Abstract
Long non-coding RNA (lncRNA) can regulate several aspects of gene expression, being associated with complex phenotypes in humans and livestock species. In taurine beef cattle, recent evidence points to the involvement of lncRNA in feed efficiency (FE), a proxy for increased productivity and sustainability. Here, we hypothesized specific regulatory roles of lncRNA in FE of indicine cattle. Using RNA-Seq data from the liver, muscle, hypothalamus, pituitary gland and adrenal gland from Nellore bulls with divergent FE, we submitted new transcripts to a series of filters to confidently predict lncRNA. Then, we identified lncRNA that were differentially expressed (DE) and/or key regulators of FE. Finally, we explored lncRNA genomic location and interactions with miRNA and mRNA to infer potential function. We were able to identify 126 relevant lncRNA for FE in Bos indicus, some with high homology to previously identified lncRNA in Bos taurus and some possible specific regulators of FE in indicine cattle. Moreover, lncRNA identified here were linked to previously described mechanisms related to FE in hypothalamus-pituitary-adrenal axis and are expected to help elucidate this complex phenotype. This study contributes to expanding the catalogue of lncRNA, particularly in indicine cattle, and identifies candidates for further studies in animal selection and management.
Highlights
The flow of information from DNA to protein synthesis comprises specific steps in which gene expression can be controlled
3665 transcripts were excluded because they showed high similarity with known proteins from the UniProt database (E-value < 10−6 ) and seven were excluded because they had coding potential according to CPC2 analysis
We were able to identify new Long non-coding RNA (lncRNA) in five tissues of Nellore cattle, which are predicted to be involved in the regulation of feed efficiency (FE) of indicine cattle
Summary
The flow of information from DNA to protein synthesis comprises specific steps in which gene expression can be controlled. LncRNA have low or no potential for protein-coding and are lowly conserved among species [3]. They present no specific sequence pattern, making categorization of lncRNA and prediction of their function challenging [2]. LncRNA are considered evolutionarily less conserved than protein-coding genes, which does not indicate a lack of function, but rather a possible fast adaptation mechanism [3]. These molecules can fold into complex structures, mediating target recognition by base pairing and by tertiary structural interactions [3]. In contrast to protein-coding genes, lncRNA are more tissue-specific, are expressed at lower levels and often contain multiple exons, polyA tail, 5’ cap and CpG islands in
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