| Summary: | Paratuberculosis is a major endemic disease caused by <i>Mycobacterium avium subspecies paratuberculosis</i> (MAP) infection and leads to huge economic loss in the dairy sector worldwide. Alternative splicing (AS) events, playing indispensable regulatory roles in many protein functions and biological pathways, are shown to be associated with complex traits and diseases. In this study, by integrating the RNA sequencing (RNA-seq) data of 24 samples from three tissues (peripheral blood, jejunum and salivary gland) of Holstein cows, we obtained 2,706,541,696 uniquely mapped reads in total that represented 12,870 expressed genes, and detected 4285 differentially expressed genes (DEGs) between MAP-infected and healthy cows (<i>p</i> < 0.05). Of them, 92 differentially expressed splicing factors (DESFs) were included. Further, 119, 150 and 68 differential alternative splicing (DAS) events between MAP-infected and healthy cows were identified in peripheral blood, jejunum and salivary glands, respectively. Of note, six DAS events were highly and significantly correlated with the DESFs (<i>R</i><sup>2</sup> > 0.9; <i>p</i> < 0.01), and their corresponding genes (<i>COPI coat complex subunit gamma 2</i><i>gene</i> (<i>COPG2</i>), <i>kinesin family member 2C gene</i> (<i>KIF2C</i>), <i>exocyst complex component 7</i> (<i>EXOC7</i>), <i>Rab9 effector protein with kelch motifs gene</i> (<i>RABEPK</i>), <i>deoxyribonuclease 1 gene</i> (<i>DNASE1</i>) and <i>early endosome antigen 1</i><i>gene</i> (<i>EEA1</i>)) were significantly enriched in immune response such as vesicle-mediated transport, regulation of acute inflammatory response and tuberculosis through gene ontology (GO) and KEGG analysis. KS test showed that the DAS events in the <i>EXOC7</i> and <i>KIF2C</i> genes indeed displayed differences between MAP-infected cows and healthy cows. The DAS in <i>EXOC7</i> might produce a new protein sequence with lack of 23 amino acids, and the DAS in <i>KIF2C</i> induced a stop codon of premature occurrence and resulted in a lack of functional domain. In summary, this study identified the DAS events and corresponding genes related to MAP-infection base on the RNA-seq data from multiple tissues of Holstein cows, providing novel insights into the regulatory mechanisms underpinning paratuberculosis in dairy cattle.
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