Potential Involvement of DNA Methylation of First Intron in Transcriptional Regulation During Bovine Subclinical Mastitis Caused by Staphylococcus Aureus

Citation

Wang, M., M. Laterrière, P.-L. Dudemaine, N. Bissonnette, D. Gagné, and E. M. Ibeagha-Awemu. 2022. PSVIII-B-15 Potential Involvement of DNA Methylation of First Intron in Transcriptional Regulation During Bovine Subclinical Mastitis Caused by Staphylococcus Aureus. Journal of Animal Science 100(Supplement_3):310-311. doi: 10.1093/jas/skac247.565 %J Journal of Animal Science

Plain language summary

: This study aimed to investigate the possible influence of DNA methylation (a biological process by which methyl groups are added to the DNA molecule) of first introns (nucleotide sequence between exon 1 and exon 2 which is not expressed or does not form part of the RNA product) (DNA-MeFI) on transcriptional activities (the process by which a cell regulates the copying of a DNA molecule to form an RNA molecule (transcription)) during subclinical mastitis caused by Staphylococcus aureus (SA). This study profiled the methylome (a set of DNA methylation modifications in an organism's genome or in a particular cell) and transcriptome (all the messenger RNA molecules expressed from the genes of an individual or organisms in response to a stimulus) of milk somatic cells from cows (n=15) with SA subclinical mastitis (SACs) and healthy cows (HCs) (n=13), followed by bioinformatics processing with standard tools. The DNA-MeFI was calculated for each of 19411 genes found as expressed in the samples, by averaging the methylation levels of all CpG sites in the first intron. At genome-wide, the DNA-MeFIs was inversely correlated with gene expression (GE). Similarly, the difference in the DNA-MeFI and GE between SACs and HCs was also inversely correlated. Then 644 genes with >10% difference in DNA-MeFI and two fold change in GE were identified and referred to as differentially methylated and expressed genes (DMEgenes). The 644 DME-genes were significantly enriched in 5 gene ontology (GO) terms (GO terms describe the molecular actions of gene products, the biological processes in which those actions occur and the cellular locations where they are present) and 11 KEGG pathways (networks of gene products with specific functions) with diseases and immune related functions, including Staphylococcus aureus infection and Natural killer cell mediated cytotoxicity pathways, etc. Furthermore, the DNA-MeFI of 264 DME-genes were found to correlate significantly with their GE, including 225 DME-genes(85.23%) with inverse correlations. 39 DME-genes with positive correlations were significantly enriched in 21 GO terms mainly related to metabolic processes. In conclusion, the DNA-MeFI possibly participate in the regulation of gene expression during bovine subclinical mastitis caused by SA.

Abstract

DNA methylation involvement in the regulation of mammary gland inflammatory defense against pathogens, including Staphylococcus aureus(SA) has been documented. However, the mechanisms are not clear. The possible influence of DNA methylation of first introns (DNA-MeFI) on transcriptional activities during subclinical mastitis was studied by profiling the methylome (whole genome methylation sequencing) and transcriptome (RNA-sequencing) of milk somatic cells from cows(n=15) with SA subclinical mastitis (SACs) and healthy cows (HCs)(n=13), followed by bioinformatics processing with standard tools. The DNA-MeFI was calculated, for each of 19411 genes found as expressed in the samples, by averaging the methylation levels of all CpG sites in the first intron. At genome-wide, the DNA-MeFIs was inversely correlated with gene expression (GE) (Pearson’s r=-0.173, p=1.60×10-122)(Figure 1-A). Similarly, the difference in the DNA-MeFI and GE between SACs and HCs was also inversely correlated (Pearson’s r=-0.149, p=4.25×10-97)(Figure 1-B). Application of machine learning by Gaussian Mixed model (GMM) using scikit-learn in python to the changes of DNA-MeFI and GE between SACs and HCs revealed 2866 outliers (GMM’s p< 0.005) that showed significant changes in the DNA-MeFI and/or GE. 644 genes with >10% difference in DNA-MeFI and |log2FC| >1 in GE were selected and referred to as differentially methylated and expressed genes (DME-genes). 644 DME-genes were significantly enriched in 5 GO terms and 11 KEGG pathways related to diseases and immune functions, including Staphylococcus aureus infection and Natural killer cell mediated cytotoxicity (Table 1). Furthermore, 74.84% DME-genes showed inverse changes in DNA-MeFI and GE. Besides, the DNA-MeFI of 264 DME-genes were found to correlate significantly with their GE (|rho| >0.3, FDR<0.05), including 225 DME-genes(85.23%) with inverse correlations(rho< -0.3, FDR< 0.05). 39 DME-genes with positive correlations were significantly enriched in 21 GO terms mainly related to metabolic processes. In conclusion, the DNA-MeFI possibly participate in the regulation of gene expression during bovine subclinical mastitis caused by SA.