Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of lamb Callipyge muscle types (ST, LD, SS, SM) at birth (T=0) and 12 weeks (T=12)

ABSTRACT: Microarrays were used for transcription profiling of skeletal muscle samples taken at birth, when the phenotype was not expressed, and 12 weeks of age from Callipyge and wild type sheep. The genes that underlie the expression of the phenotype rather than result from the fibre type change in the affected muscle have been identified. We used microarrays to detail the global programme of gene expression underlying the hypertrophy phenotype and identified distinct classes of regulated genes during this process. A working model that links the muscle hypertrophy phenotype with a core group of transcriptional coregulators is proposed. Experiment Overall Design: Gene expression analyses were performed primarily on longissimus dorsi skeletal muscle (LD) from Wild type (NN) and Callipyge (NCpat) sheep using Bovine Affymetrix GeneChip microarrays. Two developmental time-points were investigated in this study: newborn (within 5 days of birth; T0) and 11-12 weeks post-birth (T12). The muscle hypertrophy phenotype developed over the first 2-3 months and was associated with a significant change in muscle fibre type (Carpenter et al., 1996; Cockett et al., 1994; 1996; Kerth et al., 2003). One of the objectives of the gene expression analysis was to delineate between those genes that underlie the muscle hypertrophy in Callipyge sheep and those that result from the fibre type change in the affected muscle. To address this issue a comparison was undertaken of gene expression in wild type skeletal muscles with differing fibre type compositions to identify fibre type specific genes. These samples were taken from NN animals at T12. The three skeletal muscles used in this analysis were semimembranosis (SM), semitendinosis (ST) and longissimus dorsi (LD).

ORGANISM(S): Ovis aries

SUBMITTER: Ross Tellam

PROVIDER: E-GEOD-5955 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Identification of a gene network contributing to hypertrophy in callipyge skeletal muscle.

Vuocolo Tony T Byrne Keren K White Jason J McWilliam Sean S Reverter Antonio A Cockett Noelle E NE Tellam Ross L RL

Physiological genomics 20061031 3

The callipyge mutation in sheep results in postnatal skeletal muscle hypertrophy in the pelvic limbs and loins with little or no effect on anterior skeletal muscles. Associated with the phenotype are changes in the expression of a number of imprinted genes flanking the site of the mutation, which lies in an intergenic region at the telomeric end of ovine chromosome 18. The manner in which these local changes in gene expression are translated into muscle hypertrophy is not known. Microarray-based ...[more]

PMID: 17077277

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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)

Project description:The adult skeletal muscle is a plastic tissue with a remarkable ability to adapt to different levels of activity by altering its excitability, its contractile and metabolic phenotype and its mass. Knowledge on the mechanisms responsible for muscle mass comes primarily from models of muscle inactivity or denervation or from genetic models of muscle diseases. Given that the underlying exercise-induced transcriptional mechanisms regulating muscle mass are not fully understood, here we investigated the cellular and molecular adaptive mechanisms taking place in fast skeletal muscle of adult zebrafish in response to swimming. Fish were trained at low swimming speed (0.1 m/s; non-exercised) or at their optimal swimming speed (0.4 m/s; exercised). A significant increase in fibre cross-sectional area (1,290 M-BM-1 88 vs. 1,665 M-BM-1 106 M-NM-<m2) and vascularization (298 M-BM-1 23 vs. 458 M-BM-1 38 capillaries/mm2) was found in exercised over non-exercised fish. Gene expression profiling evidenced the transcriptional activation of a series of complex networks of extracellular and intracellular signaling molecules and pathways involved in the regulation of muscle mass, myogenesis and angiogenesis, many (e.g. BMP, TGFM-oM-^AM-", FGF, Notch, Wnt, MEF2, Shh, EphrinB2) not previously associated with exercise-induced contractile activity, and that recapitulate in part the transcriptional events occurring during skeletal muscle regeneration. These results demonstrate that fibre hypertrophy is responsible for the growth-promoting effects of exercise accompanied by a switch to a more oxidative capacity of white muscle fibres to fuel the increased energy demands. Importantly, our study identified novel molecular mechanisms regulating muscle mass and function in vertebrates. Adult zebrafish were subjected or not to a swim training regime consisting of swimming at the optimal swimming speed for this species for 6 h/day, 5 days/week for a total of 4 weeks (20 experimental days). Total RNA of fast muscle from individual non-exercised (n = 8) and exercised (n = 8) zebrafish was analyzed.

Dataset Information

Transcription profiling of lamb Callipyge muscle types (ST, LD, SS, SM) at birth (T=0) and 12 weeks (T=12)

Publications

Identification of a gene network contributing to hypertrophy in callipyge skeletal muscle.

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