RESUMEN
The aim of this study was to identify novel lncRNA differentially expressed (DE) between divergent animals for beef tenderness and marbling traits in Nellore cattle. Longissimus thoracis muscle samples from the 20 most extreme bulls (of 80 bulls set) for tenderness, tender (n = 10) and tough (n = 10) groups, and marbling trait, high (n = 10) and low (n = 10) groups were used to perform transcriptomic analysis using RNA-Sequencing. For tenderness, 29 lncRNA were DE (p-value ≤ 0.01) in tough beef animals in relation to tender beef animals. We observed that genic lncRNAs, for example, lncRNA_595.1, were overlapping exonic part of the PICK gene, while lncRNA_3097.2 and lncRNA_3129.5 overlapped intronic part of the genes GADL1 and PSMD6. The lncRNA associated with PICK1, GADL1, and PMD6 genes were enriched in the pathways associated with the ionotropic glutamate receptor, gamma-aminobutyric acid synthesis, and the ubiquitin-proteasome pathway. For marbling, 50 lncRNA were DE (p-value ≤ 0.01) in high marbling group compared with low marbling animals. The genic lncRNAs, such as lncRNA_3191.1, were overlapped exonic part of the ITGAL gene, and the lncRNA_512.1, lncRNA_3721.1, and lncRNA_41.4 overlapped intronic parts of the KRAS and MASP1 genes. The KRAS and ITGAL genes were enriched in pathways associated with integrin signaling, which is involved in intracellular signals in response to the extracellular matrix, including cell form, mobility, and mediates progression through the cell cycle. In addition, the lincRNAs identified to marbling trait were associated with several genes related to calcium binding, muscle hypertrophy, skeletal muscle, lipase, and oxidative stress response pathways that seem to play a role important in the physiological processes related to meat quality. These findings bring new insights to better understand the biology mechanisms involved in the gene regulation of these traits, which will be valuable for a further investigation of the interactions between lncRNA and mRNAs, and of how these interactions may affect meat quality traits.
RESUMEN
OBJECTIVE: Recent studies have implied that gene expression has high tissue-specificity, and therefore it is essential to investigate gene expression in a variety of tissues when performing the transcriptomic analysis. In addition, the gradual increase of long non-coding RNA (lncRNA) annotation database has increased the importance and proportion of mapped reads accordingly. METHODS: We employed simple statistical models to detect the sexually biased/dimorphic genes and their conjugate lncRNAs in 40 RNA-seq samples across two factors: sex and tissue. We employed two quantification pipeline: mRNA annotation only and mRNA+lncRNA annotation. RESULTS: As a result, the tissue-specific sexually dimorphic genes are affected by the addition of lncRNA annotation at a non-negligible level. In addition, many lncRNAs are expressed in a more tissue-specific fashion and with greater variation between tissues compared to protein-coding genes. Due to the genic region lncRNAs, the differentially expressed gene list changes, which results in certain sexually biased genes to become ambiguous across the tissues. CONCLUSION: In a past study, it has been reported that tissue-specific patterns can be seen throughout the differentially expressed genes between sexes in cattle. Using the same dataset, this study used a more recent reference, and the addition of conjugate lncRNA information, which revealed alterations of differentially expressed gene lists that result in an apparent distinction in the downstream analysis and interpretation. We firmly believe such misquantification of genic lncRNAs can be vital in both future and past studies.