternal callipyge allele

ABSTRACT: Lambs that inherit a callipyge allele from their dam have an up-regulation of maternally imprinted transcripts near the callipyge mutation but do not exhibit muscle hypertrophy. It is not clear what effects these maternally expressed transcripts have in the muscle or how the inheritance of a maternal callipyge allele prevents the expression of the callipyge phenotype which is seen paternal heterozygotes only. This experiment utilized bovine gene expression arrays to profile the gene expression of the semimembranosus muscle of 30 day old half-sibling lambs of all four possible genotypes with respect to the callipyge allele (+/+, C/+, +/C, and C/C). Experiment Overall Design: 10 lambs were used for this study. N=3 biological reps for C/C genotype, N=3 biological reps for Cmat/+ genotype, N=2 biological reps for +/Cpat genotype, and N=2 biological reps for +/+ genotype. Pairwise contrasts were performed to analyze the presence of a maternally inherited callipyge allele and the effect on a homozygous animal (+/C vs CC; +/+ vs C/+; and C/+ vs C/C). Experiment Overall Design: These data make up two experiments. Experiment Overall Design: [1] The maternal allele (4 genotype) experiment compares all four possible genotypes of a particular allele at one age and one tissue (30 days semimembranosus). Experiment Overall Design: [2] The paternal allele (2 genotype) experiment compares only the NC and the NN genotypes in one tissue (SM) across 4 ages (10, 20, 30, and 80 days). Experiment Overall Design: Images were interpreted with Microarray Suite version 5.0 (MAS5.0) in GCOS with no scaling or normalization (i.e., Samples GSM298143-GSM298164). Images were also interpreted by RMA using Bioconductor package of R (i.e., Samples GSM298165-GSM298186).

ORGANISM(S): Ovis aries

SUBMITTER: Christopher Bidwell

PROVIDER: E-GEOD-11780 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The callipyge phenotype is a monogenic muscular hypertrophy that is only expressed in heterozygous sheep receiving the CLPG mutation from their sire. The wild-type phenotype of CLPG/CLPG animals is thought to result from translational inhibition of paternally expressed DLK1 transcripts by maternally expressed miRNAs. To identify the miRNA responsible for this trans-effect, we used high-throughput sequencing to exhaustively catalogue miRNAs expressed in skeletal muscle of sheep of the four CLPG genotypes. We have identified 747 miRNA species of which 110 map to the DLK1-GTL2 or callipyge domain. We demonstrate that the latter are imprinted and preferentially expressed from the maternal allele. We show that the CLPG mutation affects their level of expression in cis (~3.2-fold increase) as well as in trans (~1.8-fold increase). In CLPG/CLPG animals, miRNAs from the DLK1-GTL2 domain account for ~20% of miRNAs in skeletal muscle.We show that the CLPG genotype affects the levels of A to I editing of at least five pri-miRNAs of the DLK1-GTL2 domain, but that levels of editing of mature miRNA are always minor. We present suggestive evidence that the miRNAs from the domain target the ORF of DLK1 thereby causing the trans-inhibition underlying polar overdominance. We highlight the limitations of high-throughput sequencing for digital gene expression profiling as a result of biased and inconsistent amplification of specific miRNAs. These data were used to confirm the expression levels found by the high-throughput sequencing analysis. A total of 8 samples (two animals per callipyge genotype) were analysed using the miRCury LNA microRNA array (Exiqon). On each array, the test sample labelled with Hy3 was hybridized on one channel, and a pool made with the 8 test samples (labelled with Hy5) was used on the other channel as a reference for normalization. The callipyge mutation (C) is a SNP localised in an imprinted domain. Thus, heterozygous animals will have different phenotypes. The following 4 genotypes were analyzed in this study: NN: Wild-type (+mat/+pat) CN: Maternal heterozygous (Cmat/+pat) NC: Paternal heterozygous (+mat/Cpat) CC: Homozygous mutant (Cmat/Cpat)

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Transcription profiling of lamb muscle from animals with maternal callipyge allele

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