Comprehensive Transcriptional Profiling of the Gastrointestinal Tract of Ruminants from Birth to Adulthood Reveals Strong Developmental Stage Specific Gene Expression

Abstract

One of the most significant physiological challenges to neonatal and juvenile ruminants is the development and establishment of the rumen. Using a subset of RNA-Seq data from our high-resolution atlas of gene expression in sheep (Ovis aries) we have provided the first comprehensive characterization of transcription of the entire gastrointestinal (GI) tract during the transition from pre-ruminant to ruminant. The dataset comprises 164 tissue samples from sheep at four different time points (birth, one week, 8 weeks and adult). Using network cluster analysis we illustrate how the complexity of the GI tract is reflected in tissue- and developmental stage-specific differences in gene expression. The most significant transcriptional differences between neonatal and adult sheep were observed in the rumen complex. Comparative analysis of gene expression in three GI tract tissues from age-matched sheep and goats revealed species-specific differences in genes involved in immunity and metabolism. This study improves our understanding of the transcriptomic mechanisms involved in the transition from pre-ruminant to ruminant by identifying key genes involved in immunity, microbe recognition and metabolism. The results form a basis for future studies linking gene expression with microbial colonization of the developing GI tract and provide a foundation to improve ruminant efficiency and productivity through identifying potential targets for novel therapeutics and gene editing.

Keywords: RNA-Seq; development; gastrointestinal tract; gene expression; goat; immunity; macrophage; ruminant; sheep; transcription.

Figure 1

Diagrammatic representation of the morphological changes that occur in the gastrointestinal tract of a sheep during the transition from (A) pre-ruminant to (B) ruminant. The 14 regions sampled for this study are numbered (12 samples from each of the lambs and 2 from the adult animals only – esophagus and rectum). The esophageal groove is indicated with dotted lines.

Figure 2

Gene-to-gene network graph of sheep GI tract tissues alongside alveolar macrophages, esophageal tissue and liver with the nodes collapsed by class to illustrate the relative size of each cluster. The top 20 largest clusters are annotated by function. Created using Graphia Professional with parameters Pearson’s R = 0.85, MCLi = 2.2, Minimum Component Size = 2, Minimum Cluster Size = 2.

Figure 3

Comparative analysis of the expression of five C-type lectin genes, measured as transcripts per million (TPM), across three GI tract tissues (large colon, ileum and rumen) and alveolar macrophages in sheep and goats.

Figure 4

Sample-to-sample network graph of sheep GI tract samples colored according to developmental stage. Created using Graphia Professional with parameters Pearson’s R = 0.85, MCLi = 2.2, Minimum Component Size = 2, Minimum Cluster Size = 2.

Figure 5

Principal Component Analysis of macrophage associated signatures in the sheep GI tract illustrating separation by tissue (A & B) and developmental stage (C & D) in three and four components, respectively. The mean of each group was used as the center of the circle colored-by-group with a confidence interval of 0.95 as the ellipse size.

Figure 6

The top 25 differentially expressed genes up-regulated and top 25 down-regulated genes between goat and sheep in the rumen, ileum and colon of age-matched one-week old animals.