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Genes 2018, 9(3), 142; https://doi.org/10.3390/genes9030142

Integration of lncRNA and mRNA Transcriptome Analyses Reveals Genes and Pathways Potentially Involved in Calf Intestinal Growth and Development during the Early Weeks of Life

1
Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC J1M 0C8, Canada
2
Department of Animal Science, McGill University, Ste-Anne-De Bellevue, QC H9X 3V9, Canada
3
Département des Sciences Animales, Université Laval, Québec, QC G1V 0A9, Canada
*
Author to whom correspondence should be addressed.
Received: 12 November 2017 / Revised: 15 February 2018 / Accepted: 21 February 2018 / Published: 5 March 2018
(This article belongs to the Section Animal Genetics and Genomics)
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Abstract

A better understanding of the factors that regulate growth and immune response of the gastrointestinal tract (GIT) of calves will promote informed management practices in calf rearing. This study aimed to explore genomics (messenger RNA (mRNA)) and epigenomics (long non-coding RNA (lncRNA)) mechanisms regulating the development of the rumen and ileum in calves. Thirty-two calves (≈5-days-old) were reared for 96 days following standard procedures. Sixteen calves were humanely euthanized on experiment day 33 (D33) (pre-weaning) and another 16 on D96 (post-weaning) for collection of ileum and rumen tissues. RNA from tissues was subjected to next generation sequencing and 3310 and 4217 mRNAs were differentially expressed (DE) between D33 and D96 in ileum and rumen tissues, respectively. Gene ontology and pathways enrichment of DE genes confirmed their roles in developmental processes, immunity and lipid metabolism. A total of 1568 (63 known and 1505 novel) and 4243 (88 known and 4155 novel) lncRNAs were detected in ileum and rumen tissues, respectively. Cis target gene analysis identified BMPR1A, an important gene for a GIT disease (juvenile polyposis syndrome) in humans, as a candidate cis target gene for lncRNAs in both tissues. LncRNA cis target gene enrichment suggested that lncRNAs might regulate growth and development in both tissues as well as posttranscriptional gene silencing by RNA or microRNA processing in rumen, or disease resistance mechanisms in ileum. This study provides a catalog of bovine lncRNAs and set a baseline for exploring their functions in calf GIT development. View Full-Text
Keywords: calf; rumen; ileum; gastrointestinal tract; lncRNA; mRNA; pathways; cis target gene calf; rumen; ileum; gastrointestinal tract; lncRNA; mRNA; pathways; cis target gene
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Ibeagha-Awemu, E.M.; Do, D.N.; Dudemaine, P.-L.; Fomenky, B.E.; Bissonnette, N. Integration of lncRNA and mRNA Transcriptome Analyses Reveals Genes and Pathways Potentially Involved in Calf Intestinal Growth and Development during the Early Weeks of Life. Genes 2018, 9, 142.

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