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In addition, it has been shown that genes interact with each other and can jointly affect many biological processes, and alternative splicing (AS) regulates transcription processes in almost every aspect of eukaryotic biology, which enables cells to generate different protein isoforms from a single gene. Recently, RNA-Sequencing (RNA-Seq) based transcriptomics has been gradually applied to decipher gene expression patterns in backfat, muscle, and liver tissues related to FA formation in different cattle species and breeds. Generally, rumen, liver, muscle, and backfat are the major tissues associated with hydrolysis, hydrogenation, synthesis, metabolism, and modification of FA in cattle, which jointly determine the proportion of different FAs in fat and muscle tissues. However, most ruminant studies to date have only focused on single tissue/organ, which lacks a holistic view to identify potential interactive mechanisms across different tissues. In cattle, FA synthesis and metabolism in cattle are very complex and involve in many biological processes in multiple tissues. Development of strategies to increase healthy FAs in beef, however, remains challenging due to large variations among animals in FA formation and a lack of comprehensive understanding of modes of action regulating FA synthesis at the molecular level.
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Based on the health risks associated with consuming certain types of FA by humans, some beef FAs can be defined as healthy or unhealthy FAs. This study provides an applicable pipeline for AS events based on comprehensive RNA-Seq analysis and improves our understanding of the regulatory mechanism of FAs in beef cattle.īeef is an important fatty acid (FA) source in human diets and plays a critical role in human nutrition and health. Eight key genes were identified from the integrated analysis of DE, co-expressed, and AS genes between animals with high and low healthy/unhealthy FA ratios. In addition, the healthy/unhealthy FA ratio related AS events, differential expressed (DE) genes, co-expressed genes, and their functions in four tissues were analysed.
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The highly conserved and absent AS events were detected in rumen tissue, which may contribute to its functional differences compared with the other three tissues. Using this large dataset, the alternative splicing (AS) events, one of the transcriptional regulatory mechanisms in four tissues were identified. In this study, using ~1.2 Tb high-quality RNA-Seq-based transcriptomic data of 188 samples from four key metabolic tissues (rumen, liver, muscle, and backfat) together with the contents of 49 FAs in backfat, the molecular regulatory mechanisms of these tissues contributing to FA formation in cattle were explored. However, the regulatory mechanisms ultimately resulting in FA profiles vary among animals and remain largely unknown. Increasing the healthy/unhealthy fatty acid (FA) ratio in meat is one of the urgent tasks required to address consumer concerns.
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