Special Issue "Non-Coding RNAs Roles in Animals"

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: 31 December 2021.

Special Issue Editors

Dr. Duy Ngoc Do
E-Mail Website
Guest Editor
Department of Animal Science and Aquaculture, Dalhousie University,58 River Road, Haley Institute, Truro, NS B2N 5E3, Canada
Interests: miRNAs; genomic selection; network analyses; genome-wide association studies; genetic diversity; next generation of sequencing; biomarkers; feed efficiency; milk genomics
Dr. Prashanth N Suravajhala
E-Mail Website
Guest Editor
Birla Institute of Scientific Research, Jaipur, India
Interests: systems genomics; lncRNAs; protein interactions; known unknowns; next generation sequencing
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues,

The important function of non-coding RNAs (ncRNA), such as microRNAs (miRNA), long non-coding RNAs (lncRNA), and circular RNAs (circRNA), in gene regulation in many species is increasingly appreciated. In livestock, thousands of miRNAs have been characterized and lncRNAs are beginning to be understood, thanks to the next generation of sequencing technologies. Moreover, ncRNAs are involved in many gene regulation processes and pathways related to economically important traits. In addition, ncRNAs are also considered as potential biomarkers for infectious diseases in different farm animal species.

We invite original research or review papers that allow us to better understand the roles of ncRNAs in livestock/animals. Any research related to functional characterization of ncRNAs, exploration of the roles of ncRNAs in novel phenotypes or less-approached diseases, examining the interaction among ncRNAs, and between ncRNAs and metabolites are invited. We also invited research using bioinformatics approaches or integrated omics for analyzing ncRNAs functions or linking the ncRNAs expression to the phenotypes. 

Dr. Duy Ngoc Do
Dr. Prashanth N Suravajhala
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Animals is an international peer-reviewed open access monthly journal published by MDPI.

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Keywords

  • miRNAs
  • lcRNAs
  • infectious diseases
  • feed efficiency
  • mastitis
  • circRNAs
  • pathways
  • biomarkers
  • epigenetics
  • host response

Published Papers (9 papers)

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Research

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Article
Circular PPP1R13B RNA Promotes Chicken Skeletal Muscle Satellite Cell Proliferation and Differentiation via Targeting miR-9-5p
Animals 2021, 11(8), 2396; https://doi.org/10.3390/ani11082396 - 13 Aug 2021
Viewed by 467
Abstract
Skeletal muscle plays important roles in animal locomotion, metabolism, and meat production in farm animals. Current studies showed that non-coding RNAs, especially the circular RNA (circRNA) play an indispensable role in skeletal muscle development. Our previous study revealed that several differentially expressed circRNAs [...] Read more.
Skeletal muscle plays important roles in animal locomotion, metabolism, and meat production in farm animals. Current studies showed that non-coding RNAs, especially the circular RNA (circRNA) play an indispensable role in skeletal muscle development. Our previous study revealed that several differentially expressed circRNAs among fast muscle growing broilers (FMGB) and slow muscle growing layers (SMGL) may regulate muscle development in the chicken. In this study, a novel differentially expressed circPPP1R13B was identified. Molecular mechanism analysis indicated that circPPP1R13B targets miR-9-5p and negatively regulates the expression of miR-9-5p, which was previously reported to be an inhibitor of skeletal muscle development. In addition, circPPP1R13B positively regulated the expression of miR-9-5p target gene insulin like growth factor 2 mRNA binding protein 3 (IGF2BP3) and further activated the downstream insulin like growth factors (IGF)/phosphatidylinositol 3-kinase (PI3K)/AKT serine/threonine kinase (AKT) signaling pathway. The results also showed that the knockdown of circPPP1R13B inhibits chicken skeletal muscle satellite cells (SMSCs) proliferation and differentiation, and the overexpression of circPPP1R13B promotes the proliferation and differentiation of chicken SMSCs. Furthermore, the overexpression of circPPP1R13B could block the inhibitory effect of miR-9-5p on chicken SMSC proliferation and differentiation. In summary, our results suggested that circPPP1R13B promotes chicken SMSC proliferation and differentiation by targeting miR-9-5p and activating IGF/PI3K/AKT signaling pathway. Full article
(This article belongs to the Special Issue Non-Coding RNAs Roles in Animals)
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Article
Expression Characteristics of microRNA in Pig Umbilical Venous Blood and Umbilical Arterial Blood
Animals 2021, 11(6), 1563; https://doi.org/10.3390/ani11061563 - 27 May 2021
Viewed by 917
Abstract
As the medium of material exchange between mother and fetus, umbilical cord blood is closely connected with fetal development. microRNA (miRNA) has a wide range of biological functions and has high flow characteristics. Small RNA sequencing of pig umbilical venous blood (UVB) and [...] Read more.
As the medium of material exchange between mother and fetus, umbilical cord blood is closely connected with fetal development. microRNA (miRNA) has a wide range of biological functions and has high flow characteristics. Small RNA sequencing of pig umbilical venous blood (UVB) and umbilical arterial blood (UAB) revealed that a total of 302 miRNAs were identified, and 106 and 22 miRNAs were specifically expressed in the UVB and UAB, respectively. Using the two methods of differential expression multiple and differential expression percentage, it is found that only 35% of the highly expressed miRNAs in the UVB by the two analysis modes overlap, but 56.25% of the enriched signal pathways are the same. Only 20% of the highly expressed miRNAs in the UAB overlap, but 62.07% of the signal pathways are the same. Further analysis revealed that miR-423 can be used as a characteristic miRNA of UVB and has the potential to treat muscle-related diseases. miR-122-5p can be used as a characteristic miRNA of UAB and may help to improve liver- and brain-related diseases. In summary, these results enrich understanding of miRNA in mother–fetal communication and provide a reference for the development and application of porcine cord blood products. Full article
(This article belongs to the Special Issue Non-Coding RNAs Roles in Animals)
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Article
RNA-Seq Reveals Function of Bta-miR-149-5p in the Regulation of Bovine Adipocyte Differentiation
Animals 2021, 11(5), 1207; https://doi.org/10.3390/ani11051207 - 22 Apr 2021
Viewed by 721
Abstract
Intramuscular fat is a real challenge for the experts of animal science to improve meat quality traits. Research on the mechanism of adipogenesis provides invaluable information for the improvement of meat quality traits. This study investigated the effect of bta-miR-149-5p and its underlying [...] Read more.
Intramuscular fat is a real challenge for the experts of animal science to improve meat quality traits. Research on the mechanism of adipogenesis provides invaluable information for the improvement of meat quality traits. This study investigated the effect of bta-miR-149-5p and its underlying mechanism on lipid metabolism in bovine adipocytes. Bovine adipocytes were differentiated and transfected with bta-miR-149-5p mimics or its negative control (NC). A total of 115 DEGs including 72 upregulated and 43 downregulated genes were identified in bovine adipocytes. The unigenes and GO term biological processes were the most annotated unigene contributor parts at 80.08%, followed by cellular component at 13.4% and molecular function at 6.7%. The KEGG pathways regulated by the DEGs were PI3K-Akt signaling pathway, calcium signaling pathway, pathways in cancer, MAPK signaling pathway, lipid metabolism/metabolic pathway, PPAR signaling pathway, AMPK signaling pathway, TGF-beta signaling pathway, cAMP signaling pathway, cholesterol metabolism, Wnt signaling pathway, and FoxO signaling pathway. In addition to this, the most important reactome enrichment pathways were R−BTA−373813 receptor CXCR2 binding ligands CXCL1 to 7, R−BTA−373791 receptor CXCR1 binding CXCL6 and CXCL8 ligands, R−BTA−210991 basigin interactions, R−BTA−380108 chemokine receptors binding chemokines, R−BTA−445704 calcium binding caldesmon, and R−BTA−5669034 TNFs binding their physiological receptors. Furthermore, the expression trend of the DEGs in these pathways were also exploited. Moreover, the bta-miR-149-5p significantly (p < 0.01) downregulated the mRNA levels of adipogenic marker genes such as CCND2, KLF6, ACSL1, Cdk2, SCD, SIK2, and ZEB1 in bovine adipocytes. In conclusion, our results suggest that bta-miR-149-5p regulates lipid metabolism in bovine adipocytes. The results of this study provide a basis for studying the function and molecular mechanism of the bta-miR-149-5p in regulating bovine adipogenesis. Full article
(This article belongs to the Special Issue Non-Coding RNAs Roles in Animals)
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Article
MicroRNA-148a Regulates the Proliferation and Differentiation of Ovine Preadipocytes by Targeting PTEN
Animals 2021, 11(3), 820; https://doi.org/10.3390/ani11030820 - 15 Mar 2021
Cited by 2 | Viewed by 452
Abstract
MicroRNAs (miRNAs) have been found to be involved in lipid deposition and metabolism. However, there have been no reports on the roles of miR-148a in the proliferation and adipogenesis of preadipocytes in sheep. In this study, the expression of miR-148a was profiled in [...] Read more.
MicroRNAs (miRNAs) have been found to be involved in lipid deposition and metabolism. However, there have been no reports on the roles of miR-148a in the proliferation and adipogenesis of preadipocytes in sheep. In this study, the expression of miR-148a was profiled in the eight tissues of Tibetan ewes and differentiated preadipocytes, and the role of miR-148a in differentiation and proliferation of ovine preadipocytes was investigated using Oil Red O staining, CCK-8, EdU staining, cell cycle detection, and RT-qPCR. The effect of PTEN on the differentiation of ovine preadipocytes was also investigated. The miR-148a was widely expressed in the eight tissues investigated and had significantly increased expression in liver, spleen and subcutaneous adipose tissues, and the heart. The expression of miR-148a continued to increase with the differentiation of ovine preadipocytes. The over-expression of miR-148a significantly promoted differentiation but inhibited the proliferation of ovine preadipocytes. The inhibition of miR-148a had the opposite effect on the differentiation and proliferation of ovine preadipocytes with over-expressed miR-148a. The results from the dual luciferase reporter assays showed that miR-148a mimic significantly decreased the luciferase activity of PTEN-3′UTR dual luciferase reporter vector, suggesting that PTEN is a target gene of miR-148a. In over-expressed-PTEN preadipocytes, the number of lipid droplets remarkably decreased, and the expression levels of adipogenesis marker genes PPARγ, FASN, FATP4, GLUT4, C/EBPβ and LPL were also significantly down-regulated. These results suggest that miR-148a accelerated the adipogenic differentiation of ovine preadipocytes by inhibiting PTEN expression, and also inhibited the proliferation of ovine preadipocytes. Full article
(This article belongs to the Special Issue Non-Coding RNAs Roles in Animals)
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Article
RNA-Seq Implies Divergent Regulation Patterns of LincRNA on Spermatogenesis and Testis Growth in Goats
Animals 2021, 11(3), 625; https://doi.org/10.3390/ani11030625 - 26 Feb 2021
Viewed by 583
Abstract
Long intergenic non-coding RNAs (lincRNAs) regulate testicular development by acting on protein-coding genes. However, little is known about whether lincRNAs and protein-coding genes exhibit the same expression pattern in the same phase of postnatal testicular development in goats. Therefore, this study aimed to [...] Read more.
Long intergenic non-coding RNAs (lincRNAs) regulate testicular development by acting on protein-coding genes. However, little is known about whether lincRNAs and protein-coding genes exhibit the same expression pattern in the same phase of postnatal testicular development in goats. Therefore, this study aimed to demonstrate the expression patterns and roles of lincRNAs during the postnatal development of the goat testis. Herein, the testes of Yiling goats with average ages of 0, 30, 60, 90, 120, 150, and 180 days postnatal (DP) were used for RNA-seq. In total, 20,269 lincRNAs were identified, including 16,931 novel lincRNAs. We identified seven time-specifically diverse lincRNA modules and six mRNA modules by weighted gene co-expression network analysis (WGCNA). Interestingly, the down-regulation of growth-related lincRNAs was nearly one month earlier than the up-regulation of spermatogenesis-related lincRNAs, while the down-regulation of growth-related protein-coding genes and the correspondent up-regulation of spermatogenesis-related protein-coding genes occurred at the same age. Then, potential lincRNA target genes were predicted. Moreover, the co-expression network of lincRNAs demonstrated that ENSCHIT00000000777, ENSCHIT00000002069, and ENSCHIT00000005076 were the key lincRNAs in the process of testis development. Our study discovered the divergent regulation patterns of lincRNA on spermatogenesis and testis growth, providing a fresh insight into age-biased changes in lincRNA expression in the goat testis. Full article
(This article belongs to the Special Issue Non-Coding RNAs Roles in Animals)
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Article
Long Noncoding RNA LncPGCR Mediated by TCF7L2 Regulates Primordial Germ Cell Formation in Chickens
Animals 2021, 11(2), 292; https://doi.org/10.3390/ani11020292 - 24 Jan 2021
Cited by 1 | Viewed by 647
Abstract
Although lncRNAs have been identified as playing critical roles in the development of germ cells, their potential involvement in the development of PGCs in chickens remains poorly understood. Differentially expressed lncRNAs (DELs) from previous RNA-seq of embryonic stem cells (ESCs), PGCs, and spermatogonial [...] Read more.
Although lncRNAs have been identified as playing critical roles in the development of germ cells, their potential involvement in the development of PGCs in chickens remains poorly understood. Differentially expressed lncRNAs (DELs) from previous RNA-seq of embryonic stem cells (ESCs), PGCs, and spermatogonial stem cells (SSCs) were analyzed by K-means clustering, from which a key candidate, lncRNA (lncRNA PGC regulator, LncPGCR) was obtained. We confirmed that LncPGCR plays a positive role in the development of PGCs by increasing the expression of the PGC marker gene (Cvh and C-kit), while downregulating the pluripotency-associated gene (Nanog) in vitro and in vivo. The activation and expression of LncPGCR are regulated by histone acetylation, and transcription factor TCF7L2. Mechanistically, a rescue assay was performed to further confirm that LncPGCR contributed to the development of PGCs by regulating the gga-miR-6577-5p/Btrc signaling pathway. Adsorption of gga-miR-6577-5p activated the WNT signaling cascade by relieving the gga-miR-6577-5p-dependent inhibition of Btrc expression. Taken together, our study discovered the growth-expedited role of LncPGCR in PGCs development, showing the potential LncPGCR/miR-6577-5p/Btrc pathway. The results and findings provide a novel insight into the development of PGCs. Full article
(This article belongs to the Special Issue Non-Coding RNAs Roles in Animals)
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Article
Analysis of lncRNA Expression Profile during the Formation of Male Germ Cells in Chickens
Animals 2020, 10(10), 1850; https://doi.org/10.3390/ani10101850 - 11 Oct 2020
Cited by 1 | Viewed by 710
Abstract
Germ cells have an irreplaceable role in transmitting genetic information from one generation to the next, and also play an important role in sex differentiation in poultry, while little is known about epigenetic factors that regulate germ cell differentiation. In this study, RNA-seq [...] Read more.
Germ cells have an irreplaceable role in transmitting genetic information from one generation to the next, and also play an important role in sex differentiation in poultry, while little is known about epigenetic factors that regulate germ cell differentiation. In this study, RNA-seq was used to detect the expression profiles of long non-coding RNAs (lncRNAs) during the differentiation of chicken embryonic stem cells (ESCs) into spermatogonial stem cells (SSCs). The results showed that a total of 296, 280 and 357 differentially expressed lncRNAs (DELs) were screened in ESCs vs. PGCs, ESCs vs. SSCs and PGCs vs. SSCs, respectively. Gene Ontology (GO) and KEGG enrichment analysis showed that DELs in the three cell groups were mainly enriched in autophagy, Wnt/β-catenin, TGF-β, Notch and ErbB and signaling pathways. The co-expression network of 37 candidate DELs and their target genes enriched in the biological function of germ cell development showed that XLOC_612026, XLOC_612029, XLOC_240662, XLOC_362463, XLOC_023952, XLOC_674549, XLOC_160716, ALDBGALG0000001810, ALDBGALG0000002986, XLOC_657380674549, XLOC_022100 and XLOC_657380 were the key lncRNAs in the process of male germ cell formation and, moreover, the function of these DELs may be related to the interaction of their target genes. Our findings preliminarily excavated the key lncRNAs and signaling pathways in the process of male chicken germ cell formation, which could be helpful to construct the gene regulatory network of germ cell development, and also provide new ideas for further optimizing the induction efficiency of germ cells in vitro. Full article
(This article belongs to the Special Issue Non-Coding RNAs Roles in Animals)
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Article
RNA-Seq Reveals the Expression Profiles of Long Non-Coding RNAs in Lactating Mammary Gland from Two Sheep Breeds with Divergent Milk Phenotype
Animals 2020, 10(9), 1565; https://doi.org/10.3390/ani10091565 - 03 Sep 2020
Cited by 2 | Viewed by 614
Abstract
Long non-coding RNAs (lncRNAs) are a kind of non-coding RNA with >200 nucleotides in length. Some lncRNAs have been proven to have clear regulatory functions in many biological processes of mammals. However, there have been no reports on the roles of lncRNAs in [...] Read more.
Long non-coding RNAs (lncRNAs) are a kind of non-coding RNA with >200 nucleotides in length. Some lncRNAs have been proven to have clear regulatory functions in many biological processes of mammals. However, there have been no reports on the roles of lncRNAs in ovine mammary gland tissues. In the study, the expression profiles of lncRNAs were studied using RNA-Seq in mammary gland tissues from lactating Small-Tailed Han (STH) ewes and Gansu Alpine Merino (GAM) ewes with different milk yield and ingredients. A total of 1894 lncRNAs were found to be expressed. Compared with the GAM ewes, the expression levels of 31 lncRNAs were significantly up-regulated in the mammary gland tissues of STH ewes, while 37 lncRNAs were remarkably down-regulated. Gene Ontogeny (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that the target genes of differentially expressed lncRNAs were enriched in the development and proliferation of mammary epithelial cells, morphogenesis of mammary gland, ErbB signaling pathway, and Wnt signaling pathway. Some miRNA sponges of differentially expressed lncRNAs, reported to be associated with lactation and mammary gland morphogenesis, were found in a lncRNA-miRNA network. This study reveals comprehensive lncRNAs expression profiles in ovine mammary gland tissues, thereby providing a further understanding of the functions of lncRNAs in the lactation and mammary gland development of sheep. Full article
(This article belongs to the Special Issue Non-Coding RNAs Roles in Animals)
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Review

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Review
Long Non-Coding RNAs in Insects
Animals 2021, 11(4), 1118; https://doi.org/10.3390/ani11041118 - 14 Apr 2021
Cited by 1 | Viewed by 671
Abstract
Only a small subset of all the transcribed RNAs are used as a template for protein translation, whereas RNA molecules that are not translated play a very important role as regulatory non-coding RNAs (ncRNAs). Besides traditionally known RNAs (ribosomal and transfer RNAs), ncRNAs [...] Read more.
Only a small subset of all the transcribed RNAs are used as a template for protein translation, whereas RNA molecules that are not translated play a very important role as regulatory non-coding RNAs (ncRNAs). Besides traditionally known RNAs (ribosomal and transfer RNAs), ncRNAs also include small non-coding RNAs (sncRNAs) and long non-coding RNAs (lncRNAs). The lncRNAs, which were initially thought to be junk, have gained a great deal attention because of their regulatory roles in diverse biological processes in animals and plants. Insects are the most abundant and diverse group of animals on this planet. Recent studies have demonstrated the role of lncRNAs in almost all aspects of insect development, reproduction, and genetic plasticity. In this review, we describe the function and molecular mechanisms of the mode of action of different insect lncRNAs discovered up to date. Full article
(This article belongs to the Special Issue Non-Coding RNAs Roles in Animals)
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