Transcriptional modulation by abundant milk protein genes in the bovine mammary gland

Objectives: A few proteins are known to be highly abundant in milk. The transcription of these milk protein genes could be expected to dilute the pool of non-abundant transcripts during lactation. Therefore, we developed a method to adjust for this dilution and investigated the degree to which non-abundant transcripts are affected during lactation. Methods: Raw count data for quantitative mRNA expression from one replicate each of bovine mammary gland tissue collected during pre-puberty and lactation was extracted from the bovine gene atlas ( Technical replicates were generated using a Poisson distribution based on the expression values in the biological replicate to achieve a set of three expression profiles for each developmental stage. A threshold for “high abundance” transcripts was empirically determined from the data and an adjustment factor was calculated to adjust the gene expression levels. Differential expression between the pre-puberty and lactation sets was completed using both the adjusted and non-adjusted data sets (DESeq, R). Results: During lactation, high abundance genes exhibited expression counts orders of magnitude larger than the low abundance genes. The six high abundance genes included casein-κ, casein-α-s1, β-lactoglobulin, α-lactalbumin, GLYCAM1, and steroyl-coA desaturase. Cumulatively, these genes were responsible for 68.6% of total expression in the mammary gland during lactation while equating to less than 1% of the total number of genes expressed (~16,000). No high abundance transcripts were observed in the data set derived from the pre-pubescent gland. Using the original data set, there were 1,910 genes up-regulated and 3,231 genes down-regulated during lactation relative to pre-puberty. After adjustment to account for the dilution by high-abundance transcripts, there were 2,987 genes up-regulated and 2,046 genes downregulated during lactation. Conclusions: We have developed a method to quantify the effect of high-abundance milk proteins on the dilution of the mammary transcriptome during lactation. During lactation, the transcription of some genes appears to be down-regulated, when they are not. Meanwhile, the transcription of another subset appears to be unchanged, when these genes are actually up-regulated. While the dilution of transcripts could be expected to directly regulate protein levels, quantification of this dilution is nevertheless vital to dissect the underlying mechanisms of genetic transcription during lactation.

Download PDF