The beef fatty acid profile contributes to its sensory properties and plays a significant role in determining the quality of the final product from a health perspective. Therefore, it is essential to select animals with the genetic potential to produce healthier beef by increasing the levels of CLA and maintaining the optimal ratio of PUFA to SFA and ω6 to ω3. Our study identified significant genetic differences between animals (p-value < 0.05), which were classified into three groups based on their FA profile (Fig. 1). The C1 cluster showed higher levels of PUFA/SFA, PUFA, ω6, ω3, linolenic, and α-linolenic compared with C2 and C3, which have helpful activities in human metabolism, making C1 a potential group for animal selection. The C2 cluster exhibited intermediate fatty acid profile and cluster C3 showed a lower PUFA/SFA ratio and higher levels of SFA, MUFA (including OA), and CLA compared to the other groups. The simultaneous presence of elevated SFA, MUFA and CLA in cluster C3 may be related to activities of the Δ9 desaturase enzyme. This enzyme converts SFA into MUFA and transvaccenic acid (MUFA) into its corresponding conjugated linoleic acid (CLA), contributing to them being metabolically interconnected and mutually dependent 24.
The genome produces numerous lncRNAs, which are transcripts with more than 200 nucleotides and do not encode protein-coding gene. Studies have indicated that the structure of lncRNA is one of the most critical factors regulating different biological processes at the epigenetic, transcriptional, and translational levels 25,26. When involved in transcriptional regulation act as ligands and often interact with transcription factors to form complexes and control gene transcription 27. LncRNAs can be classified into different categories depending on their location, structure, and function. In this study, we categorized lncRNAs based on their genomic location as genic lncRNAs (Table 3) and intergenic lncRNAs (lincRNA) (Tables 4 and 5). Genic lncRNAs are long non-coding RNAs that overlap coding proteins and may intersect gene exons, introns, or an entire gene, respectively 25. LincRNA is defined by the absence of direct overlap with intergenic noncoding RNA and protein-coding genes. They exhibit distinct attributes setting them apart from mRNA-coding genes and serve functions such as chromatin and genome architecture remodeling, transcriptional regulation and RNA stabilization 28.
In this study, 25 DE genic lncRNAs were found to be annotated in the bovine genome reference (ARS.UCD 1.2), 46 DE novel transcript was associated with annotated lncRNA and 194 DE novel lincRNA were identified and associated with FA content in beef cattle. These lncRNAs are important in regulating the expression of genes related to beef FA profile deposition by affecting FA biosynthesis pathway and lipid metabolism. However, the specific functions of these lncRNAs still need to be further explored.
Among the DE genic lncRNAs found to the C1 vs. C2 comparison, we can highlight the lncRNA_16456.3, downregulated in C1 in relation to C2 and interacting with the genes FAM126A (Family with sequence similarity 126 member A) and IL6 (Interleukin-6) (Table 3). Although the function of FAM126A is unclear, some studies have reported it as important for lipid metabolism and lipid homeostasis 29–31. The FAM126A gene encodes the Hyccin protein, which is essential for function of protein complex, known as the phosphatidylinositol-5-phosphate synthesis complex (PI5P4K). This complex may interfere with phospholipid synthesis 32. Phospholipids (PLs) are essential structural lipids in cell membranes, and their fatty acid composition plays a critical role in determining membrane properties and functions 33. Intramuscular fat consists mainly of triglycerides (TG) and PLs 34. In general, the PL fraction is rich in PUFA due to the preferential incorporation of PUFA into PL associated with cell membranes, while SFA and MUFA are mainly deposited in the TG fraction 35–37. In this regard, the phospholipid content in intramuscular fat can influence the composition of fatty acids in meat. Thus, DE lncRNA_16456.3 may be influencing in phospholipid synthesis through interaction with the FAM126A gene, contributing to a profile with lower PUFA content in C2.
The Interleukin 6 (IL6) is a pro-inflammatory adipokine produced by adipose tissue, skeletal muscle, and macrophages 38. The IL6 was enriched to the biological process GO terms such as cellular response to lipid (GO:0071396) and it plays a role in immune response, regulates lipid homeostasis, fatty acid oxidation, lipolysis in adipocytes, skeletal muscle tissue, and hepatocytes 39,40. According to in vitro studies, palmitic acid can stimulate the transcription of IL6 in different biological tissues 41–43. This is possible due to the inflammatory response triggered by palmitic acid responsible for the positive regulation of IL6 44. Furthermore, study conducted on pigs, found that IL6 polymorphism exhibited a significant association with PUFA levels 45. IL6 in swine is located near the QTL regions associated with PUFA, CLA, and SFA content 46–50. These studies showed that the IL6 gene may have a pleiotropic effect on the composition of fatty acids. It is associated with the concentration of both SFA, MUFA and PUFA. Our results showed lncRNA_13894.1 was downregulated for high PUFA, ω3, ω6 and low SFA, MUFA, CLA, and oleic acid; C1), suggesting that its negative regulation and associated with IL6 may contribute to a genetic profile with lower PUFA and higher SFA, MUFA, CLA an oleic acid.
Still comparing C1 vs. C2, lncRNA_15786.3 interacted with the CCN1 gene (Cellular communication network factor 1) and was upregulated compared with C1 cluster (Table 3). CCN1 encodes a protein associated with the extracellular matrix that is essential regulating cellular processes such as proliferation, migration, and cell adhesion 51. A study showed that CCN1 regulates the lipogenic gene FASN (Fatty acid synthase), crucial for fatty acid synthesis, contributing to lipid formation and fat accumulation in cells 52. Li et al53 in a study of SNP in Chinese Holstein dairy cattle, they reported that homozygous genotypes for FASN were associated with higher levels of PUFAs in milk. Zhang et al. (2008) identified SNPs associated with lower levels of myristic acid, palmitic acid, and total SFA in the Longissimus dorsi muscle of American Angus bulls. These findings support our results, in which C1 showed significant differences in FA content, such as higher levels of PUFA and lower levels of SFA, myristic acid, and palmitic acid compared to the FA profile of the C2 cluster. This suggests that animals in C1 would have a genetic profile associated with a healthy and desirable FA composition, characterized by higher PUFA and lower SFA content. In this context, lncRNA_15786.3 may influence the concentration of these fatty acids through its interaction with the CCN1 gene, contributing to a healthy fatty acid profile.
For C1 vs. C2 comparison, 17 DE long intergenic RNA (lincRNA) were upregulated and 36 were downregulated in C1 in relation to C2. The lncRNA_18383.11 was associated with the DDIT4L (DNA Damage Inducible Transcript 4 Like) gene and was upregulated compared with C1 cluster (Table 3). This DDIT4L gene, also known as REDD2 (Regulated in Development and DNA Damage Responses 2) acts as an inhibitor of the mTOR signaling pathway, responsible for regulating cell growth and proliferation, and for been involved in the stress response 54,55. Zhao et al. 56 observed that decrease mTORC1 signaling pathway activity triggered increased FA oxidation in mice. Liu et al. 57 reported that diets with a high level of PUFAs (ω3/ω6) were able to inhibit the activity of the mTORC1 signaling pathway, reducing the cellular response to growth stimulus and consequently preventing metabolic syndromes such as weight loss, insulin resistance, inflammation and mitochondrial dysfunction in mice. In addition, when PUFAs are oxidized, there is a reduction in the supply of free fatty acids for the synthesis of pro-inflammatory lipids, such as SFA 58–60. In this study, C1 showed a significantly higher difference in PUFAs, including ω6, ω3 linoleic and alpha-linolenic, with lower values for palmitic acid and myristic acid than C2. Our results support these findings and suggest that the interaction between lncRNA_18383.11 and the DDIT4L gene may affecting concentration of PUFA in C1, influencing FA oxidation by inhibiting of the mTORC signaling pathway. In this sense, lncRNA_18383.11 may contribute to a healthier beef fatty acid profile with higher PUFA and lower SFA.
For the C1 vs. C3 comparison, the lncRNAs lncRNA_13894.1 and lncRNA_12504 interacted with SOX4 (SRY-Box transcription factor 4), respectively) and BNIP3 (BCL2/Adenovirus E1B 19 kDa protein-interacting protein 3) (Table 3). These genes were enriched by GO biological function terms related to mitochondrial transport (GO:0006839), fat cell differentiation (GO:0045444), and canonical Wnt signaling pathway (GO:0060070) (Table S2). The lncRNA_12504 was downregulated (Table 3) in animals from the C1 compared with C3. In this study, C1 showed significant differences in the content of total PUFAs, including linoleic acid, α-linolenic acid, ω3, ω6, and PUFA/SFA ratio, compared to the fatty acid profile of C3, while the content of SFA, stearic acid, myristic acid, palmitic acid was significantly lower in C1. The Wnt pathay enriched the SOX4 gene which is an important developmental transcription factor that regulates stem cell characteristics, neuronal differentiation 61 and osteoblast development 62. SOX4 plays a role in fat development that remains to be clarified 63. A recent study investigated the role of SOX4 protein in forming white adipocytes in mice under obese conditions 63. These authors demonstrated that SOX4 can control white adipose tissue hyperplasia by inhibiting preadipocyte determination. Adipose tissue hyperplasia can also be induced by a high rate of SFA 64 Despite the above authors' promising results, there are still questions about the exact role of SOX4 in fat development in cattle. In this study, C1 had a lower SFA content compared to C3 and identified that lncRNA_12504 interacted with the SOX4 gene downregulated in C1 animals, suggesting the relationship of lncRNA_13894.1 in the control of hyperplasia in adipose tissue. However, more studies are needed to understand better these interactions and the role of SOX4 and how they can affect the fatty acid profile of beef in Nellore cattle. The BNIP3 encodes a protein in the outer mitochondrial membrane, where it functions in mitophagy and mitochondrial dynamics 65. This gene acts in different metabolic pathways, such as lipid metabolism 65 glycolysis 66 and mitochondrial bioenergetics 67. The BNIP3 gene directly interacts with acetyl-CoA acyltransferase 2 (ACAA2), an enzyme involved in lipid metabolism that facilitates the final stage of β-oxidation within mitochondria 68,69. The ACAA2 enzyme plays a crucial role in malonyl-CoA formation, essential for elongating fatty acid chains 70. Studies on single nucleotide polymorphisms in sheep showed that the ACAA2 gene was associated with the ω6/ω3 ratio in milk 71. Our study showed that C1 has high levels of ω6, ω3, linoleic, alpha-linolenic and ω6/ω3 in relation to C3 and found lncRNA_13894.1 interacted with the BNIP3 gene upregulated in animals from C1, suggesting the relationship of the lncRNA_13894.1 in the FA determination, contributing to PUFA concentration in bovine muscle tissue.
For the C2 vs. C3 comparison, the lncRNA_16618.6 and lncRNA_11324.5 interact with GPR85 (G Protein-Coupled Receptor 85) and ENSBTAG00000019048, respectively. The lncRNA_16618.6 was upregulated in animals from the C2 in relation to C3 and interacted with GPR85. The GPR85 is a gene involved in G protein-coupled receptors (GPCRs). This protein superfamily (GPCRs) has a wide chemical diversity of possible ligands, including lipids 72. Studies have shown that GPCRs play an essential role in binding extracellular FAs, including small, medium, and long-chain FAs 73–76. Additionally, G proteins can regulate the cAMP-mediated signaling pathway 77–79. In the context of lipid metabolism, the cAMP/PKA pathway may play an important role in the regulation of lipolysis80, FA oxidation81, adipogenesis82 and anti-inflammatory83,84 through stimulation of PUFA fatty acids such as oleic acid, docosahexaenoic acid (DHA). In this study, the C2-fatty acid profile exhibited significant differences in PUFA, ω3 and ω6 content compared to the C3-fatty acid profile, indicating that this lncRNA lncRNA_16618.6 and its interaction with GPR85 may influence the concentration of ω6 and ω3 fatty acids, thereby contributing to a beef fatty acid profile with higher PUFA levels in C2. The lncRNA_11324.5 was downregulated in animals from the C2 in relation to C3 and interacted with ENSBTAG00000019048. The ENSBTAG00000019048 (Mediator complex subunit 28 - MED28), also known as magicin, is expressed in numerous cell lines and tissues 85. MED28 has been shown to regulate smooth muscle cell differentiation negatively 86. This gene has been identified as associated with IMF content and carcass traits in cattle in GWAS studies 87,88. However, there are no reports of the role of MED28 in lipid metabolism. In the present study, C2 showed lower content of total SFA, including myristic, palmitic and stearic acids in relation to C3. IMF content in bovine is characterized by its abundant SFA, especially palmitic acid and stearic acid 89. These findings suggest that downregulation of lncRNA_11324.5 and interaction with MED28 may be acting toward a fatty acid profile with higher levels lows for SFA. However, further studies are needed to better understand these interactions, and the role of MED28 and how they might affect the beef fatty acid profile in Nellore cattle.
The novel transcript lengths, lncRNA_19922.3 and lncRNA_17096.3, were associated with ENSBTAT00000067459 and ENSBTAT00000066814 lncRNAs, and interacted with NR2F1 (COUP transcription factor 1) and MNX1 (Motor neuron and pancreas homeobox 1) genes, respectively. These transcripts were downregulated in C1 vs. C2 and C1 vs. C3 comparisons (Table 3). For the C1 vs. C2 comparison, NR2F1 was enriched by GO biological function terms related to cellular lipid response (GO: 0071396), while for the C1 vs. C3 comparison, this gene was enriched by GO biological function terms related to cellular response to steroid hormone stimulus (GO:0071383). The NR2F1 gene (also known as nuclear receptor 2F1, or COUP-TF1) is a sterol-binding transcription factor involved in the regulation of synthesis and transport of triglycerides in enterocytes and associated to lipid, cholesterol, and carbohydrate metabolism 90–92. Researchers have validated NR2F1 as a candidate gene for IMF deposition using multi-omic data in Longissimus dorsi and gluteus medius tissues of pigs 93,94. In a genomic association study in pigs conducted by Pena et al. (2019), the NR2F1 gene was identified in genomic regions that regulate a relevant percentage of genetic variance for the composition of fatty acids, being these palmitoleic, oleic acid and MUFA. In this study, the C3 showed significant differences in the total content of SFAs, including myristic, palmitic, stearic acid, and oleic acid compared to the C1 and C2 fatty acid profiles. MUFA and oleic contents were very similar between C2 and C3, differing significantly from C1 with small values for MUFA and oleic contents. These results suggest that animals in the C2 would have a genetic profile associated with more balanced MUFA and SFA contents.
The MNX1 gene regulates the development of motor neurons and pancreatic beta cells, playing a crucial role in the proper formation of these tissues during embryonic development 95. Although the function of this gene in cattle remains unclear, Zhang et al. 96 demonstrated that MNX1 enhances lipid synthesis by stimulating the expression of SREBP1 gene and fatty acid synthesis in humans. GWAS using SNPs markers indicated that the bovine SREBP1 polymorphism is associated with proportions of SFA, palmitic acid, stearic acid, and triglycerides in the fat composition in Simmental and Korean Hanwoo bulls 97,98. In this context, the interaction of the novel transcripts lncRNA_19922.3 and lncRNA_17096.3 with potential genes such as NR2F1 and MNX1, suggest an important role in the regulation of elements associated with the high content of MUFA and SFA, including individual FAs such as palmitic and stearic fatty acids as observed in C3 and C2.
The lncRNA_5415.4 associated with the BTG2 (BTG Anti-Proliferation Factor 2) gene was upregulated in C1 vs. C3 and C2 vs. C3 comparisons (Table 3). C1 and C2 presented significant differences in the contents of ω3 and ω6, in addition to linoleic and alpha-linolenic in relation to C3. Omegas 3 and 6 play a significant role in reducing coronary heart disease, regulating the immune system, maintaining cerebral activities, as well as aiding visual and cognitive development 99–101. For C1 vs. C3 comparison, BTG2 was enriched by GO biological function terms related with negative regulation of macromolecule biosynthetic process (GO:0010558) and central nervous system neuron differentiation (GO:0021953) (Table 8). While for C2 vs. C3 this gene was enriched by GO biological function terms related with negative regulation of cell proliferation (GO:0008285) and central nervous system neuron differentiation (GO:0006839) (Table 9). BTG2 gene encodes a multifunctional protein capable of inhibiting cell proliferation, inducing apoptosis and modulating gene expression. This gene is induced by the TP53 gene, leading to the cessation of cellular proliferation 102. Scherma et al 103 investigated the effects of ω6 and ω3 FAs on submandibular gland tumorigenesis in mice and, reported that ω3 rich diet significantly reduced the number and size of tumors compared to the control diet. In addition, the ω3 rich diet increased the expression of the TP53 gene, which is involved in apoptosis and tumor suppression. Several studies have suggested ω3 and ω6 as biologically effective classes of lipids for the treatment of cancer and their potential influence on the regulation of several pathways and genes responsible for tumor suppressor action 84,104–107. Our data suggest that lncRNA_5415.4 may participate in cell proliferation regulation and be involved in programmed cell death under the influence of ω3 and ω6 fatty acids.
Additionally, we can highlight the lncRNA_20062.7, which interacts with the genes IFN-TAU (Interferon Tau), IFNAG (Interferon-gamma), IFNA5 (Interferon Alpha 5), and IFNW1 (Interferon Omega 1) and was downregulated in the C1 vs. C3 and C2 vs. C3 comparisons (Table 3). These genes were enriched by GO biological function terms related to cell activation involved in immune response (GO:0002263), leukocyte activation involved in immune response (GO:0002366), lymphocyte activation involved in immune response (GO:0002285), adaptive immune response (GO:0002250), B cell activation (GO:0042113) in C2 vs. C3 comparison (Table 9). These genes belong to the interferon superfamily, are cytokines and play a fundamental role in the immune response 108, regulate the production of inflammatory cytokines and control cell growth and proliferation 109. Furthermore, they may play a role in adipogenesis, lipid accumulation, and fatty acid metabolism in mammalian muscle tissue 110. In vitro studies with Huh-7 cells have shown that oleic acid and palmitic acid increase the expression of interferon-stimulated genes and NF-κβ-dependent pro-inflammatory genes 111. While high levels of ω3 PUFA block gene expression pathways related to interferon in mouse 112, which corroborates with our findings. C3 presented a profile with a higher oleic and palmitic concentration of acid and lower ω3 compared with other clusters (C1 and C2). In this sense, lncRNA_20062 can interact with interferons in response to the higher content of these fatty acids in meat.
Some lincRNAs (lncRNA_18394.1 and lncRNA_2526.3) were downregulated in C1 vs. C2 and C1 vs. C3 comparisons (Table 3) and were associated with the EIF4E (Eukaryotic Translation Initiation Factor 4E) and DDX1 (DEAD-Box Helicase 1) genes. These genes were enriched by GO biological function terms related to RNA splicing (GO:0008380) and cellular response to lipid (GO:0071396) for C1 vs. C2. Whereas for the C1 vs. C3 comparison, these genes were enriched by GO biological function terms related to negative regulation of macromolecule biosynthetic process (GO:0010558) and cytoplasmic stress granule (GO:0010494) (Table 8). The EIF4E (eukaryotic initiation factor 4E) gene encodes an RNA-binding protein that plays a crucial role in regulation of translation and protein synthesis in eukaryotic cells 113. EIF4E can regulate several metabolic pathways, including lipid metabolism. Studies in mice have shown that EIF4E is a key regulator of lipid homeostasis and energy metabolism adipose tissue, through the synthesis and oxidation of FAs 114. Furthermore, in bovine mammary epithelial cells, it was observed that EIF4E is an important regulator in the synthesis of milk fatty acids through the mTOR/eIF4E signaling pathway 115. DDX1 gene is a member of the DEAD box family of RNA helicases and involved in many of biological processes, DNA repair, microRNA processing, tRNA maturation and mRNA transport 116. Li et al117 observed that exposure to saturated FAs such as palmitic acid, decreases in insulin production in pancreatic beta cells, which may contribute to the development of insulin resistance and diabetes. Additionally, they found that the molecular mechanism underlying this reduction in insulin production has been attributed to the interaction of the DDX1 protein with the untranslated region of insulin mRNA, which inhibits of its translation. It is recognized that SFA contributes to the development of insulin resistance 118–122. In this study, the content of total SFA, including palmitic acid, myristic acid and stearic acid, MUFA, CLA and oleic acid were significantly lower in C1 compared to C2 and 3, which may be influenced by the downregulation of the lincRNAs lncRNA_18394.1 and lncRNA_2526.3 for a genetic profile with higher MUFA and SFA.
The lincRNAs, lncRNA_17681.1 and lncRNA_17194.2 were downregulated in C1 vs. C3 and C2 vs. C3 comparison, respectively, and were associated with the APOL3 (Apolipoprotein L3) and HOXC10 (Homeobox C10) genes (Tables 5 and 6). The APOL3, is a member of the apolipoprotein L protein family (APOL-I to VI) and associated with the transport/recycling of cholesterol and sphingolipids in skeletal muscle and other human tissues 123. In beef cattle this gene has been associated with IMF deposition and identified as a highly duplicated gene in the genome 124,125. The HOXC10 gene, a member of the HOX gene family, plays crucial roles in mammalian physiological processes such as limb regeneration126 and differentiation of lumbar motor neurons 127. HOXC10 is also associated with angiogenesis 128, fat metabolism129,130 and sexual regulation 131. Kang et al132 studied the transcriptome of fat-tailed sheep and reported the HOXC10 as a candidate gene for adipose deposition. In humans, evidence suggests that the HOXC10 may play an important role in the development of obesity, adverse fat distribution, and subsequent changes in whole-body metabolism and function 133. In this study, C3 showed significant differences in the total SFA content, including myristic, palmitic, stearic and oleic acid compared to the C1 and C2 fatty acid profile, while the MUFA and oleic acid contents were similar between C2 and C3, and differed significantly from C1 which interestingly had small values for MUFA, oleic content, SFAs. In this sense, lincRNAs (lncRNA_17681.1 and lncRNA_17194.2) associated with APOL3 and HOXC10 genes can regulate a genetic profile with higher SFA and MUFA content, presented in C3.
The DE lincRNA, lncRNA_17393.3, was upregulated in C1 vs. C2 and C2 vs. C3 comparisons (Table 3) and interacted with the CNOT2 (CCR4-NOT Transcription Complex Subunit 2) gene. In both comparisons, CNOT2 was enriched by GO biological function terms related to response to organic cyclic compound (GO:0014070), response to hormone (GO:0009725) and cellular response to lipid (GO:0071396) (Tables 7 and 9). The CNOT2 gene encodes the synthesis of the CCR4-NOT2 protein involved in the regulation of gene expression, acting in mRNA degradation, transcription, protein synthesis and cell cycle control 134,135. The CCR4-NOT2 protein has been associated with several cellular processes, immune response and lipid synthesis 136,137. Sohn et al. 138 investigated the role of the CCR4-NOT2 gene in adipocyte differentiation and lipogenesis in 3T3-L1 cells. The authors reported that overexpression of the CCR4-NOT2 gene promotes adipocyte differentiation and lipogenesis by upregulating transcription factors such as PPARγ and CEBPα. In addition, the presence of ω3 PUFA in cells promoted increased mRNA expression of transcription factors PPARγ and CEBPα that act in the adipogenesis process 139,140, which has been confirmed by the vast majority of in vivo and in vitro studies 141,142. In this study, C1 showed significant differences in total PUFA/SFA, PUFA, including ω3, ω6, linoleic and α-linoleic compared to the C2 fatty acid profile, and these differ significantly from C3 which interestingly had small values for the same fatty acids.
In all comparisons C1 vs. C2, C1 vs. C3, and C2 vs. C3, the lincRNAs (lncRNA_10184.1 lncRNA_10184.3; lncRNA_11659.1, lncRNA_11659.3, lncRNA_11659.14, lncRNA_11659.17, lncRNA_11659.21; lncRNA_20515.10, lncRNA_20515.12, lncRNA_20515.13; lncRNA_12128.6 lncRNA_12128.7; lncRNA_3024.5, lncRNA_3024.7) were DE and associated with the SMN2 (Survival Of Motor Neuron 2, Centromeric), RUVBL1 (RuvB Like ATPase 1), AUH (AU RNA Binding Methylglutaconyl-CoA Hydratase), TRIM27 (Tripartite Motif Containing 27), and SMAD9 (SMAD Family Member 9) genes, respectively (Table 4, 5, and 6). These genes were enriched by GO biological function terms related to RNA splicing, RNA localization, adaptive immune response, regulation of protein polymerization, response to organic cyclic compound, response to organic cyclic compound. Among these genes, only the AUH gene was associated with GO biological function terms related to lipid metabolism, such as cellular lipid metabolic process, FA metabolic process, and lipid oxidation. AUH is a gene that encodes an RNA-binding protein specific for AU and has intrinsic enoyl-CoA hydratase activity, an enzyme involved in the degradation of fatty acids (regardless of its degree of saturation) 143. Thus, AUH is essential in maintaining energy homeostasis and regulating metabolism. As the function of AUH in cattle has not been studied yet, it is worth investigating the mechanism by which the interaction between lincRNAs and AUH may contribute to the fatty acid profile investigation in beef future studies.
Overall, enrichment analyses revealed gene ontology (GO) terms related to immune response in the C2 vs. C3 comparison. These GO terms include cell activation involved in immune response (GO:0002263), adaptive immune response (GO:0002250), leukocyte activation involved in immune response (GO:0002366), lymphocyte activation involved in immune response (GO:0002285), and B cell activation (GO:0042113). Studies have shown that SFAs can promote inflammation in adipose tissue through various mechanisms. SFAs activate pattern recognition receptors (PRRs) and toll-like receptor 4 (TLR4), leading to the production of pro-inflammatory cytokines, including tumor necrosis factor-alpha (TNF-α) and interleukin-6 (IL6) 59,144,145. Moreover, SFAs induce endoplasmic reticulum stress and activate inflammatory signaling pathways, such as nuclear factor-kappa B (NF-κB), further exacerbating adipose tissue inflammation 146. These events triggered to accelerate inflammation in adipose tissue (SUGANAMI et al., 2007). These studies support that the composition of beef fatty acids, particularly SFAs, plays a crucial role in modulating inflammatory responses and immune activation in adipose tissue. In this study, the C2 and C3 profiles, which exhibit a high content of SFA compared to the C1, may be contributing to the enrichment of immune system-associated gene ontology terms.
The present study has identified several differentially expressed genic and intergenic lncRNA. However, further in-depth investigations are required to better understand the molecular mechanisms through which these lncRNAs regulate beef fatty acid metabolism, to more accurately discern their impact on Nellore cattle beef quality traits.