Figure 1.
Venn diagrams of miRNA target sites at the 3′-UTRs of SLA-1, SLA-3 and SLA-6.
Predictions were performed by TargetScan, PACMIT and TargetSpy algorithms.
Table 1.
miRNA-binding sites and poly-miRTSs (created and disrupted sites predicted by TargetScan, PACMIT and TargetSpy) in SLA-1, SLA-3 and SLA-6 porcine genes.
Figure 2.
Influence of sequence variants on predicted miRNA target sites at the 3′-UTRs of SLA-3.
Known alleles (17 sequences) were retrieved from NCBI database. TargetScan (blue), PACMIT (green), TargetSpy (brown). The miRNAs targeting the VEGA reference are indicated in text. The complete list of miRNAs targeting the altered target sites in SLA-3 alleles is reported in Table S2.
Table 2.
Mapping statistics (number of reads) of 144 M RNA-Seq reads obtained from different pig tissues.
Figure 3.
Co-expression patterns of four poly-miRTSs and their cognate miRNAs.
RNA-Seq and Small RNA-Seq reads were obtained from abdominal fat (AF), liver (LI) and longissimus dorsi muscle (LD) of two individual pigs (pig 2268 and pig 2270). Left y-axis: ratios of the number of reads of reference allele vs. variant allele at poly-miRTSs positions; right y-axis: expression levels of targeting miRNAs. Numbers in parenthesis indicate the position of the poly-miRTSs in the 3′-UTR. The asterisks indicate significant differences between tissues (p-values <0.05).
Figure 4.
Allele-specific expression at two poly-miRTSs in SLA-DQA.
RNA-Seq reads were obtained from alveolar macrophages (A) and whole blood (B) libraries. The asterisk indicates a significant difference between reads bearing the reference and the variant alleles assessed by a binomial test, p-value <0.001.