Gene expression studies of developing bovine longissimus muscle from two different beef cattle breeds
Sigrid A. Lehnert,Sigrid A. Lehnert,Antonio Reverter,Antonio Reverter,Keren Byrne,Keren Byrne,Yonghong Wang,Yonghong Wang,Greg Nattrass,Greg Nattrass,Nicholas J. Hudson,Nicholas J. Hudson,Paul L. Greenwood,Paul L. Greenwood +13 more
TLDR
The developing longissimus muscle of fetuses carrying the Piedmontese mutation shows an emphasis on glycolytic muscle biochemistry and a large-scale up-regulation of the translational machinery at birth, as well as gene expression differences that may underpin the phenotype differences between the two breeds.Abstract:
The muscle fiber number and fiber composition of muscle is largely determined during prenatal development. In order to discover genes that are involved in determining adult muscle phenotypes, we studied the gene expression profile of developing fetal bovine longissimus muscle from animals with two different genetic backgrounds using a bovine cDNA microarray. Fetal longissimus muscle was sampled at 4 stages of myogenesis and muscle maturation: primary myogenesis (d 60), secondary myogenesis (d 135), as well as beginning (d 195) and final stages (birth) of functional differentiation of muscle fibers. All fetuses and newborns (total n = 24) were from Hereford dams and crossed with either Wagyu (high intramuscular fat) or Piedmontese (GDF8 mutant) sires, genotypes that vary markedly in muscle and compositional characteristics later in postnatal life. We obtained expression profiles of three individuals for each time point and genotype to allow comparisons across time and between sire breeds. Quantitative reverse transcription-PCR analysis of RNA from developing longissimus muscle was able to validate the differential expression patterns observed for a selection of differentially expressed genes, with one exception. We detected large-scale changes in temporal gene expression between the four developmental stages in genes coding for extracellular matrix and for muscle fiber structural and metabolic proteins. FSTL1 and IGFBP5 were two genes implicated in growth and differentiation that showed developmentally regulated expression levels in fetal muscle. An abundantly expressed gene with no functional annotation was found to be developmentally regulated in the same manner as muscle structural proteins. We also observed differences in gene expression profiles between the two different sire breeds. Wagyu-sired calves showed higher expression of fatty acid binding protein 5 (FABP5) RNA at birth. The developing longissimus muscle of fetuses carrying the Piedmontese mutation shows an emphasis on glycolytic muscle biochemistry and a large-scale up-regulation of the translational machinery at birth. We also document evidence for timing differences in differentiation events between the two breeds. Taken together, these findings provide a detailed description of molecular events accompanying skeletal muscle differentiation in the bovine, as well as gene expression differences that may underpin the phenotype differences between the two breeds. In addition, this study has highlighted a non-coding RNA, which is abundantly expressed and developmentally regulated in bovine fetal muscle.read more
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MEN ε/β nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles
Hongjae Sunwoo,Marcel E. Dinger,Jeremy E. Wilusz,Paulo P. Amaral,John S. Mattick,David L. Spector +5 more
TL;DR: The findings indicate that the MEN epsilon/beta non-coding RNAs are essential structural/organizational components of paraspeckles.
Journal ArticleDOI
A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation
TL;DR: A new algorithm is proposed that correctly identifies the gene containing the causal mutation from microarray data alone and yields the correct answer, “myostatin”, the myostatin mutation that releases the brakes on Piedmontese muscle growth by translating a dysfunctional protein.
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Genome-wide association study of growth in crossbred beef cattle.
Warren M Snelling,M. F. Allan,John W. Keele,Larry A. Kuehn,Tara G. McDaneld,Timothy P. L. Smith,Tad S. Sonstegard,R. M. Thallman,Gary L. Bennett +8 more
TL;DR: Most SNPassociated with BWT and postnatal growth affected components in the same direction, although detection of SNP associated with one component independent of others presents a possible opportunity for SNP-assisted selection to increase postnatalgrowth relative to BWT.
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Gene expression patterns during intramuscular fat development in cattle.
Yonghong Wang,Yonghong Wang,Neil I. Bower,Neil I. Bower,Antonio Reverter,Antonio Reverter,Siok Hwee Tan,Siok Hwee Tan,N. De Jager,N. De Jager,Ran Wang,Sean McWilliam,L. M. Cafe,L. M. Cafe,Paul L. Greenwood,Paul L. Greenwood,Sigrid A. Lehnert,Sigrid A. Lehnert +17 more
TL;DR: This study provides clear evidence of early molecular changes associated with marbling and also identifies specific time frames when intramuscular fat development in cattle muscle can be detected by using gene expression.
Journal ArticleDOI
Neat1 is a p53-inducible lincRNA essential for transformation suppression.
Stephano S. Mello,Carolyn Sinow,Nitin Raj,Pawel K. Mazur,Kathryn T. Bieging-Rolett,Daniela Kenzelmann Broz,Jamie F. Conklin Imam,Hannes Vogel,Laura D. Wood,Julien Sage,Tetsuro Hirose,Shinichi Nakagawa,John L. Rinn,Laura D. Attardi +13 more
TL;DR: This work identifies Neat1, a noncoding RNA (ncRNA) constituent of paraspeckles, as a p53 target gene broadly induced by mouse and human p53 in different cell types and by diverse stress signals, providing fundamental new insight into p53-mediated tumor suppression.
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