Transcriptional profiling of bovine milk using RNA sequencing

Abstract

BackgroundCow milk is a complex bioactive fluid consumed by humans beyond infancy. Even though the chemical and physical properties of cow milk are well characterized, very limited research has been done on characterizing the milk transcriptome. This study performs a comprehensive expression profiling of genes expressed in milk somatic cells of transition (day 15), peak (day 90) and late (day 250) lactation Holstein cows by RNA sequencing. Milk samples were collected from Holstein cows at 15, 90 and 250 days of lactation, and RNA was extracted from the pelleted milk cells. Gene expression analysis was conducted by Illumina RNA sequencing. Sequence reads were assembled and analyzed in CLC Genomics Workbench. Gene Ontology (GO) and pathway analysis were performed using the Blast2GO program and GeneGo application of MetaCore program.ResultsA total of 16,892 genes were expressed in transition lactation, 19,094 genes were expressed in peak lactation and 18,070 genes were expressed in late lactation. Regardless of the lactation stage approximately 9,000 genes showed ubiquitous expression. Genes encoding caseins, whey proteins and enzymes in lactose synthesis pathway showed higher expression in early lactation. The majority of genes in the fat metabolism pathway had high expression in transition and peak lactation milk. Most of the genes encoding for endogenous proteases and enzymes in ubiquitin-proteasome pathway showed higher expression along the course of lactation.ConclusionsThis is the first study to describe the comprehensive bovine milk transcriptome in Holstein cows. The results revealed that 69% of NCBI Btau 4.0 annotated genes are expressed in bovine milk somatic cells. Most of the genes were ubiquitously expressed in all three stages of lactation. However, a fraction of the milk transcriptome has genes devoted to specific functions unique to the lactation stage. This indicates the ability of milk somatic cells to adapt to different molecular functions according to the biological need of the animal. This study provides a valuable insight into the biology of lactation in the cow, as well as many avenues for future research on the bovine lactome.

Milk Protein Synthesis in the Lactating Mammary Gland: Insights from Transcriptomics Analyses

“…Despite those limitations, there is a relatively good agreement between the abundance of mRNA and microarray signal (i.e., number of cDNA with dyes bound to the oligos); thus, despite not being absolute, the comparison between microarray signals can be used to provide an initial idea of relative abundance between mRNA species. The high similarity in relative transcript abundance among caseins and between casein genes and alpha-lactalbumin in mammary gland of dairy cows is consistent with transcriptomics analysis of bovine milk somatic cells using the more accurate RNA sequencing technology [94]. In the figure are reported the relative percentage of the signal of the genes of interest compared to CSN1S1 or Csn1s1.…”

Global differential gene expression in the pituitary gland and the ovaries of pre- and postpubertal Brahman heifers

“…All the samples analyzed passed all the quality control parameters having the same length (100 bp); 100% coverage in all bases; 25% of A, T, G, and C nucleotide contributions; 50% GC on base content; and less than 0.1% over-represented sequences, indicating good quality of sequencing outputs. Only transcripts with RPKM ≥ 0.2 in at least 1 tissue were considered expressed genes; otherwise, they were discarded from further analyses (Wickramasinghe et al, 2012;Cánovas et al, 2014a). Uniform RPKM values across tissues may serve to identify ubiquitous genes or tissue-specific genes, but these analyses should be performed across all studied tissues and is beyond the current study, which is focused on pituitary gland and ovarian expression.…”

Biosynthesis of milk fat, protein, and lactose: roles of transcriptional and posttranscriptional regulation

“…The use of large transcriptomic analysis (i.e., microarray or RNA sequencing) by which to study the adaptation of mammary gland to lactation and/or change in milk production under specific conditions has been carried out in mouse (4,54,122,123,143,189,191,217,236,256), rat (3,47,187), bovine (31,36,56,75,96,144,183,209,218,233,239), sheep (209), goat (71,163,164), human (121,139,147), pig (204), kangaroo (120), and seal (144). It is beyond the scope of the current review to present a thorough discussion of the results from those studies.…”