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Mammary gland transcriptome profiling reveals an abundance of transcripts for cell maintenance and protein turnover.

L. Beckett

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06-22-2020

Abstract:

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Mammary gland transcriptome profiling reveals an abundance of transcripts for cell maintenance and protein turnover.
L. Beckett*, J. Thimmapuram, S. Xie, T. Casey, S. S. Donkin. Purdue University West Lafayette, IN.

Identifying gene networks that support milk synthesis is critical to understanding mechanisms that control efficient milk production and response to nutrient supply. The objective of this study was to analyze the coding mammary transcriptome in early lactation cows across magnitudes of normalized RNA-seq read counts as a relative indicator of their importance in supporting milk synthesis. Forty-five mL of milk was collected from multiparous cows (n = 6; DIM 68 � 3 d) following 2 treatment periods of a post-ruminal lysine infusion of 0 and 63 g/d for 10 d, which was part of a larger study. Total RNA was isolated (n = 12 samples), libraries prepared, and paired end reads were sequenced on an Illumina HiSeq2500 platform. Of the total reads (236M � 39M), 79% mapped to the ENSEMBL bovine genome. EBseq analysis found no significant effect of lysine infusion on the transcriptome, therefore, reads were averaged across both treatments. Gene transcripts (12,730) with a normalized read count mean ≥ 5 were divided into 9 categories by magnitude of read counts (Table 1) for functional annotation analysis. The 13 most abundant transcripts were casein and whey proteins, regulators of milk fat synthesis and secretion, a ubiquitinating protein, and a tRNA transporter and together accounted for 67% of the 23M coding reads. Ingenuity pathway analysis revealed mTOR, JAK/STAT, PPARα, and ubiquitin proteasome pathways were enriched with reads ≥ 200. Genes with < 200 reads corresponded to tissue homeostasis and immune response. Some of the most abundant genes corresponded to maintenance of translation, protein turnover, and amino acid recycling suggesting their importance in supporting mammary function and milk synthesis.Table 1. Magnitude of read count categories for functional annotation analysis

Magnitude of normalized read countsNo. of Genes% ReadsOntological category
≥50k1367Milk protein
<50k to ≥5k1476.9Translation
<5k to ≥1k8136.6Glycolysis
<1k to ≥5001,2253.7Proteasome
<500 to ≥2002,8504.0Ubiquitin
<200 to ≥1002,3141.5Mitochondria
<100 to ≥501,8580.6DNA repair
<50 to ≥102,7610.3Immune response
<10 to ≥57490.023Complement cascades
<53,8039.4
Total16,533100

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