Transcript profiling of expressed sequence tags from semimembranosus muscle of commercial and naturalized pig breeds

Nascimento, Carlos Souza do; Peixoto, J. O.; Verardo, Lucas Lima; Campos, Carolina; Weller, Mathias; Faria, Vinícius Ribeiro; Botelho, Margareth Evangelista; Martins, Marta Fonseca; Machado, Marcos Antônio; Silva, F.F.; Lopes, Paulo Sávio; Guimarães, Simone Eliza Facioni

doi:10.4238/2012.june.15.1

Cited by 4 publications

(10 citation statements)

References 21 publications

(25 reference statements)

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“…Previous studies have shown breed differences in mitochondrial function in muscle and fat in the pig [27,28]. The transcript profiling of ESTs from the semimembranosus muscle demonstrates elevated expression of mitochondrial related enzymes (NADH dehydrogenase, cytocrome c oxidase and cytocrome b reductase) in the skeletal muscle of Piau, a naturalized Brazilian pig breed with slow growth rate, high fat deposition and favorable meat quality, compared to commercial breeds (Large White and Duroc), implicating breed differences in oxidative and glycolytic metabolism [29]. Similar breed differences were reported in Korean native pigs who demonstrate higher expression of the 3 mitochondrial proteins: succinate dehydrogenase, NADH-ubiquinone oxidoreductase, and glycerol-3-phosphate dehydrogenase in the muscle as compared with Landrace [4].…”

Section: Discussionmentioning

confidence: 99%

Glucocorticoid receptor is involved in the breed-dependent transcriptional regulation of mtDNA- and nuclear-encoded mitochondria genes in the liver of newborn piglets

Zou

Jia

et al. 2013

BMC Vet Res

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BackgroundMitochondria, which are essential for the functionality of eukaryotic cells, are particularly important in metabolically active tissues such as liver. Different breeds of pigs demonstrate distinct metabolic profiles in the liver, yet little is known whether the expression and transcriptional regulation of mitochondrial genes differ between breeds.ResultsHere we used male newborn Large White (LW) and Erhualian (EHL) piglets to delineate the difference in hepatic mitochondrial gene regulation between breeds. The hepatic content of ATP was significantly higher (p < 0.01) in EHL piglets, which was associated with lower mtDNA copy number (p < 0.05). Most of the mtDNA-encoded genes (10 of 13), however, were more abundantly expressed in EHL compared to LW piglets. We also detected 3 differentially expressed nuclear-encoded mitochondrial genes, among which isocitrate dehydrogenase 2 (IDH2) and ATP synthase, H+ transporting, mitochondrial Fo complex, subunit d (ATP5H) were expressed significantly lower, while adenylate kinase 1 (AK1) was significantly over expressed in EHL piglets. Compared to LW, the over expression of mtDNA-encoded genes in EHL was associated with significantly higher (p < 0.01) glucocorticoid receptor (GR) binding to the control region of mtDNA with no alterations in the methylation status. For nuclear-encoded genes, however, a negative correlation was observed between GR binding and mRNA expression of AK1 and ATP5H. Moreover, higher expression of AK1 in EHL piglets was also associated with lower cytosine methylation (p < 0.05) and hydroxymethylation (p < 0.05). In the promoter region.ConclusionsThese results indicate a role of the GR in the breed-dependent regulation of mitochondrial genes in the liver of newborn piglets.

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Section: Discussionmentioning

confidence: 99%

Glucocorticoid receptor is involved in the breed-dependent transcriptional regulation of mtDNA- and nuclear-encoded mitochondria genes in the liver of newborn piglets

Zou

Jia

et al. 2013

BMC Vet Res

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“…The ESTs used in this study were generated from three different pig breeds' skeletal muscle tissue cDNA libraries (Duroc, Large White and a Local Breed Piau) constructed by Nascimento et al (2012).…”

Section: Est Datasetmentioning

confidence: 99%

“…Functional annotation of ESTs for the three datasets was performed using the program BLASTX (Altschul et al 1997), against the data base of transcripts from SwissProt (http://www.expasy.ch/sprot/). More details can be obtained at Nascimento et al (2012).…”

Section: Differentially Expressed Genes Identificationmentioning

confidence: 99%

“…A number of 3670 unique sequences representing putative transcripts from pig breeds forming 905 contigs (merged overlapping sequences) and 2765 singletons were obtained, defined as sequences that did not assemble into contigs using the defined assembly parameters. More details about cDNA Library construction, reads sequencing and sequence assembly can be obtained at Nascimento et al (2012).…”

Section: Differentially Expressed Genes Identificationmentioning

confidence: 99%

“…AC1-2, AC1-3, Fisher1-2, Fisher1-3, Chi 2 1-2, Chi 2 1-3, R, Chi 2 ANKRD2 AC1-2, AC1-3, Fisher1-2, Fisher1-3, Chi 2 1-2, Chi 2 1-3, R, Chi 2 ATP5A1 AC1-2, AC1-3, Fisher1-2, Fisher1-3, Chi 2 1-2, Chi 2 1-3, R, Chi 2 ATP6V1H AC1-2, AC1-3, Fisher1-2, Fisher1-3, Chi 2 1-2, Chi 2 1-3, R, Chi 2 CA3 AC1-3 CGGBP1 AC1-2, AC1-3, Fisher1-2, Fisher1-3, Chi 2 1-2, Chi 2 1-3, R, Chi 2 DCTN1 AC1-2, AC1-3, AC2-3, Fisher1-2, Fisher2-3, Chi 2 1-2, Chi 2 2-3, R, Chi 2 DYSFIP1 AC1-2, AC1-3, Fisher1-2, Fisher1-3, Chi 2 1-2, Chi 2 1-3, R, Chi 2 ENO3 AC1-3, AC2-3, Fisher1-2, Fisher1-3, Chi21-3 EXOSC8 AC1-2, AC1-3, Fisher1-2, Fisher1-3, Chi 2 1-2, Chi 2 1-3, R, Chi 2 MT-COX3 AC1-3, AC2-3, Fisher1-2, Fisher1-3, Chi 2 1-3 MyBPC1 AC1-2, AC1-3, Fisher1-2, Fisher1-3, Chi 2 1-2, Chi 2 1-3, R, Chi 2 MyBPH AC1-2, AC1-3, Fisher1-2, Fisher1-3, Chi 2 1-2, Chi 2 1-3, R, Chi 2 MyH7 AC1-2, AC1-3, Fisher1-2, Fisher1-3, Chi 2 1-2, Chi 2 1-3, R, Chi 2 MyL2 AC1-3 NAGA AC1-2, AC1-3, Fisher1-2, Fisher1-3, Chi 2 1-2, Chi 2 1-3, R, Chi 2 NDUFA9 AC1-2, AC1-3, Chi 2 1-2, Chi 2 1-3, R, Chi 2 PDLIM5 AC1-2 RPL10A AC1-2, AC1-3, Fisher1-2, Fisher1-3, Chi 2 1-2, Chi 2 1-3, R, Chi 2 SDHS AC1-2, AC2-3, Chi 2 1-2 MARCD3 AC1-2, AC1-3, Chi 2 1-2, Chi 2 1-3, R, Chi 2 TCBE2 AC1-2, AC1-3, Chi 2 1-2, Chi 2 1-3, R, Chi 2 TPM2 AC1-2, AC1-3 TRIM54 AC1-2, AC1-3, Fisher1-2, Fisher1-3, Chi 2 1-2, Chi 2 1-3, R, Chi 2 ZCRB1 AC1-2, AC1-3, Fisher1-2, Fisher1-3, Chi 2 1-2, Chi 2 1-3, R, Chi 2 a According to Nascimento et al (2012). b IDEG6 tests that showed differential expression, AC: Audic and Claverie statistic, Fisher: Fisher test, GT: Greller and Tobin statistic, R: R statistic and Chi 2 : chi-squared test.…”

Section: Gene Network Analysesmentioning

confidence: 99%

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Identification and validation of differentially expressed genes from pig skeletal muscle

Verardo

Nascimento

Silva

et al. 2012

J Animal Breeding Genetics

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Pig is an important animal for meat production; this is generally associated with characteristics determined prenatally during myogenesis. Expressed sequence tags (EST) can provide direct information on the transcriptome and indirect information on the relation between the genome and phenotype, giving information about differentially expressed genes (DEG). In this work, the identification and annotation of DEG from EST libraries of three pig breeds (Duroc, Large White and Local Breed Piau) were performed followed by real-time PCR analyses during pre- and postnatal stages (21, 40, 70 and 90 days of pregnancy and 107, 121 and 171 days postnatal) from commercial breed animals for analysis of genes expression levels. Therefore, 34 genes differentially expressed were identified, of which 21 grouped in a network related with muscle development. From this, the expression profile of 13 genes was measured, to confirm their relationship with myogenesis like ANKRD2, MYBPC1, NEB and MYL2. These genes showed a prenatal high expression in this study. Besides, novels candidates for muscle development (TP53 and DCTN1) were listed. These findings can contribute to better explaining gene function mechanism and are helpful in uncovering the pathways that mediate pre- and postnatal skeletal muscle development in vertebrates.

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Identification and expression levels of pig miRNAs in skeletal muscle

et al. 2013

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MicroRNAs are a class of naturally occurring non-coding RNAs. Typically they are $ 22 nucleotides long and suppress translation of their targets genes. Several laboratories have attempted to identify miRNAs from pig muscle and the bioinformatics strategies using ESTs have proved to be successful for this aim. In this study we report an in silico identification of ncRNA in pig EST libraries focusing on novel pig miRNAs and further investigated the differential expression of pigs miRNAs (known and novel) by quantitative real-time PCR during pre-and postnatal stage from Commercial and local breed Piau pigs skeletal muscle tissue. We identified two miRNAs not yet described in pigs: hsa-miR-1207-5p and hsa-miR-665. Besides, we found 288 target genes for hsa-miR-1207-5p and 214 for hsa-miR-665; from them, four are muscle specific genes. Through expression analyses, differences were found between pre-and postnatal stages and genetics groups. The findings of miRNAs and their muscle-specific targets in pigs will be helpful for understanding the function and processing of this RNA class in the future. Besides, the miRNAs differentially expressed between Commercial and Piau breeds suggest that they can be used to uncover phenotypic differences across different genetic groups.

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Transcript profiling of expressed sequence tags from semimembranosus muscle of commercial and naturalized pig breeds

Cited by 4 publications

References 21 publications

Glucocorticoid receptor is involved in the breed-dependent transcriptional regulation of mtDNA- and nuclear-encoded mitochondria genes in the liver of newborn piglets

Glucocorticoid receptor is involved in the breed-dependent transcriptional regulation of mtDNA- and nuclear-encoded mitochondria genes in the liver of newborn piglets

Identification and validation of differentially expressed genes from pig skeletal muscle

Identification and expression levels of pig miRNAs in skeletal muscle

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