Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Molecular regulation of enhanced muscle mass in developing Blond Aquitaine foetuses compared to Charolais

ABSTRACT: Background : The Blonde Aquitaine (BA) is a French beef breed with enhanced muscularity of unknown genetic origin. Targeted sequencing has shown that the BA is not a carrier of any of the bovine MSTN mutations. At the protein level the BA shows a transition to a faster muscle isoform phenotype with a greater proportion of type IIX and a smaller proportion of type I fibres than comparison Charolais (CH). Associated modifications in the activity of oxidative and glycolytic enzymes were also previously detected. Collectively, these changes are often observed in breeds of production species selected for enhanced growth and efficiency, but the underlying molecular mechanisms are unknown. Method : We examined the transcriptome of the Longissimus thoracis muscle at 4 gestational stages (110, 180, 210, and 260 dpc) in BA and CH foetuses. These time points coincide with primary and secondary myogenesis and functional differentiation. Total RNA was hybridised to the Agilent one-colour microarray platform containing 45,220 probes mapped to 17646 protein coding bovine genes. Following normalisation, we used a combination of differential expression (limma method, Smyth & al 2005) and a network theory method based on differential co-expression analysis (Hudson & al 2009) to compare and contrast the two muscle transcriptomes. Conclusions : In both breeds the most developmentally-regulated genes included: embryonic muscle subunit isoforms (e.g. MYL4) whose expression dropped dramatically prior to birth when they are replaced by the adult isoforms; metabolic enzymes (e.g. the mitochondrially-localised sarcomeric creatine kinase CKMT2) that prepare the foetus for functional independence postpartum, and 1 probe out of 4 representing a gene of unknown function (C13H20ORF194) also previously published as highly developmentally regulated in Wagyu by Hereford longissimus muscle (Hudson & al 2013). In contrasting the breeds, MSTN was the 2nd most differentially expressed muscle gene between the breeds, being approximately 4-fold down-regulated in CH at each of the time points. Given MSTN is a growth inhibitor, this result may reflect either divergent muscle mass or fibre composition in foetuses and could account for the low muscle development of BA calves at birth. Among the most differentially connected transcriptional regulators we prioritised expected molecules like MSTN, but also unexpected ones like PROX1, NMI, MBD1, NRIP2 and TAF12. Although not differentially expressed at the transcript level these molecules are transcriptionally rewired between the breeds and may form attractive new candidates for the development of differential muscle mass and fibre composition in cattle. 2 beef breeds: Blond Aquitaine (BA) and Charolais (CH) ; 4 gestational stages per breed (110, 180, 210, and 260 dpc); 3 animals (biological replicats) per stage and per breed, except for BA 180 dpc, BA 260 dpc and CH 110 dpc (only 2 animals due to technical problem during hybridization).

ORGANISM(S): Bos taurus

SUBMITTER: Isabelle Cassar-Malek

PROVIDER: E-GEOD-60844 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Similar Datasets

Project description:Background : The Blonde Aquitaine (BA) is a French beef breed with enhanced muscularity of unknown genetic origin. Targeted sequencing has shown that the BA is not a carrier of any of the bovine MSTN mutations. At the protein level the BA shows a transition to a faster muscle isoform phenotype with a greater proportion of type IIX and a smaller proportion of type I fibres than comparison Charolais (CH). Associated modifications in the activity of oxidative and glycolytic enzymes were also previously detected. Collectively, these changes are often observed in breeds of production species selected for enhanced growth and efficiency, but the underlying molecular mechanisms are unknown. Method : We examined the transcriptome of the Longissimus thoracis muscle at 4 gestational stages (110, 180, 210, and 260 dpc) in BA and CH foetuses. These time points coincide with primary and secondary myogenesis and functional differentiation. Total RNA was hybridised to the Agilent one-colour microarray platform containing 45,220 probes mapped to 17646 protein coding bovine genes. Following normalisation, we used a combination of differential expression (limma method, Smyth & al 2005) and a network theory method based on differential co-expression analysis (Hudson & al 2009) to compare and contrast the two muscle transcriptomes. Conclusions : In both breeds the most developmentally-regulated genes included: embryonic muscle subunit isoforms (e.g. MYL4) whose expression dropped dramatically prior to birth when they are replaced by the adult isoforms; metabolic enzymes (e.g. the mitochondrially-localised sarcomeric creatine kinase CKMT2) that prepare the foetus for functional independence postpartum, and 1 probe out of 4 representing a gene of unknown function (C13H20ORF194) also previously published as highly developmentally regulated in Wagyu by Hereford longissimus muscle (Hudson & al 2013). In contrasting the breeds, MSTN was the 2nd most differentially expressed muscle gene between the breeds, being approximately 4-fold down-regulated in CH at each of the time points. Given MSTN is a growth inhibitor, this result may reflect either divergent muscle mass or fibre composition in foetuses and could account for the low muscle development of BA calves at birth. Among the most differentially connected transcriptional regulators we prioritised expected molecules like MSTN, but also unexpected ones like PROX1, NMI, MBD1, NRIP2 and TAF12. Although not differentially expressed at the transcript level these molecules are transcriptionally rewired between the breeds and may form attractive new candidates for the development of differential muscle mass and fibre composition in cattle.

Project description:Obese and lean pig breeds showed obvious phenotypic variations and physiological differences in skeletal muscle growth. Prenatal muscle development programs postnatal performance. In this study we initially conducted full transcriptional profiling of prenatal skeletal muscle from Tongcheng pigs (obese) and Landrace pigs (lean) at 33, 65 and 90 days post coitus (dpc), using long serial analysis of gene expression (LongSAGE). We subsequently sequenced 317,115 LongSAGE tags and identified 1400 and 1201 differentially expressed transcripts that showed eight expression patterns for Tongcheng and Landrace, respectively. These two breeds had more significant differences in their gene expression profiles at 65 than that at 33 and 90 dpc. We also identified 532, 653 and 459 transcripts that were differentially expressed at 33, 65 and 90 dpc between the two breeds, respectively. The cellular function of the differentially expressed transcripts that matched annotated genes revealed that each stage had a uniquely altered profile between the two breeds in various functional categories including muscle fiber constitute and contraction, apoptosis, protein synthesis, and signalling transduction. Our results suggest that skeletal muscle development potentially has a greater lag in its growth rate at 33-65 dpc in Tongcheng pigs when compared with their Landrace counterparts. Our analyses therefore not only will provide valuable resources in the further identification of candidate genes for meat production traits, but also assist in the elucidation of the development of prenatal skeletal muscle in pigs and other vertebrates. Keywords: comparative transcriptome analysis Three Tongcheng and Landrace sows were mated with the same boar of each corresponding breed, respectively. The sows were then sacrificed at a commercial slaughterhouse and the uteri containing the embryos were collected immediately. The longissimus muscle tissues were then rapidly dissected from each of the embryos at 33, 65 and 90 dpc for both the Tongcheng and Landrace pigs. These samples were snap-frozen in liquid nitrogen and stored at -80°C until further use in the LongSAGE experiments. For the skeletal muscles from the six different samples, that is, Tongcheng (T33, T65 and T90, respectively) and Landrace (L33, L65 and L90, respectively), equal quantities of total RNA from each individual (n=4) were pooled. Six LongSAGE libraries were subsequently generated using I-SAGETM Long kits (Invitrogen, USA) according to the manufacturer’s instructions. Transforming clones were sequenced with the help of an ABI PRIZM 3730 DNA sequencer.

Dataset Information

Molecular regulation of enhanced muscle mass in developing Blond Aquitaine foetuses compared to Charolais

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure