Bioinformatics Analysis Of Allele-Specific Expression Regulation Of Porcine Alveolar Macrophages

The porcine alveolar macrophages play an important role in resisting pathogen invasion and immune response as important cellular immune cells.Some studies have shown that the specific expression of alleles is closely related to the occurrence of certain susceptible diseases,but the research progress abou the allele-specific expression and disease,immune is not much,What's more,the regulation mechanism of allele-specific expression is not very thorough.Therefore,in this study,we will focus on the allele-specific expression of porcine alveolar macrophage cell line 3D4 / 21 before and after Poly(I: C)stimulation and the possible transcriptional regulatory factors such as transcription factor binding,histone modification and haplotype chromosome interaction differences and other aspects for the analysis,the main results are as follows:Based on the RNA-seq data,we identified the preferentially expressed alleles of the PAM cell line 3D4 / 21 under Poly(I: C)stimulation and non-stimulation respectively.After a comprehensive comparison,it was found that some alleles associated with pathogen infection and immune response showed different expression preferences after stimulation and the overall expression of alleles was significantly higher than that in the case of non-stimulation.We speculated that these genes contains mutations that are resistant to pathogen invasion and can be used as candidate disease resistance genes for further validation.In order to further understand the mechanism of unbalanced expression of alleles,we correlate with ChIP-seq data.The results showed that the haplotype preference of transcription factor binding and histone modification is highly correlated with the preference of allele expression.And we can see that the preference of haplotype chromatin interaction is consistent with the preference of allele expression by observed CTCF and RNAPII-mediated chromatin interaction information at the haplotype level.Our results provide some useful revelation for exploring the ability to improve the disease resistance and immunity of pigs,which also have some reference significance for understanding the relationship between the allele-specific expression and the relevant regulatory factors.