Transcriptomic profile of semitendinosus muscle of bulls of different breed and performance

Abstract The aim of the study was to compare the transcriptomic profiles of fully differentiated skeletal muscle derived from bulls belonging to different breeds of varying performance. Microarray analyses were performed to determine the differences in the expression profiles of genes between semitendinosus muscles of 15-month-old beef-breed bulls (Limousin—LIM and Hereford—HER) and dairy-breed bulls (Holstein Friesian—HF). These analyses allowed for the identification of those genes the expression of which is similar and characteristic of fully differentiated muscle in beef breeds, but differs in skeletal muscle of a typical dairy breed. The analysis revealed 463 transcripts showing similar expression in the semitendinosus muscle of beef breeds (LIM/HER), in comparison with the dairy breed (HF). Among the identified genes, 227 were upregulated and 236 were downregulated in beef breeds. The ontological analyses revealed that the largest group of genes similarly expressed in LIM and HER was involved in the processes of protein metabolism and development of muscle organ. In beef breeds, some genes involved in protein synthesis and proteolysis showed an upregulation, including ctsd, ctsf, fhl2, fhl3, fst, sirt1, and trim63, whereas some were downregulated, including bmpr1a, bmpr2, mstn, smad2, hspa8, gsk3β, and tgfβ2. The expression of the chosen genes was confirmed by RT-qPCR technique. Thus, it can be assumed that the identified genes involved in the regulation of growth and development of muscle tissue and the processes of protein metabolism in the examined cattle breeds may be responsible for the greater gain of muscle mass in beef-breed bulls.

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Transcriptomic Profile of Primary Culture of Skeletal Muscle Cells Isolated from Semitendinosus Muscle of Beef and Dairy Bulls

International Journal of Molecular Sciences ◽

10.3390/ijms21134794 ◽

2020 ◽

Vol 21 (13) ◽

pp. 4794

Author(s):

Anna Ciecierska ◽

Tomasz Motyl ◽

Tomasz Sadkowski

Keyword(s):

Muscle Cells ◽

Contractile Apparatus ◽

Proliferating Cells ◽

Semitendinosus Muscle ◽

Expression Of Genes ◽

Holstein Friesian ◽

Dairy Bulls ◽

Microarray Analyses ◽

Dairy Breed ◽

Transcriptome Level

The aim of the study was to identify differences in the transcriptomic profiles of primary muscle cell cultures derived from the semitendinosus muscle of bulls of beef breeds (Limousin (LIM) and Hereford (HER)) and a dairy breed (Holstein-Friesian (HF)) (n = 4 for each breed). Finding a common expression pattern for proliferating cells may point to such an early orientation of the cattle beef phenotype at the transcriptome level of unfused myogenic cells. To check this hypothesis, microarray analyses were performed. The analysis revealed 825 upregulated and 1300 downregulated transcripts similar in both beef breeds (LIM and HER) and significantly different when compared with the dairy breed (HF) used as a reference. Ontological analyses showed that the largest group of genes were involved in muscle organ development. Muscle cells of beef breeds showed higher expression of genes involved in myogenesis (including erbb-3, myf5, myog, des, igf-1, tgfb2) and those encoding proteins comprising the contractile apparatus (acta1, actc1, myh3, myh11, myl1, myl2, myl4, tpm1, tnnt2, tnnc1). The obtained results confirmed our hypothesis that the expression profile of several groups of genes is common in beef breeds at the level of proliferating satellite cells but differs from that observed in typical dairy breeds.

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Dynamic transcriptome profiles of postnatal porcine skeletal muscle growth and development

BMC Genomic Data ◽

10.1186/s12863-021-00984-1 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yanping Wang ◽

Jiying Wang ◽

Hongmei Hu ◽

Huaizhong Wang ◽

Cheng Wang ◽

...

Keyword(s):

Skeletal Muscle ◽

Protein Metabolism ◽

Growth And Development ◽

Molecular Mechanisms ◽

Expression Profiles ◽

Muscle Growth ◽

Postnatal Period ◽

Skeletal Muscle Growth ◽

Cytoskeleton Organization ◽

Go Terms

Abstract Background Skeletal muscle growth and development are closely associated with the quantity and quality of pork production. We performed a transcriptomic analysis of 12 Longissimus dorsi muscle samples from Tibetan piglets at four postnatal stages of 0, 14, 30, and 60 days using RNA sequencing. Results According to the pairwise comparisons between the libraries of the muscle samples at the four postnatal stages, a total of 4115 differentially expressed genes (DEGs) were identified in terms of |log2(fold change)| ≥ 1 and an adjusted P value < 0.01. Short-time series expression miner (STEM) analysis of the DEGs identified eight significantly different expression profiles, which were divided into two clusters based on the expression pattern. DEGs in cluster I displayed a pattern of decreasing to a nadir, and then a rise, and the significantly enriched gene ontology (GO) terms detected using them were involved in multiple processes, of which the cell cycle, immunocyte activation and proliferation, as well as actin cytoskeleton organization, were the top three overrepresented processes based on the GO terms functional classification. DEGs in cluster II displayed a pattern of increasing to a peak, then declining, which mainly contributed to protein metabolism. Furthermore, besides the pathways related to immune system, a few diseases, and protein metabolism, the DEGs in clusters I and II were significantly enriched in pathways related to muscle growth and development, such as the Rap1, PI3K-Akt, AMPK, and mTOR signaling pathways. Conclusions This study revealed GO terms and pathways that could affect the postnatal muscle growth and development in piglets. In addition, this study provides crucial information concerning the molecular mechanisms of muscle growth and development as well as an overview of the piglet transcriptome dynamics throughout the postnatal period in terms of growth and development.

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The Effect of Dietary Protein on Protein Metabolism and Performance in Endurance-trained Males

Medicine & Science in Sports & Exercise ◽

10.1249/mss.0000000000001791 ◽

2019 ◽

Vol 51 (2) ◽

pp. 352-360 ◽

Cited By ~ 9

Author(s):

ERIC WILLIAMSON ◽

HIROYUKI KATO ◽

KIMBERLY A. VOLTERMAN ◽

KATSUYA SUZUKI ◽

DANIEL R. MOORE

Keyword(s):

Dietary Protein ◽

Protein Metabolism ◽

And Performance

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Time Dependent Gene Expression Changes in the Liver of Mice Treated with Benzene

Biomarker Insights ◽

10.4137/bmi.s590 ◽

2008 ◽

Vol 3 ◽

pp. BMI.S590 ◽

Cited By ~ 3

Author(s):

Han-Jin Park ◽

Jung Hwa Oh ◽

Seokjoo Yoon ◽

S.V.S. Rana

Keyword(s):

Gene Expression ◽

Expression Profiles ◽

Gene Expression Profiles ◽

General Purpose ◽

Time Dependent ◽

Expression Data ◽

Benzene Exposure ◽

Microarray Analyses ◽

First Time ◽

Affymetrix Gene Chip

Benzene is used as a general purpose solvent. Benzene metabolism starts from phenol and ends with p-benzoquinone and o-benzoquinone. Liver injury inducted by benzene still remains a toxicologic problem. Tumor related genes and immune responsive genes have been studied in patients suffering from benzene exposure. However, gene expression profiles and pathways related to its hepatotoxicity are not known. This study reports the results obtained in the liver of BALB/C mice (SLC, Inc., Japan) administered 0.05 ml/100 g body weight of 2% benzene for six days. Serum, ALT, AST and ALP were determined using automated analyzer (Fuji., Japan). Histopathological observations were made to support gene expression data. c-DNA microarray analyses were performed using Affymetrix Gene-chip system. After six days of benzene exposure, twenty five genes were down regulated whereas nineteen genes were up-regulated. These gene expression changes were found to be related to pathways of biotransformation, detoxification, apoptosis, oxidative stress and cell cycle. It has been shown for the first time that genes corresponding to circadian rhythms are affected by benzene. Results suggest that gene expression profile might serve as potential biomarkers of hepatotoxicity during benzene exposure.

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22 Characterization of tRNA Expression Profiles in Large Offspring Syndrome

Journal of Animal Science ◽

10.1093/jas/skab235.022 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 13-14

Author(s):

Anna K Goldkamp ◽

Yahan Li ◽

Rocio M Rivera ◽

Darren Hagen

Keyword(s):

Skeletal Muscle ◽

Expression Profiles ◽

Expression Patterns ◽

Tumor Development ◽

Gene Clusters ◽

Tissue Type ◽

Trna Genes ◽

Translational Machinery ◽

Trna Species

Abstract Differentially methylated regions (DMRs) have been associated with Large Offspring Syndrome (LOS) in cattle. Some DMRs overlap transfer RNA (tRNA) gene clusters, potentially altering tRNA expression patterns uniquely by treatment group or tissue type. tRNAs are classified as adapter molecules, serving a key role in the translational machinery implementing genetic code. Variation in tRNA expression has been identified in several disease pathways suggesting an important role in the regulation of biological processes. tRNAs also serve as a source of small non-coding RNAs. To better understand the role of tRNA expression in LOS, total RNA was extracted from skeletal muscle and liver of 105-day fetuses and the tRNAs sequenced. Although there are nearly three times the number of tRNA genes in cattle as compared to human (1,659 vs 597), there is a shared occurrence of transcriptionally silent tRNA genes in both species. This study detected expression of 474 and 487 bovine tRNA genes in skeletal muscle and liver, respectively, with the remainder being very lowly expressed or transcriptionally silent. Eleven tRNA isodecoders are transcriptionally silent in both skeletal muscle and liver and another isodecoder is silent in the liver (SerGGA). Further, the highest expressed isodecoders differ by treatment or tissue type with roughly half correlated to codon frequency. While the absence of certain isodecoders may be relieved by wobble base pairing, missing tRNA species could likely increase the likelihood of mistranslation or mRNA degradation. Differential expression of tissue- and treatment-specific tRNA genes may modulate translation during protein homeostasis or cellular stress, altering regulatory products targeting genes associated with overgrowth in skeletal muscle and/or tumor development in the liver of LOS individuals.

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PSIV-6 Differential gene expression of fibro/adipogenic progenitors between Wagyu and Brahman cattle: A possible contribution to their different meat quality

Journal of Animal Science ◽

10.1093/jas/skab235.553 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 301-301

Author(s):

Chaoyang Li ◽

Qianglin Liu ◽

Matt Welborn ◽

Leshan Wang ◽

Yuxia Li ◽

...

Keyword(s):

Gene Expression ◽

Skeletal Muscle ◽

Meat Quality ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Cattle Breed ◽

Intramuscular Fat ◽

Brahman Cattle ◽

Differential Gene ◽

The Difference

Abstract The amount of intramuscular fat directly influences the meat quality. However, significant differences in the ability to accumulate intramuscular fat are present among different beef cattle breeds. While Wagyu, a cattle breed that originated from Japan, is renowned for abundant intramuscular fat, Brahman cattle generally have very little intramuscular fat accumulation and produce tougher meat. We identified that bovine intramuscular fat is derived from a group of bipotent progenitor cells named fibro/adipogenic progenitors (FAPs) which also give rise to fibroblasts. Thus, the variation in intramuscular fat development between Wagyu and Brahman is likely attributed to the difference in FAPs between these two breeds. In order to understand the gene expression difference between FAPs of the two breeds, single-cell RNA-seq was performed using total single-nucleated cells isolated from the longissimus muscle of young purebred Wagyu, purebred Brahman, and Wagyu-Brahman cross cattle. FAPs constitute the largest single-nucleated cell population in both Wagyu and Brahman skeletal muscle. Multiple subpopulations of FAPs with different gene expression profiles were identified, suggesting that FAP is a heterogeneous population. A unique FAP cluster expressing lower levels of fibrillar collagen and extracellular remodeling enzyme genes but higher levels of select proadipogenic genes was identified exclusively in Wagyu skeletal muscle, which likely contributes to the robust intramuscular adipogenic efficiency of Wagyu FAPs. In conclusion, the difference in the cellular composition and gene expression of FAPs between Wagyu and Brahman cattle likely contribute to their distinct meat quality.

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