Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

Ngoc, Duy; Dudemaine, Pier-Luc; Fomenky, Bridget E.; Ibeagha‐Awemu, Eveline M.

doi:10.5772/intechopen.69872

Cited by 7 publications

(6 citation statements)

References 227 publications

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“…It is well documented that lncRNAs may act in cis or trans to regulate the activities of genes [ 15 , 68 , 69 , 70 , 71 , 72 ]. Due to current lack of information, the functions of bovine lncRNAs can be inferred either by their physical position to protein coding genes such as their potential cis target genes (genes neighboring lncRNAs) or by their co-expression relationship with mRNAs (guilt by association methods) [ 73 , 74 , 75 , 76 ]) or determined experimentally. To infer the function of lncRNAs, we identified their cis target genes (genes located within 50 Kb flanking regions of lncRNAs), especially those having significant co-expression correlation (p.BH < 0.05) with lncRNAs.…”

Section: Discussionmentioning

confidence: 99%

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

Ibeagha‐Awemu

Ngoc

Dudemaine

et al. 2018

Genes

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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.

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Section: Discussionmentioning

confidence: 99%

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

Ibeagha‐Awemu

Ngoc

Dudemaine

et al. 2018

Genes

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“…In addition to these classic epigenetic processes (DNA methylation, histone modification, and chromatin remodeling), ncRNAs also play important regulatory roles in gene expression and chromatin modification impacting livestock production and health ( Do et al, 2017a ; Benmoussa et al, 2020 ). ncRNAs are a class of RNA species that mediate their functions as RNA (are not translated into proteins) and generally regulate gene expression at the transcriptional and posttranscriptional levels.…”

Section: Epigenetic Processes and Impacts On Gene Regulationmentioning

confidence: 99%

“…Continued technological advances have further promoted the implementation of genomic selection in livestock production ( Georges et al, 2019 ; Gurgul et al, 2019 ). Sequence analysis of livestock genomes uncovered the general molecular and regulatory mechanisms of the coding and non-coding genome underlying production and health traits, which have supported advances in trait improvement ( Kamath et al, 2016 ; Do et al, 2017a ; Wara et al, 2019 ). These factors still fall short of accounting for the optimal level of variation that is required to achieve continued improvements in livestock health and productivity.…”

Section: Introductionmentioning

confidence: 99%

Impacts of Epigenetic Processes on the Health and Productivity of Livestock

Wang

Ibeagha‐Awemu

2021

Front. Genet.

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The dynamic changes in the epigenome resulting from the intricate interactions of genetic and environmental factors play crucial roles in individual growth and development. Numerous studies in plants, rodents, and humans have provided evidence of the regulatory roles of epigenetic processes in health and disease. There is increasing pressure to increase livestock production in light of increasing food needs of an expanding human population and environment challenges, but there is limited related epigenetic data on livestock to complement genomic information and support advances in improvement breeding and health management. This review examines the recent discoveries on epigenetic processes due to DNA methylation, histone modification, and chromatin remodeling and their impacts on health and production traits in farm animals, including bovine, swine, sheep, goat, and poultry species. Most of the reports focused on epigenome profiling at the genome-wide or specific genic regions in response to developmental processes, environmental stressors, nutrition, and disease pathogens. The bulk of available data mainly characterized the epigenetic markers in tissues/organs or in relation to traits and detection of epigenetic regulatory mechanisms underlying livestock phenotype diversity. However, available data is inadequate to support gainful exploitation of epigenetic processes for improved animal health and productivity management. Increased research effort, which is vital to elucidate how epigenetic mechanisms affect the health and productivity of livestock, is currently limited due to several factors including lack of adequate analytical tools. In this review, we (1) summarize available evidence of the impacts of epigenetic processes on livestock production and health traits, (2) discuss the application of epigenetics data in livestock production, and (3) present gaps in livestock epigenetics research. Knowledge of the epigenetic factors influencing livestock health and productivity is vital for the management and improvement of livestock productivity.

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“…Not only the growth of the number of ncRNAs, but also more functions of ncRNAs in livestock have been described. Several reviews have examined the roles of ncRNAs in livestock phenotypes [ 6 , 12 , 13 , 17 , 18 , 19 ]. Given the importance of feed efficiency, it is essential to explore the miRNAs roles in the regulation of feed efficiency.…”

Section: Introductionmentioning

confidence: 99%

Emerging Roles of Non-Coding RNAs in the Feed Efficiency of Livestock Species

Ngoc

Davoudi

et al. 2022

Genes

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A global population of already more than seven billion people has led to an increased demand for food and water, and especially the demand for meat. Moreover, the cost of feed used in animal production has also increased dramatically, which requires animal breeders to find alternatives to reduce feed consumption. Understanding the biology underlying feed efficiency (FE) allows for a better selection of feed-efficient animals. Non-coding RNAs (ncRNAs), especially micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs), play important roles in the regulation of bio-logical processes and disease development. The functions of ncRNAs in the biology of FE have emerged as they participate in the regulation of many genes and pathways related to the major FE indicators, such as residual feed intake and feed conversion ratio. This review provides the state of the art studies related to the ncRNAs associated with FE in livestock species. The contribution of ncRNAs to FE in the liver, muscle, and adipose tissues were summarized. The research gap of the function of ncRNAs in key processes for improved FE, such as the nutrition, heat stress, and gut–brain axis, was examined. Finally, the potential uses of ncRNAs for the improvement of FE were discussed.

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Transcriptome Analysis of Non‐Coding RNAs in Livestock Species: Elucidating the Ambiguity

Cited by 7 publications

References 227 publications

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

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

Impacts of Epigenetic Processes on the Health and Productivity of Livestock

Emerging Roles of Non-Coding RNAs in the Feed Efficiency of Livestock Species

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