Comprehensive transcriptional profiling of the gastrointestinal tract of ruminants from birth to adulthood reveals strong developmental stage specific gene expression

Stephen J. Bush, Mary E.B. McCulloch, Charity Muriuki, Mazdak Salavati, Gemma M. Davis, Iseabail L. Farquhar, Zofia M. Lisowski, Alan L. Archibald, David A. Hume, Emily L. Clark*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)

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 tissueand 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.

Original languageEnglish
Pages (from-to)359-373
Number of pages15
JournalG3: Genes, Genomes, Genetics
Volume9
Issue number2
DOIs
Publication statusPrint publication - 1 Feb 2019
Externally publishedYes

Keywords

  • Development
  • Gastrointestinal
  • Gene expression
  • Goat
  • Immunity
  • Macrophage
  • RNA-Seq
  • Ruminant
  • Sheep
  • Tract
  • Transcription

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