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 (http://bovineatlas.arl.arizona.edu/). 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.

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