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.

A Mini-Atlas of Gene Expression for the Domestic Goat (Capra hircus)

“…Throughout the GI tract, there was a strong immune signature, similar to that observed in neonatal and adult sheep (Bush et al, 2019), which was greatest in clusters 10 and 19 ( Table 3 ) where expression was high in the ileum and Peyer’s patches, thymus, and spleen. Cluster 10 had a more general immune related profile with higher expression in the spleen and significant GO terms associated with cytokine receptor activity (p = 1.3x10 -8 ) and T-cell receptor complex (p = 0.00895).…”

“…Even at this early stage of development, the typical epithelial signature of the rumen (Xiang et al, 2016a; Xiang et al, 2016b) was observed. Genes coexpressed in the rumen (clusters 7 and 13 – Table 3 ) were typical of a developing rumen epithelial signature (Bush et al, 2019) and were associated with GO terms for epidermis development (p = 0.00016), keratinocyte differentiation (p = 1.5x10 -14 ), and skin morphogenesis (p = 8.2x10 -6 ). Large colon (cluster 12) included several genes associated with GO terms for microvillus organization (p = 1x10 6 ) and microvillus (p = 6.3x10 6 ) including MYO7B which is found in the brush border cells of epithelial microvilli in the large intestine.…”

A Gene Expression Atlas of the Domestic Water Buffalo (Bubalus bubalis)

“…Although ruminant species have anatomically equivalent gastrointestinal tracts, we considered that GI tract gene expression may differ due to differences in diet, metabolism, or habitat. To test this hypothesis, we compared gene expression in the GI tract between buffalo and sheep, using gene expression data from the sheep atlas (Clark et al, 2017), which have also been the focus of a separate analysis (Bush et al, 2018). Equivalent datasets from both species were clustered using Graphia Professional with genes expressed in the forestomach and small and large intestines compared between species.…”

“…The new transcript models created (732 protein-coding transcripts, representing 631 genes, plus 6,756 lncRNAs) were then integrated with the “second pass” Kallisto index to create a “third pass” index, with expression quantification repeated as above. Transcript models were retained only if they could be robustly annotated, using the criteria described in Clark et al (2017) for protein-coding genes, and the criteria described in Bush et al (2018) for lncRNAs.…”

Elimination of Reference Mapping Bias Reveals Robust Immune Related Allele-Specific Expression in Crossbred Sheep

“…We chose to focus this analysis on immune-related tissues in part because of the depth of available sequence in those tissues, and in part because they contain abundant immune cell populations. The diversity of cell populations is reflected in the transcriptional complexity of immune tissues and cell types in the sheep gene expression atlas data set (Clark et al, 2017; Bush et al, 2019). As such, this subset of tissues gave us a transcriptionally rich data set in which to measure ASE.…”