BACKGROUND
lipids are a class of molecules present in all cell types.
they contribute to cellular structure, energy storage and several biological functions from transcriptional regulation to physiological processes  <cit> .
over the last couple decades, it has been reported that consumption of fatty acids is associated with fat deposition and may have metabolic effects, such as altered blood lipid and lipoprotein content  <cit> .
however, there are still contrasting opinions about the role of dietary fatty acids on human health, which can be observed in previous reviews and meta-analysis studies conducted in the last years  <cit> .
lipid composition in beef has become an important discussion point.
although meat is a significant source of fat in the human diet, it contains high saturated fat content that is associated with some diseases such as obesity, cancer and coronary heart disease  <cit> .
on the other hand, meat has high nutritional value and is an important source of unsaturated fatty acids such as oleic acid  and conjugated linoleic acid , which have beneficial effects on human health  <cit> .
thus, there is a need to improve the nutritional value of meat and better understand the biological and molecular processes associated with fatty acid composition in skeletal muscle.
previous studies have shown that oa as well as other fatty acids such as linoleic acid , docosahexaenoic acid , eicosapentaenoic acid  and cla can regulate gene transcription in tissues such as muscle, liver, adipose, monocytes and blood mononuclear cells  <cit> .
activation of nuclear receptors such as peroxisome proliferator-activated receptors  and coactivators of the sterol response element binding protein  can mediate this regulation.
both ppars and srebps play a role in preadipocyte differentiation, lipid homeostasis and peroxisomal beta-oxidation regulation by controlling the transcription of acyl-coa oxidase and other enzymes involved in adipocyte development .
while elevated intracellular levels of stearic  and palmitic  acids were associated with apoptotic death  <cit>  and inflammatory process  <cit> .
however, the effective involvement of these fatty acids in molecular and physiological processes in skeletal muscle remains unclear.
the present investigation was undertaken to identify differentially expressed genes  and functional pathways associated with seven fa content in beef cattle.
our hypothesis was that variation in fa content could be associated with difference in gene expression in skeletal muscle.
our study revealed that up regulation of stearoyl-coa desaturase  is associated with deposition of unsaturated fa and that increased levels of oa and cla are associated with expression of genes that have protective function associated with important human diseases.
RESULTS
phenotypes and sequencing data
seven different fas, important to beef quality and human health, were used in this transcriptome study, including: oleic acid , palmitic acid , stearic acid , linoleic acid , conjugated linoleic acid cis <dig> trans <dig> , eicosapentaenoic acid  and docosahexaenoic acid .
the skeletal muscle samples analyzed were chosen based on their extreme values for each fa studied .
when ranked by fatty acids content in skeletal muscle, the statistical test of means performed between the high  and low  groups according to fa had significant differences  for oa, pa, sa, cla-c9t <dig>  la, epa and dha, but no difference in imf content or backfat thickness .
however, animals with extreme phenotypes for oa, pa, sa, cla-c9t <dig>  la, epa and dha also had significant differences for other fas.
for example, animals with high levels of oa had significantly  lower levels for sa and pa, but high levels for cla-c9t <dig>  while extreme animals for cla-c9t <dig> had significant low levels for sa and pa, but high levels for oa and dha.
the correlation between any two fas tended to be low .
however, there were some fas that high negative correlations, e.g.
oa and pa  and oa and sa  or high positive correlations, e.g.
epa and la  and epa and dha  .table  <dig> phenotypic correlation between the groups of extreme values of fatty acids content in skeletal muscle
apalmitic acid
bstearic acid
coleic acid
dlinoleic acid
econjugated linoleic acid cis <dig>  trans 11
feicosapentaenoic acid
gdocosahexaenoic acid
the average number of mapped read pairs per sample before and after filtering were  <dig>  million and  <dig>  million respectively , which means that on average  <dig> % of total read pairs were mapped to the bos taurus umd <dig>  reference genome assembly.
after filtering for transcript expression level, a total of  <dig> ;  <dig> ;  <dig> ;  <dig> ;  <dig> ;  <dig>  and  <dig>  annotated genes were used for differential expression analysis for oa, pa, sa, cla-c9t <dig>  epa, dha and la content, respectively.
differential expression analysis
differential gene expression analysis was performed for each fa by camparing gene expression level between the h and l fa content groups.
no degs were identified for la and sa , while  <dig>   <dig> and  <dig> degs were identified for epa, dha and pa, respectively .
in contrast,  <dig> and  <dig> degs for oa and cla-c9t <dig>  respectively, were identified between h and l groups .
a volcano plot of log <dig> fold-change  versus − log <dig> fdr-corrected p-value  for oa is shown in fig.
<dig>  the volcano plot of other fas are shown in additional file  <dig>  of the  <dig> degs for oa,  <dig> genes were up-regulated and  <dig> were down-regulated and of the  <dig> degs for cla-c9t <dig>   <dig> genes were up-regulated and  <dig> were down-regulated in the l group relative to the h group.
the expression level, fold change, adjusted p-value and annotation of all degs for oa and cla-c9t <dig> are shown in more detail in additional files  <dig> and  <dig> fig.
<dig> volcano plot of log2fold-change  versus − log10fdr-corrected p-value in rna-seq data for oleic acid content
functional enrichment analysis for oleic acid content
in this study, two different tools of pathway analysis were performed: david and ingenuity pathway analysis® .
according to david enrichment analysis, several ontology terms were significantly enriched  for the differentially expressed gene lists .
cellular component go terms related to mitochondrial envelope , mitochondrial membrane , respiratory chain , mitochondrial matrix  and intracellular organelle lumen  were associated with degs for oa content.
in addition, six kegg pathways  that were associated with oxidative phosphorylation , ribosome  and proteasome  were also identified.
these pathways are involved with oxidative phosphorylation and oxidative stress diseases such as huntington , parkinson  and alzheimer  .table  <dig> pathways identified from differentially expressed genes list between high and low oleic acid content
anumber of differentially expressed genes involved in the term
bpercentage of differentially expressed genes involved in the term
c
p-value adjusted for multiple tests by benjamin and hochberg
the ipa® software  was also performed for functional enrichment using the global functional analysis  and global canonical pathways  analysis from the degs list for oa content .
global canonical pathways analysis estimates the likelihood that the association between a set of degs in a pathway is due to random chance using a right-tailed fishers exact test.
significance was set at bh-adj-pvalue ≤  <dig> , which indicated a non-random association.
several canonical pathways  were identified by gcp analysis, including oxidative phosphorylation , mitochondrial dysfunction , insulin receptor signaling , lps-stimulated mapk signaling , role of nfat in cardiac hypertrophy  and huntington’s disease signaling  .
twenty-five networks were enriched as a function of oa content as identified by ipa®gfa analyses .
one in particular, shown in fig.
<dig>  was associated with lipid metabolism and energy production.
this network contained molecules and genes such as cholesterol , very-low-density lipoprotein , perilipin  <dig> , scd, low-density lipoprotein carnitine palmitoyltransferase i  and carnitine palmitoyltransferase i , respectively .
among these only scd was up-regulated in the h group as shown in red in fig.
<dig> fig.
<dig> a gene network associated with lipid metabolism and energy production is impacted by oa content.
genes presented in red are up-regulated in the high oleic acid content  group.
genes presented in green are down-regulated in the h group.
the intensity of the colors is related to the estimated of fold change.
molecules in white are not in the de list, but were incorporated into the network through relationships with other molecules
to further explore the observed changes in gene expression, ipa® upstream regulator analyses were performed to identify the cascade of upstream transcriptional regulators that could be involved in the gene expression changes in skeletal muscle due to oa content.
the ipa® program estimated the effects between transcriptional regulators and their target genes based on prior knowledge stored in the ingenuity® knowledge base.
upstream regulators were identified from the list of degs for oa content , which were connected via mechanistic networks detected by ipa®.
peroxisome proliferator-activated receptor gamma, coactivator  <dig> alpha  was among the top predicted upstream regulators.
ppargc1a and ten other transcription factors  such as forkhead box o <dig> , peroxisome proliferator-activated receptor gamma, coactivator  <dig> beta , estrogen-related receptor gamma , sterol regulatory element binding transcription factor  <dig> , tumor protein p <dig> , forkhead box o <dig> , v-myc avian myelocytomatosis viral oncogene homolog  and myogenic differentiation  <dig>  were predicted to be inhibited , whereas the transcription factors forkhead box o <dig>  and sterol regulatory element binding transcription factor  <dig>  were predicted to be activated .fig.
<dig> the mechanistic network of the upstream regulators and their relationship predicted by ipa®.
the molecules shown in blue are predicted to be inhibited, while the molecules shown in orange are predicted to be activated as a result of oa content.
color intensity represents the level of inhibition or activation.
the lines and arrows in blue represent a direct interaction and activation, respectively.
the interrupted lines in yellow represents direct inhibition.
the gray lines represent the interactions that oa content did not affect, but have been reported in the literature
the functional enrichment analysis using the ipa® program identified several statically significantly enriched biological functions  from the oa degs list , e.g.
processing of rna , transcription of rna , expression of rna , transcription of dna , expression of mrna , catabolism of fatty acid , beta-oxidation of palmitic acid , depletion of triacylglycerol .
the indirect inhibitory interaction between scd and β-oxidation and the depletion of triacylglycerol, which was associated with lipid metabolism and energy production are shown in fig.
<dig>  in the network shown in fig.
<dig> it is also possible to observe the indirect interaction between scd, ldl-cholesterol, vldl-cholesterol, cpt <dig>  cpt1b, plin <dig> and ucp <dig> fig.
<dig> biological functions that include stearoyl-coa desaturase such as  beta-oxidation of palmitic acid and  agpat <dig> depletion of triacylglycerol.
genes shown in red are up-regulated in the high oleic acid content group, while genes shown in green are down-regulated
functional enrichment analysis for conjugated linoleic acid cis <dig> trans <dig> content
the enrichment analysis performed by david software using the list of degs for cla-c9t <dig> content identified one kegg pathway, which was related to ribosome function .
among the molecular functions identified by david associated  with the cla-c9t <dig> de genes identified between the groups with extreme values of cla-c9t <dig> were nucleotide binding , atp binding  and structural constituent of ribosome  .
the top five canonical pathways identified for cla-c9t <dig> content by gfa and gcp analysis using ipa® program were protein ubiquitination , interferon signaling , hypoxia signaling in the cardiovascular system , angiopoietin signaling  and mtor signaling  .
the top five upstream regulators identified from the list of degs for cla-c9t <dig>  associated network functions and toxicology list  for cla-c9t <dig> content are shown in additional file  <dig>  among the top upstream regulators were: interferon, lambda  <dig> , tumor necrosis factor , retinoic acid, signal transducer and activator of transcription  <dig> , and interferon regulatory factor  <dig> , which were predicted as activated in this study .
however other important cytokines and transcription regulators were identified as activated/inhibited such as ifnk , ccl <dig>  ligand 5) and, prl , trim <dig> , nfkb1a , srebf <dig>  foxo <dig>  tp <dig> and myc, respectively .
figure  <dig> shows the foxo <dig> network, which has been associated with the metabolic disorder dyslipidemia.fig.
<dig> the network of the upstream regulator foxo <dig> by ipa®.
genes presented in red are up-regulated in the high oleic acid content  group.
genes presented in green are down-regulated in the h group.
the intensity of the colors is related to the estimated of the fold change.
the interrupted lines in orange represents direct inhibition.
the blue represents direct activation.
the gray lines represent the no interactions have been reported in the literature
the top five associated network functions detected from the list of cla-c9t <dig> degs between the groups with extreme values of cla-c9t <dig> were related to rna damage, repair and post-transcriptional modification; developmental disorder; metabolic disorder; lipid metabolism, molecular transport, rna trafficking and; cell death and survival .
figure  <dig> illustrates the network associated with lipid and nucleic acid metabolism and small molecule biochemistry, which presents epidermal growth factor receptor  as a central gene and which was down-regulated in animals with high cla-c9t <dig> content .
figure  <dig> shows a network associated with molecular transport, rna trafficking, rna post-transcriptional modification that contained ribonucleoproteins , which were up-regulated in animals with high cla-c9t <dig> content.
the top five toxicology terms were associated with cardiac necrosis/cell death , cardiac hypertrophy , hypoxia-inducible factor signaling , increases liver steatosis  and, ppara/rxra activation  .fig.
<dig> network associated with lipid metabolism, nucleic-acid metabolism and small molecule biochemistry impacted by cla-c9t <dig> content.
genes presented in red are up-regulated in the high cla-c9t <dig> content  group.
genes presented in green are down-regulated in the h group.
the intensity of the colors is related to estimate of the fold change.
molecules in white are not in the de list, but were incorporated into the network through relationships with other molecules
fig.
<dig> network associated with molecular transport, rna trafficking and rna post-transcriptional modification impacted by cla-c9t <dig> content.
genes presented in red are up-regulated in the high cla-c9t <dig> content  group.
genes presented in green are down-regulated in the h group.
the intensity of the colors is related to estimate of the fold change.
molecules in white are not in the de list, but were incorporated into the network through relationships with other molecules
validation of differentially expressed genes
the quantitative real-time polymerase chain reaction  results and the relative quantification of degs selected to validate the present rna-seq study are shown in additional file  <dig>  nine genes differently expressed between high and low oa groups were tested by qpcr and seven genes  confirmed the rnaseq data , one gene confirmed but not at a significant level and one gene disagreed with rnaseq data .
discussion
skeletal muscle is important for energy homeostasis, as it is a site of energy storage and insulin-stimulated glucose.
metabolic diseases such as obesity and coronary disorders could be a consequence of insulin resistance, i.e.
the inability of insulin to drive glucose into the skeletal muscle and other tissues as liver, which can be caused by excessive body fat deposition  <cit> .
fatty acids in skeletal muscle play an important role in the structural and functional processes that influence the fluidity and stability of membrane structures, which impacts membrane functions such as transport, cell signaling, responses to oxidative damage and apoptosis.
studies have reported that the fatty acid profile of skeletal muscle phospholipids and triacylglycerides can be influenced by the fatty acid composition of human and animal diets  <cit> .
several saturated and unsaturated fatty acids have been implicated, both positively and negatively, in different biological processes in skeletal muscle and other tissues such as liver and cardiac tissue  <cit> .
in contrast, meta-analysis studies reported no evidence that a human diet, which was rich in monounsaturated fatty acids  and polyunsaturated fatty acids  and depleted for saturated fatty acid , had beneficial effects on coronary heart disease  <cit> .
in this study, all animals were of the same breed, sex, similar age and fed the same diet.
however, different levels of fa content were observed in skeletal muscle.
this maybe due to genetic variation among the animals  <cit>  given that the environmental variables were similar across all animals.
transcriptomic analyses  indicated that many genes were differentially expressed  between animals with high and low oa and cla-c9t <dig> content.
while, only a few genes were differentially expressed among the extreme groups for pa, sa, epa and dha and none for la and sa.
additionally, previous studies reported only a few genes were affected by different levels of intramuscular fat content  <cit>  and tenderness  <cit>  in this same population.
because the samples used for oa and cla-c9t <dig> analysis also differed significantly for other fas , we cannot be certain that the observed de genes for oa and cla-c9t <dig> are associated solely with these fas.
despite the use of some samples in the analysis of several fa extremes, the lists of differentially expressed genes, and identified pathways were very different.
this may not be surprising given the generally low correlation between fas .
thus it is very likely that utilization of only a couple samples in several analyses does not have an negative impact on other analyses.
finally, these findings indicate the biological importance of oa and cla-c9t <dig> for skeletal muscle physiology.
however, a word of caution is necessary because, a direct relation between gene expression level and protein abundance was not establish  <cit> .
these fatty acids may play an important role in transcription regulation and consequently in energy homeostasis and metabolic diseases such as obesity and diabetes as also presented by ntambi  <cit> .
the most abundant mufa found in skeletal muscle fat is oleic acid   <cit> .
it is present in membrane phospholipids, triglycerides and cholesterol esters.
human oa consumption has been associated with low levels of low-density lipoprotein  and also with the potential increase of high-density lipoprotein  levels in the blood.
furthermore, oa is converted to oleoylethanolamide , a small molecule in the intestine, which is involved in appetite control  <cit> .
previous studies have reported an important contribution of oa intake to general human health, which could lead to a decrease in cholesterol levels, atherosclerosis risk and diabetes occurrence.
further, oa has protective effects against viral infection and cancer development .
beef has a high unsaturated fatty acid profile, primarily oa  <cit> .
it is considered an important source of oa in human nutrition, and health .
another important aspect of the oa content in beef is its relationship to meat quality traits such as tenderness, flavor and shelf-life  <cit> .
thus, it is appealing to improve our knowledge about biological processes associated with oa content in skeletal muscle, which could both help to improve the nutritional value and quality of beef.
in mammals, the biosynthesis of the oa is dependent on the activity of stearoyl-coa desaturase .
this soluble enzyme catalyzes the introduction of a cis-double bond at the 9th carbon position of stearic acid , to form the mufa, oleic acid   <cit> .
scd is also required for the synthesis of highly unsaturated essential fatty acids or pufas such as eicosopentaenoic  and docosahexaenoic acids ; synthesized from a-linolenic acid , and arachidonic acid , which are dependent on the presence of oleic acid  <cit> .
in ruminants, such as beef cattle, the concentration of oa in adipose tissue depends more on the concentration of stearic acid hydrogenated by ruminal microorganisms than from stearic acid desaturation by scd in the tissues  <cit> .
epa and dha are omega- <dig>  long-chain pufa, which are dietary fats associated with health benefits.
they are present in cell membranes and play a role in anti-inflammatory processes and in the viscosity of cell membranes  <cit> .
epa and dha are also precursors of several metabolites that are potent lipid mediators, considered by many investigators to be beneficial in the prevention or treatment of several diseases such as cardiovascular, obesity and alzheimer .
however, in this study both epa and dha did not appear to have much of an effect on skeletal muscle gene expression, which may mean that they do not have a biological effect on skeletal muscle.
it is interesting to speculate that deg analyses of other tissues such as liver and adipose may be able to identify tissues responsive to these fatty acids.
in contrast, conjugated linoleic acid cis <dig>  trans <dig> has a large effect on gene expression.
this fa is associated with human health, specifically related with diseases such as cancer, immune and inflammatory responses and obesity  <cit>  and is naturally present in food sources such as fats in milk and meat of ruminant animals  <cit> .
this may indicate that skeletal muscle is a primary target of conjugated linoleic acid cis <dig>  trans <dig>
the enriched transcript clusters identified by david based on biological process go terms  from the list of degs were associated with electron transport chain, mrna translation and generation of precursor metabolites and energy.
fas like oa and cla-c9t <dig> are involved in both extracellular and intracellular activities, which are in a partially dissociated state at physiological ph with part of the molecules diffused into the cytosol and other part integrating the membrane structure.
these fas impact several molecular functions in the cell such as:  ion transport across membranes;  activate intracellular enzymes;  modulation of na+/k + -atpase activation,  modulation of hormone/receptor interactions;  gene transcription and;  mrna translation .
oa can be obtained by either dietary consumption or de novo lipogenesis.
de novo lipogenesis of oa can occur from both dietary carbohydrates  and fat.
the enzyme responsible for mufa oa biosynthesis is scd  <cit> , which is considered as a key enzyme in de novo lipogenesis, a process that is associated with obesity, synthesis of cholesterol and apoptosis.
in the present study, scd was up-regulated in the group of animals with high oa content.
this was expected as this gene function is linked to oa synthesis.
hulver et al.
<cit>  suggested that elevated expression of scd <dig> in human skeletal muscle contributes to abnormal lipid metabolism and progression of obesity.
however, in this study, the imf content between the l and h group was not statistically different , as the h group had an average imf content of  <dig> % and the l group had an imf of  <dig> %.
in this study, the fatty acid synthase  and acetyl-coa carboxylase, responsible for fatty acid metabolism, were not differentially expressed between the groups h an l for any fa studied, considering that the diet was the same for all animals.
this may indicate: 1) the increased scd <dig> in this study was associated just with higher synthesis of oa and not with higher fat deposition; 2) a difference in how bovine and human skeletal muscles respond to oa content.
schrauwen  <cit> , clapham et al.
<cit>  reported that mice which overexpressed ucp <dig> in skeletal muscle had lower body weights and increased ampk activity, elevated metabolic rate, lower fasting plasma glucose and insulin levels compared to wild type mice.
in the first instance ucp <dig>  which was down-regulated in the group of animals with high oa content was associated with regulation of energy homeostasis, but according to schrauwen et al.
<cit>  ucp <dig> played an important role in the protection of mitochondria against lipid-induced oxidative damage by ros production.
this protection was the result of better fatty acid exportation by mitochondria and less production of hydrogen peroxide , which caused oxidative damage to proteins and phospholipids.
plin <dig>  which was down-regulated in the group of animals with high oa content, in turn is a protein associated with lipid droplet that maintains the balance between lipogenesis and lipolysis and regulates fatty acid oxidation in oxidative tissues.
these proteins recruit mitochondria to the surface of lipid droplets, which regulates their homeostasis by storing fatty acids in the form of triglycerides and releasing fatty acids for fatty acid oxidation by mitochondria  <cit> .
cpt <dig>  which was up-regulated in the group of animals with high oa content and cpt1b, which was down-regulated in the group of animals with high oa content, are important for the beta-oxidation of long chain fatty acids, which are involved in the long chain fatty acids transport to the mitochondrial matrix and associated with type  <dig> diabetes and insulin resistance.
the inhibition of cpt <dig> decreases the ability of muscles to oxidize fatty acids due to decreased long chain fatty acids transport into muscle mitochondria that could in turn be responsible for fat accumulation in skeletal muscle  <cit> .
in this study, animals with lower values of oa content presented higher expression levels  of ucp <dig>  plin <dig>  cpt <dig> and cpt1b and lower expression level of scd, corroborating with these previous studies  where the expression level of these genes were associated with fatty acid metabolism, energy homeostasis and animal health.
herein, networks associated with reactive oxygen species  generation such as oxidative phosphorylation and mitochondrial dysfunction were detected, results that corroborate previous studies that reported the role of oa  <cit>  and fatty acids  <cit>  in the control of lipid oxidation.
mitochondria, where β-oxidation occurs, are the major source of ros generation.
fatty acid molecules are broken down to generate acetyl-coa, which enters the citric acid cycle, and nadh and fadh <dig> co-enzymes are used in the electron transport chain  <cit> .
tizioto et al.
<cit>  performed deg gene analysis between animals that showed high  and low  residual feed intake from the same population used in this study, and indicated the metabolic processes that underlie oxidative stress are a primarily network related to lipid metabolism and energy required for maintenance.
these authors also observed the important role of fatty acids in energy metabolism and mitochondrial action on lipid oxidation process similar to that reported in this study.
one of the major transcription factors identified in our study was ppargc1a, which was differentially expressed between the h and l groups for cla-c9t <dig> and down-regulated in h group.
ppargc1a is a transcriptional coactivator that regulates genes involved in energy metabolism and provides a link between external physiological stimuli and the regulation of mitochondrial biogenesis.
ppargc1a regulates global oxidative metabolism by controlling both the induction of mitochondrial metabolism and the removal of its ros by-products, which could elevate oxidative metabolism and minimize the impact of ros on cell physiology in muscle  <cit> .
a review by puigserver and spiegelman  <cit>  reported that the ppargc1a transcriptional coactivator could be activated or not in response to environmental stimuli or by cellular signals such as camp and cytokine pathways, which control energy and nutrient homeostasis.
activated ppargc1a stimulates mitochondrial oxidative metabolism, fiber-type switching in skeletal muscle, and the fasted response in liver  <cit> .
these effects of ppargc1a are the result of gene expression regulation by interacting specifically with other transcription factors such as nuclear hormone receptors, nuclear respiratory factors, and muscle-specific transcription factors.
another important tf associated with lipid metabolism, foxo <dig>  which regulates the transcriptional cascades of glucose metabolism was differentially expressed in the current study for cla-c9t <dig>  foxo <dig>  which was down-regulated in the group of animals with high cla-c9t <dig> content, is highly expressed in tissues such as pancreas, liver, skeletal muscle and adipose tissue in response to insulin and is associated with metabolic disorders as dyslipidemia .
dyslipidemia is a metabolic disorder that contributes to the development of atherosclerosis due to the elevation of plasma cholesterol, triglycerides  or low high-density lipoprotein level  <cit> .
these results are in agreement with a previous study, which indicated that the level of cla in human diet can influence atherosclerosis in animal models  <cit> .
the functional annotation analysis by ipa® for transcripts associated with fas with many deg  included important tfs, such as ppargc1a, srebf <dig>  tp <dig>  foxo <dig> and myc as upstream regulators.
in addition, biological processes, which can cause damage to human and animals health, were identified as enriched.
several disorders, diseases, molecular and cellular functions were also identified as associated with oa or cla-c9t <dig> fa content in skeletal muscle by transcriptome profiling .
two important genes associated with lipid metabolism, gene expression and cancer were identified as degs between animals with high and low cla-c9t <dig>  specifically, epidermal growth factor receptor  and rnps .
egfr is a tyrosine protein kinase, which has been implicated in several biological processes such as cell growth, survival, and migration.
the overexpression of egfr was associated with breast, lung and colon cancers  <cit> .
in this study, the egfr was down-regulated in animals with high cla-c9t <dig> content, result that agree with the association between cla-c9t <dig> content and cancer prevention.
rnps, which was up-regulated in the group of animals with high cla-c9t <dig> content, can affect several basic functions such as protein synthesis, gene expression, and chromosome stability.
it is responsible for pseudouridylation of ribosomal and spliceosomal small nuclear rnas, ribosomal rnas processing, and rna telomerase stabilization  <cit> .
macdonald  <cit>  and park et al.
<cit>  reported that association of cla-c9t <dig> transcriptome level can regulate cell proliferation and differentiation.
CONCLUSIONS
the effective involvement of oa and cla-c9t <dig> in biological processes like transcriptional regulation is still unclear.
however, this transcriptome profiling study, which used longissimus dorsi muscle from cattle with extreme values of oa and cla-c9t <dig> content, demonstrated that both oa and cla-c9t <dig> content had large effects on the expression level of genes related to important biological processes associated with oxidative phosphorylation, cell growth, survival, and migration.
it is tempting to speculate that these fatty acids have direct and maybe indirect physiological effects on skeletal muscle, while other fatty acids do not.
additional nutrigenomic and metabolomic studies are necessary to elucidate the metabolic mechanisms by which these fatty acids influence cell growth, survival, and migration, which are interestingly also associated with several human diseases directly related to human dietary intake of fatty acids.

 lipids are a class of molecules present in all cell types. they contribute to cellular structure, energy storage and several biological functions from transcriptional regulation to physiological processes. over the last couple decades, it has been reported that consumption of fatty acids is associated with fat deposition and may have metabolic effects, such as altered blood lipid and lipoprotein content. however, there are still contrasting opinions about the role of dietary fatty acids on human health, which can be observed in previous reviews and meta-analysis studies conducted in the last years. lipid composition in beef has become an important discussion point. although meat is a significant source of fat in the human diet, it contains high saturated fat content that is associated with some diseases such as obesity, cancer and coronary heart disease. on the other hand, meat has high nutritional value and is an important source of unsaturated fatty acids such as oleic acid and conjugated linoleic acid, which have beneficial effects on human health. thus, there is a need to improve the nutritional value of meat and better understand the biological and molecular processes associated with fatty acid composition in skeletal muscle. previous studies have shown that oa as well as other fatty acids such as linoleic acid, docosahexaenoic acid, eicosapentaenoic acid and cla can regulate gene transcription in tissues such as muscle, liver, adipose, monocytes and blood mononuclear cells. activation of nuclear receptors such as peroxisome proliferator-activated receptors and coactivators of the sterol response element binding protein can mediate this regulation. both ppars and srebps play a role in preadipocyte differentiation, lipid homeostasis and peroxisomal beta-oxidation regulation by controlling the transcription of acyl-coa oxidase and other enzymes involved in adipocyte development. while elevated intracellular levels of stearic and palmitic acids were associated with apoptotic death and inflammatory process. however, the effective involvement of these fatty acids in molecular and physiological processes in skeletal muscle remains unclear. the present investigation was undertaken to identify differentially expressed genes and functional pathways associated with seven fa content in beef cattle. our hypothesis was that variation in fa content could be associated with difference in gene expression in skeletal muscle. our study revealed that up regulation of stearoyl-coa desaturase is associated with deposition of unsaturated fa and that increased levels of oa and cla are associated with expression of genes that have protective function associated with important human diseases.  phenotypes and sequencing data seven different fas, important to beef quality and human health, were used in this transcriptome study, including: oleic acid, palmitic acid, stearic acid, linoleic acid, conjugated linoleic acid cis trans, eicosapentaenoic acid and docosahexaenoic acid. the skeletal muscle samples analyzed were chosen based on their extreme values for each fa studied. when ranked by fatty acids content in skeletal muscle, the statistical test of means performed between the high and low groups according to fa had significant differences for oa, pa, sa, cla-c9t la, epa and dha, but no difference in imf content or backfat thickness. however, animals with extreme phenotypes for oa, pa, sa, cla-c9t la, epa and dha also had significant differences for other fas. for example, animals with high levels of oa had significantly lower levels for sa and pa, but high levels for cla-c9t while extreme animals for cla-c9t had significant low levels for sa and pa, but high levels for oa and dha. the correlation between any two fas tended to be low. however, there were some fas that high negative correlations, e.g. oa and pa and oa and sa or high positive correlations, e.g. epa and la and epa and dha.table phenotypic correlation between the groups of extreme values of fatty acids content in skeletal muscle apalmitic acid bstearic acid coleic acid dlinoleic acid econjugated linoleic acid cis trans 11 feicosapentaenoic acid gdocosahexaenoic acid the average number of mapped read pairs per sample before and after filtering were million and million respectively, which means that on average % of total read pairs were mapped to the bos taurus umd reference genome assembly. after filtering for transcript expression level, a total of;;;;; and annotated genes were used for differential expression analysis for oa, pa, sa, cla-c9t epa, dha and la content, respectively. differential expression analysis differential gene expression analysis was performed for each fa by camparing gene expression level between the h and l fa content groups. no degs were identified for la and sa, while and degs were identified for epa, dha and pa, respectively. in contrast, and degs for oa and cla-c9t respectively, were identified between h and l groups. a volcano plot of log fold-change versus − log fdr-corrected p-value for oa is shown in fig.  the volcano plot of other fas are shown in additional file of the degs for oa, genes were up-regulated and were down-regulated and of the degs for cla-c9t genes were up-regulated and were down-regulated in the l group relative to the h group. the expression level, fold change, adjusted p-value and annotation of all degs for oa and cla-c9t are shown in more detail in additional files and fig. volcano plot of log2fold-change versus − log10fdr-corrected p-value in rna-seq data for oleic acid content functional enrichment analysis for oleic acid content in this study, two different tools of pathway analysis were performed: david and ingenuity pathway analysis®. according to david enrichment analysis, several ontology terms were significantly enriched for the differentially expressed gene lists. cellular component go terms related to mitochondrial envelope, mitochondrial membrane, respiratory chain, mitochondrial matrix and intracellular organelle lumen were associated with degs for oa content. in addition, six kegg pathways that were associated with oxidative phosphorylation, ribosome and proteasome were also identified. these pathways are involved with oxidative phosphorylation and oxidative stress diseases such as huntington, parkinson and alzheimer.table pathways identified from differentially expressed genes list between high and low oleic acid content anumber of differentially expressed genes involved in the term bpercentage of differentially expressed genes involved in the term c p-value adjusted for multiple tests by benjamin and hochberg the ipa® software was also performed for functional enrichment using the global functional analysis and global canonical pathways analysis from the degs list for oa content. global canonical pathways analysis estimates the likelihood that the association between a set of degs in a pathway is due to random chance using a right-tailed fishers exact test. significance was set at bh-adj-pvalue ≤ , which indicated a non-random association. several canonical pathways were identified by gcp analysis, including oxidative phosphorylation, mitochondrial dysfunction, insulin receptor signaling, lps-stimulated mapk signaling, role of nfat in cardiac hypertrophy and huntington’s disease signaling. twenty-five networks were enriched as a function of oa content as identified by ipa®gfa analyses. one in particular, shown in fig.  was associated with lipid metabolism and energy production. this network contained molecules and genes such as cholesterol, very-low-density lipoprotein, perilipin, scd, low-density lipoprotein carnitine palmitoyltransferase i and carnitine palmitoyltransferase i, respectively. among these only scd was up-regulated in the h group as shown in red in fig.  fig. a gene network associated with lipid metabolism and energy production is impacted by oa content. genes presented in red are up-regulated in the high oleic acid content group. genes presented in green are down-regulated in the h group. the intensity of the colors is related to the estimated of fold change. molecules in white are not in the de list, but were incorporated into the network through relationships with other molecules to further explore the observed changes in gene expression, ipa® upstream regulator analyses were performed to identify the cascade of upstream transcriptional regulators that could be involved in the gene expression changes in skeletal muscle due to oa content. the ipa® program estimated the effects between transcriptional regulators and their target genes based on prior knowledge stored in the ingenuity® knowledge base. upstream regulators were identified from the list of degs for oa content, which were connected via mechanistic networks detected by ipa®. peroxisome proliferator-activated receptor gamma, coactivator alpha was among the top predicted upstream regulators. ppargc1a and ten other transcription factors such as forkhead box o, peroxisome proliferator-activated receptor gamma, coactivator beta, estrogen-related receptor gamma, sterol regulatory element binding transcription factor, tumor protein p, forkhead box o, v-myc avian myelocytomatosis viral oncogene homolog and myogenic differentiation were predicted to be inhibited, whereas the transcription factors forkhead box o and sterol regulatory element binding transcription factor were predicted to be activated.fig. the mechanistic network of the upstream regulators and their relationship predicted by ipa®. the molecules shown in blue are predicted to be inhibited, while the molecules shown in orange are predicted to be activated as a result of oa content. color intensity represents the level of inhibition or activation. the lines and arrows in blue represent a direct interaction and activation, respectively. the interrupted lines in yellow represents direct inhibition. the gray lines represent the interactions that oa content did not affect, but have been reported in the literature the functional enrichment analysis using the ipa® program identified several statically significantly enriched biological functions from the oa degs list, e.g. processing of rna, transcription of rna, expression of rna, transcription of dna, expression of mrna, catabolism of fatty acid, beta-oxidation of palmitic acid, depletion of triacylglycerol. the indirect inhibitory interaction between scd and β-oxidation and the depletion of triacylglycerol, which was associated with lipid metabolism and energy production are shown in fig.  in the network shown in fig.  it is also possible to observe the indirect interaction between scd, ldl-cholesterol, vldl-cholesterol, cpt cpt1b, plin and ucp fig. biological functions that include stearoyl-coa desaturase such as beta-oxidation of palmitic acid and agpat depletion of triacylglycerol. genes shown in red are up-regulated in the high oleic acid content group, while genes shown in green are down-regulated functional enrichment analysis for conjugated linoleic acid cis trans content the enrichment analysis performed by david software using the list of degs for cla-c9t content identified one kegg pathway, which was related to ribosome function. among the molecular functions identified by david associated with the cla-c9t de genes identified between the groups with extreme values of cla-c9t were nucleotide binding, atp binding and structural constituent of ribosome. the top five canonical pathways identified for cla-c9t content by gfa and gcp analysis using ipa® program were protein ubiquitination, interferon signaling, hypoxia signaling in the cardiovascular system, angiopoietin signaling and mtor signaling. the top five upstream regulators identified from the list of degs for cla-c9t associated network functions and toxicology list for cla-c9t content are shown in additional file among the top upstream regulators were: interferon, lambda, tumor necrosis factor, retinoic acid, signal transducer and activator of transcription, and interferon regulatory factor, which were predicted as activated in this study. however other important cytokines and transcription regulators were identified as activated/inhibited such as ifnk, ccl ligand 5) and, prl, trim, nfkb1a, srebf foxo tp and myc, respectively. figure  shows the foxo network, which has been associated with the metabolic disorder dyslipidemia.fig. the network of the upstream regulator foxo by ipa®. genes presented in red are up-regulated in the high oleic acid content group. genes presented in green are down-regulated in the h group. the intensity of the colors is related to the estimated of the fold change. the interrupted lines in orange represents direct inhibition. the blue represents direct activation. the gray lines represent the no interactions have been reported in the literature the top five associated network functions detected from the list of cla-c9t degs between the groups with extreme values of cla-c9t were related to rna damage, repair and post-transcriptional modification; developmental disorder; metabolic disorder; lipid metabolism, molecular transport, rna trafficking and; cell death and survival. figure  illustrates the network associated with lipid and nucleic acid metabolism and small molecule biochemistry, which presents epidermal growth factor receptor as a central gene and which was down-regulated in animals with high cla-c9t content. figure  shows a network associated with molecular transport, rna trafficking, rna post-transcriptional modification that contained ribonucleoproteins, which were up-regulated in animals with high cla-c9t content. the top five toxicology terms were associated with cardiac necrosis/cell death, cardiac hypertrophy, hypoxia-inducible factor signaling, increases liver steatosis and, ppara/rxra activation.fig. network associated with lipid metabolism, nucleic-acid metabolism and small molecule biochemistry impacted by cla-c9t content. genes presented in red are up-regulated in the high cla-c9t content group. genes presented in green are down-regulated in the h group. the intensity of the colors is related to estimate of the fold change. molecules in white are not in the de list, but were incorporated into the network through relationships with other molecules fig. network associated with molecular transport, rna trafficking and rna post-transcriptional modification impacted by cla-c9t content. genes presented in red are up-regulated in the high cla-c9t content group. genes presented in green are down-regulated in the h group. the intensity of the colors is related to estimate of the fold change. molecules in white are not in the de list, but were incorporated into the network through relationships with other molecules validation of differentially expressed genes the quantitative real-time polymerase chain reaction results and the relative quantification of degs selected to validate the present rna-seq study are shown in additional file nine genes differently expressed between high and low oa groups were tested by qpcr and seven genes confirmed the rnaseq data, one gene confirmed but not at a significant level and one gene disagreed with rnaseq data. discussion skeletal muscle is important for energy homeostasis, as it is a site of energy storage and insulin-stimulated glucose. metabolic diseases such as obesity and coronary disorders could be a consequence of insulin resistance, i.e. the inability of insulin to drive glucose into the skeletal muscle and other tissues as liver, which can be caused by excessive body fat deposition. fatty acids in skeletal muscle play an important role in the structural and functional processes that influence the fluidity and stability of membrane structures, which impacts membrane functions such as transport, cell signaling, responses to oxidative damage and apoptosis. studies have reported that the fatty acid profile of skeletal muscle phospholipids and triacylglycerides can be influenced by the fatty acid composition of human and animal diets. several saturated and unsaturated fatty acids have been implicated, both positively and negatively, in different biological processes in skeletal muscle and other tissues such as liver and cardiac tissue. in contrast, meta-analysis studies reported no evidence that a human diet, which was rich in monounsaturated fatty acids and polyunsaturated fatty acids and depleted for saturated fatty acid, had beneficial effects on coronary heart disease. in this study, all animals were of the same breed, sex, similar age and fed the same diet. however, different levels of fa content were observed in skeletal muscle. this maybe due to genetic variation among the animals given that the environmental variables were similar across all animals. transcriptomic analyses indicated that many genes were differentially expressed between animals with high and low oa and cla-c9t content. while, only a few genes were differentially expressed among the extreme groups for pa, sa, epa and dha and none for la and sa. additionally, previous studies reported only a few genes were affected by different levels of intramuscular fat content and tenderness in this same population. because the samples used for oa and cla-c9t analysis also differed significantly for other fas, we cannot be certain that the observed de genes for oa and cla-c9t are associated solely with these fas. despite the use of some samples in the analysis of several fa extremes, the lists of differentially expressed genes, and identified pathways were very different. this may not be surprising given the generally low correlation between fas. thus it is very likely that utilization of only a couple samples in several analyses does not have an negative impact on other analyses. finally, these findings indicate the biological importance of oa and cla-c9t for skeletal muscle physiology. however, a word of caution is necessary because, a direct relation between gene expression level and protein abundance was not establish. these fatty acids may play an important role in transcription regulation and consequently in energy homeostasis and metabolic diseases such as obesity and diabetes as also presented by ntambi. the most abundant mufa found in skeletal muscle fat is oleic acid. it is present in membrane phospholipids, triglycerides and cholesterol esters. human oa consumption has been associated with low levels of low-density lipoprotein and also with the potential increase of high-density lipoprotein levels in the blood. furthermore, oa is converted to oleoylethanolamide, a small molecule in the intestine, which is involved in appetite control. previous studies have reported an important contribution of oa intake to general human health, which could lead to a decrease in cholesterol levels, atherosclerosis risk and diabetes occurrence. further, oa has protective effects against viral infection and cancer development. beef has a high unsaturated fatty acid profile, primarily oa. it is considered an important source of oa in human nutrition, and health. another important aspect of the oa content in beef is its relationship to meat quality traits such as tenderness, flavor and shelf-life. thus, it is appealing to improve our knowledge about biological processes associated with oa content in skeletal muscle, which could both help to improve the nutritional value and quality of beef. in mammals, the biosynthesis of the oa is dependent on the activity of stearoyl-coa desaturase. this soluble enzyme catalyzes the introduction of a cis-double bond at the 9th carbon position of stearic acid, to form the mufa, oleic acid. scd is also required for the synthesis of highly unsaturated essential fatty acids or pufas such as eicosopentaenoic and docosahexaenoic acids; synthesized from a-linolenic acid, and arachidonic acid, which are dependent on the presence of oleic acid. in ruminants, such as beef cattle, the concentration of oa in adipose tissue depends more on the concentration of stearic acid hydrogenated by ruminal microorganisms than from stearic acid desaturation by scd in the tissues. epa and dha are omega- long-chain pufa, which are dietary fats associated with health benefits. they are present in cell membranes and play a role in anti-inflammatory processes and in the viscosity of cell membranes. epa and dha are also precursors of several metabolites that are potent lipid mediators, considered by many investigators to be beneficial in the prevention or treatment of several diseases such as cardiovascular, obesity and alzheimer. however, in this study both epa and dha did not appear to have much of an effect on skeletal muscle gene expression, which may mean that they do not have a biological effect on skeletal muscle. it is interesting to speculate that deg analyses of other tissues such as liver and adipose may be able to identify tissues responsive to these fatty acids. in contrast, conjugated linoleic acid cis trans has a large effect on gene expression. this fa is associated with human health, specifically related with diseases such as cancer, immune and inflammatory responses and obesity and is naturally present in food sources such as fats in milk and meat of ruminant animals. this may indicate that skeletal muscle is a primary target of conjugated linoleic acid cis trans the enriched transcript clusters identified by david based on biological process go terms from the list of degs were associated with electron transport chain, mrna translation and generation of precursor metabolites and energy. fas like oa and cla-c9t are involved in both extracellular and intracellular activities, which are in a partially dissociated state at physiological ph with part of the molecules diffused into the cytosol and other part integrating the membrane structure. these fas impact several molecular functions in the cell such as: ion transport across membranes; activate intracellular enzymes; modulation of na+/k + -atpase activation, modulation of hormone/receptor interactions; gene transcription and; mrna translation. oa can be obtained by either dietary consumption or de novo lipogenesis. de novo lipogenesis of oa can occur from both dietary carbohydrates and fat. the enzyme responsible for mufa oa biosynthesis is scd, which is considered as a key enzyme in de novo lipogenesis, a process that is associated with obesity, synthesis of cholesterol and apoptosis. in the present study, scd was up-regulated in the group of animals with high oa content. this was expected as this gene function is linked to oa synthesis. hulver et al. suggested that elevated expression of scd in human skeletal muscle contributes to abnormal lipid metabolism and progression of obesity. however, in this study, the imf content between the l and h group was not statistically different, as the h group had an average imf content of % and the l group had an imf of %. in this study, the fatty acid synthase and acetyl-coa carboxylase, responsible for fatty acid metabolism, were not differentially expressed between the groups h an l for any fa studied, considering that the diet was the same for all animals. this may indicate: 1) the increased scd in this study was associated just with higher synthesis of oa and not with higher fat deposition; 2) a difference in how bovine and human skeletal muscles respond to oa content. schrauwen, clapham et al. reported that mice which overexpressed ucp in skeletal muscle had lower body weights and increased ampk activity, elevated metabolic rate, lower fasting plasma glucose and insulin levels compared to wild type mice. in the first instance ucp which was down-regulated in the group of animals with high oa content was associated with regulation of energy homeostasis, but according to schrauwen et al. ucp played an important role in the protection of mitochondria against lipid-induced oxidative damage by ros production. this protection was the result of better fatty acid exportation by mitochondria and less production of hydrogen peroxide, which caused oxidative damage to proteins and phospholipids. plin which was down-regulated in the group of animals with high oa content, in turn is a protein associated with lipid droplet that maintains the balance between lipogenesis and lipolysis and regulates fatty acid oxidation in oxidative tissues. these proteins recruit mitochondria to the surface of lipid droplets, which regulates their homeostasis by storing fatty acids in the form of triglycerides and releasing fatty acids for fatty acid oxidation by mitochondria. cpt which was up-regulated in the group of animals with high oa content and cpt1b, which was down-regulated in the group of animals with high oa content, are important for the beta-oxidation of long chain fatty acids, which are involved in the long chain fatty acids transport to the mitochondrial matrix and associated with type diabetes and insulin resistance. the inhibition of cpt decreases the ability of muscles to oxidize fatty acids due to decreased long chain fatty acids transport into muscle mitochondria that could in turn be responsible for fat accumulation in skeletal muscle. in this study, animals with lower values of oa content presented higher expression levels of ucp plin cpt and cpt1b and lower expression level of scd, corroborating with these previous studies where the expression level of these genes were associated with fatty acid metabolism, energy homeostasis and animal health. herein, networks associated with reactive oxygen species generation such as oxidative phosphorylation and mitochondrial dysfunction were detected, results that corroborate previous studies that reported the role of oa and fatty acids in the control of lipid oxidation. mitochondria, where β-oxidation occurs, are the major source of ros generation. fatty acid molecules are broken down to generate acetyl-coa, which enters the citric acid cycle, and nadh and fadh co-enzymes are used in the electron transport chain. tizioto et al. performed deg gene analysis between animals that showed high and low residual feed intake from the same population used in this study, and indicated the metabolic processes that underlie oxidative stress are a primarily network related to lipid metabolism and energy required for maintenance. these authors also observed the important role of fatty acids in energy metabolism and mitochondrial action on lipid oxidation process similar to that reported in this study. one of the major transcription factors identified in our study was ppargc1a, which was differentially expressed between the h and l groups for cla-c9t and down-regulated in h group. ppargc1a is a transcriptional coactivator that regulates genes involved in energy metabolism and provides a link between external physiological stimuli and the regulation of mitochondrial biogenesis. ppargc1a regulates global oxidative metabolism by controlling both the induction of mitochondrial metabolism and the removal of its ros by-products, which could elevate oxidative metabolism and minimize the impact of ros on cell physiology in muscle. a review by puigserver and spiegelman reported that the ppargc1a transcriptional coactivator could be activated or not in response to environmental stimuli or by cellular signals such as camp and cytokine pathways, which control energy and nutrient homeostasis. activated ppargc1a stimulates mitochondrial oxidative metabolism, fiber-type switching in skeletal muscle, and the fasted response in liver. these effects of ppargc1a are the result of gene expression regulation by interacting specifically with other transcription factors such as nuclear hormone receptors, nuclear respiratory factors, and muscle-specific transcription factors. another important tf associated with lipid metabolism, foxo which regulates the transcriptional cascades of glucose metabolism was differentially expressed in the current study for cla-c9t foxo which was down-regulated in the group of animals with high cla-c9t content, is highly expressed in tissues such as pancreas, liver, skeletal muscle and adipose tissue in response to insulin and is associated with metabolic disorders as dyslipidemia. dyslipidemia is a metabolic disorder that contributes to the development of atherosclerosis due to the elevation of plasma cholesterol, triglycerides or low high-density lipoprotein level. these results are in agreement with a previous study, which indicated that the level of cla in human diet can influence atherosclerosis in animal models. the functional annotation analysis by ipa® for transcripts associated with fas with many deg included important tfs, such as ppargc1a, srebf tp foxo and myc as upstream regulators. in addition, biological processes, which can cause damage to human and animals health, were identified as enriched. several disorders, diseases, molecular and cellular functions were also identified as associated with oa or cla-c9t fa content in skeletal muscle by transcriptome profiling. two important genes associated with lipid metabolism, gene expression and cancer were identified as degs between animals with high and low cla-c9t specifically, epidermal growth factor receptor and rnps. egfr is a tyrosine protein kinase, which has been implicated in several biological processes such as cell growth, survival, and migration. the overexpression of egfr was associated with breast, lung and colon cancers. in this study, the egfr was down-regulated in animals with high cla-c9t content, result that agree with the association between cla-c9t content and cancer prevention. rnps, which was up-regulated in the group of animals with high cla-c9t content, can affect several basic functions such as protein synthesis, gene expression, and chromosome stability. it is responsible for pseudouridylation of ribosomal and spliceosomal small nuclear rnas, ribosomal rnas processing, and rna telomerase stabilization. macdonald and park et al. reported that association of cla-c9t transcriptome level can regulate cell proliferation and differentiation.  the effective involvement of oa and cla-c9t in biological processes like transcriptional regulation is still unclear. however, this transcriptome profiling study, which used longissimus dorsi muscle from cattle with extreme values of oa and cla-c9t content, demonstrated that both oa and cla-c9t content had large effects on the expression level of genes related to important biological processes associated with oxidative phosphorylation, cell growth, survival, and migration. it is tempting to speculate that these fatty acids have direct and maybe indirect physiological effects on skeletal muscle, while other fatty acids do not. additional nutrigenomic and metabolomic studies are necessary to elucidate the metabolic mechanisms by which these fatty acids influence cell growth, survival, and migration, which are interestingly also associated with several human diseases directly related to human dietary intake of fatty acids. 
lipids are a class of molecules that play an important role in cellular structure and metabolism in all cell types. skeletal muscle transcriptome analysis of nellore steers revealed no differentially expressed genes for samples with extreme values for linoleic acid or stearic acid, and only a few degs for eicosapentaenoic acid, docosahexaenoic acid and palmitic acid, while large numbers of degs were associated with oleic acid and conjugated linoleic acid cis trans. to gain insight into biological processes associated with fatty acid content in skeletal muscle, the aim of the present study was to identify differentially expressed genes and functional pathways related to gene expression regulation associated with fa content in cattle. several fatty acids have been both positively and negatively implicated in different biological processes in skeletal muscle and other tissues. oa and cla-c9t content had significant effects on the expression level of genes related to important biological processes associated with oxidative phosphorylation, and cell growth, survival, and migration. functional annotation and functional enrichment from oa degs identified important genes, canonical pathways and upstream regulators such as scd, plin ucp cpt cpt1b, oxidative phosphorylation mitochondrial dysfunction, ppargc1a, and foxo two important genes associated with lipid metabolism, gene expression and cancer were identified as degs between animals with high and low cla-c9t specifically, epidermal growth factor receptor and rnps. these results contribute to our understanding of how some fas modulate metabolism and may have protective health function. in the last few decades, it has been reported that long-chain fatty acids are involved in several biological functions from transcriptional regulation to physiological processes. only two out of seven classes of molecules of fa studied were associated with large changes in the expression profile of skeletal muscle.
 lipids are a class of molecules that play an important role in cellular structure and metabolism in all cell types. in the last few decades, it has been reported that long-chain fatty acids are involved in several biological functions from transcriptional regulation to physiological processes. several fatty acids have been both positively and negatively implicated in different biological processes in skeletal muscle and other tissues. to gain insight into biological processes associated with fatty acid content in skeletal muscle, the aim of the present study was to identify differentially expressed genes and functional pathways related to gene expression regulation associated with fa content in cattle.  skeletal muscle transcriptome analysis of nellore steers revealed no differentially expressed genes for samples with extreme values for linoleic acid or stearic acid, and only a few degs for eicosapentaenoic acid, docosahexaenoic acid and palmitic acid, while large numbers of degs were associated with oleic acid and conjugated linoleic acid cis trans. functional annotation and functional enrichment from oa degs identified important genes, canonical pathways and upstream regulators such as scd, plin ucp cpt cpt1b, oxidative phosphorylation mitochondrial dysfunction, ppargc1a, and foxo two important genes associated with lipid metabolism, gene expression and cancer were identified as degs between animals with high and low cla-c9t specifically, epidermal growth factor receptor and rnps.  only two out of seven classes of molecules of fa studied were associated with large changes in the expression profile of skeletal muscle. oa and cla-c9t content had significant effects on the expression level of genes related to important biological processes associated with oxidative phosphorylation, and cell growth, survival, and migration. these results contribute to our understanding of how some fas modulate metabolism and may have protective health function. electronic supplementary material the online version of this article contains supplementary material, which is available to authorized users. keywords lipidsrna-seqbos indicusglobal oxidative metabolismhuman healthfapesp2014/22884-02012/23638-8embrapamacroprograma 01/2005issue-copyright-statement© the author 2016 