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.
Highlights
Calves undergo major physiological and dietary changes including adaptation to extrauterine life, pre-ruminant stage (3 to 5 months of age) and weaning [1]
Next-generation RNA sequencing of 48 libraries from ileum and rumen tissues of calves generated a total of 2.5 billion reads (Supplementary Table S2)
A total of 24,616 expressed messenger RNA (mRNA) were retained after removing transcripts that were not annotated to Ensemble bovine gene annotation release 84
Summary
Calves undergo major physiological and dietary changes including adaptation to extrauterine life (first week of life), pre-ruminant stage (3 to 5 months of age) and weaning [1]. Sufficient colostrum ingestion and microbial colonization is crucial for adequate development of the gastro-intestinal tract (GIT) and mucosal immune system [1,2]. These developmental transitions are accompanied by rapid changes in gene expression controlled by signal-mediated coordination of transcriptional and post-transcriptional mechanisms [3]. The transcriptional mechanisms include the activities of non-coding RNA (ncRNA) and transcription factors as well as epigenetic modifications. While only about 2% of the mammalian genome is transcribed as proteins, about 75–90% is transcribed as ncRNA, the vast majority being long non-coding RNA (lncRNA) [4].
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
