RNA-seq analysis of mammary tissue reveals persistent changes in gene expression profiles dependent upon the level of folic acid intake in C56BL/6 mice.

Purpose: To identify, using RNA-sequencing, differentially expressed genes in the mammary gland of mice supplemented with FA. We aimed to ascertain whether gene expression is persistently altered after increased FA supplementation, whether such alterations are related to genes implicated in epigenetic regulation and disease risk. Methods: Mammary gland mRNA profiles of mice 4 weeks after folic acid supplementation (5mg/kg vs 1mg/kg) during adulthood were generated by deep sequencing using RNA sequencing. The sequence reads that passed quality filters were aligned to the mouse genome using TopHat and analyzed at the gene level using DESeq2. qRT–PCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow, we mapped reads to the mouse genome (build mm10) and identified 222 genes differentially expressed between the two group (adjsuted p value <0.05). 191 of these were upregulated and 31 were downregulated. Geneset enrichment analysis identified several enriched pathways, including epithelial mesenchymal transition and myogenesis. Conclusions: Our study provides novel insights into the persistent effects of FA intake on the C57BL/6 mammary transcriptome and identifies putative gene targets and molecular pathways that help to understand how increasing FA intake may modulate the long term expression of gene networks and disease pathways. C57BL/6 Mammary gland RNA transcriptomes 4 weeks after a follic acid supplemntation (5mg/kg or 1mg/kg).