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Non-Coding RNAs Roles in Animals

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

Deadline for manuscript submissions: closed (31 December 2021) | Viewed by 40845

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Special Issue Editors

Dr. Duy Ngoc Do

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Guest Editor

Department of Animal Science and Aquaculture, Dalhousie University, Truro, Canada
Interests: genomic selection; feed efficiency; miRNAs; statistical genomics

Dr. Prashanth N Suravajhala

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Guest Editor

Amrita School of Biotechnology, Amrita University, Kerala 690525, India
Interests: systems genomics; lncRNAs; protein interactions; known unknowns; next generation sequencing
Special Issues, Collections and Topics in MDPI journals

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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

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Keywords

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

Published Papers (14 papers)

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Editorial

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3 pages, 177 KiB

Open AccessEditorial

Editorial: Role of Non-Coding RNAs in Animals

by Duy Ngoc Do and Prashanth Suravajhala

Animals 2023, 13(5), 805; https://doi.org/10.3390/ani13050805 - 23 Feb 2023

Viewed by 1131

Abstract

The importance of non-coding RNAs (ncRNAs), such as microRNAs (miRNA), long non-coding RNAs (lncRNA), and circular RNAs (circRNA), in gene regulation is increasingly being appreciated in many species [...] Full article

(This article belongs to the Special Issue Non-Coding RNAs Roles in Animals)

Research

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17 pages, 3730 KiB

Open AccessArticle

Dynamic miRNA Landscape Links Mammary Gland Development to the Regulation of Milk Protein Expression in Mice

by Wenjing Wang, Xupeng Zang, Yonglun Liu, Yunyi Liang, Gengyuan Cai, Zhenfang Wu and Zicong Li

Animals 2022, 12(6), 727; https://doi.org/10.3390/ani12060727 - 14 Mar 2022

Cited by 5 | Viewed by 2077

Abstract

Mammary gland morphology varies considerably between pregnancy and lactation status, e.g., virgin to pregnant and lactation to weaning. Throughout these critical developmental phases, the mammary glands undergo remodeling to accommodate changes in milk production capacity, which is positively correlated with milk protein expression. The purpose of this study was to investigate the microRNA (miRNA) expression profiles in female ICR mice’s mammary glands at the virgin stage (V), day 16 of pregnancy (P16d), day 12 of lactation (L12d), day 1 of forced weaning (FW1d), and day 3 of forced weaning (FW3d), and to identify the miRNAs regulating milk protein gene expression. During the five stages of testing, 852 known miRNAs and 179 novel miRNAs were identified in the mammary glands. Based on their expression patterns, the identified miRNAs were grouped into 12 clusters. The expression pattern of cluster 1 miRNAs was opposite to that of milk protein genes in mammary glands in all five different stages. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that the predicted target genes of cluster 1 miRNAs were related to murine mammary gland development and lactation. Furthermore, fluorescence in situ hybridization (FISH) analysis revealed that the novel-mmu-miR424-5p, which belongs to the cluster 1 miRNAs, was expressed in murine mammary epithelial cells. The dual-luciferase reporter assay revealed that an important milk protein gene—β-casein (CSN2)—was regarded as one of the likely targets for the novel-mmu-miR424-5p. This study analyzed the expression patterns of miRNAs in murine mammary glands throughout five critical developmental stages, and discovered a novel miRNA involved in regulating the expression of CSN2. These findings contribute to an enhanced understanding of the developmental biology of mammary glands, providing guidelines for increasing lactation efficiency and milk quality. Full article

(This article belongs to the Special Issue Non-Coding RNAs Roles in Animals)

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17 pages, 4300 KiB

Open AccessArticle

CircEZH2 Regulates Milk Fat Metabolism through miR-378b Sponge Activity

by Dongyang Wang, Zhengjiang Zhao, Yiru Shi, Junyi Luo, Ting Chen, Qianyun Xi, Yongliang Zhang and Jiajie Sun

Animals 2022, 12(6), 718; https://doi.org/10.3390/ani12060718 - 12 Mar 2022

Cited by 6 | Viewed by 2134

Abstract

In this study, we evaluated the roles of heat-induced circEZH2 in the regulation of milk fat metabolism. CircEZH2 overexpression increased HC11 cell proliferation and decreased apoptosis. These changes were accompanied by increased expression of proliferation marker proteins (PCNA, Cyclin D, and Cyclin E) and the anti-apoptotic protein Bcl2, while expression of the pro-apoptotic proteins Bax and cleaved-caspase was reduced. SiRNA-mediated silencing of EZH2 in HC11 cells had the opposite effects. CircEZH2 overexpression promoted the uptake of a fluorescent fatty acid (Bodipy) as well as expression of the fatty acid transport-related protein CD36, lipolysis-related protein LPL, and unsaturated fatty acid metabolism-related proteins FADS1 and SCD1. Dual luciferase reporter assays verified the targeting relationship of the two ceRNA networks, circEZH2-miR378b-LPL and circEZH2-miR378b-CD36. This information provides further clarification of the role of circRNAs in milk fat regulation in addition to a theoretical basis for alleviating the effects of heat stress on milk production by dairy cows. Full article

(This article belongs to the Special Issue Non-Coding RNAs Roles in Animals)

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13 pages, 4524 KiB

Open AccessArticle

miR-F4-C12 Functions on the Regulation of Adipose Accumulation by Targeting PIK3R1 in Castrated Male Pigs

by Qiao Xu, Jie Chen, Ximing Liu, Yabiao Luo, Tianzuo Wang and Meiying Fang

Animals 2021, 11(11), 3053; https://doi.org/10.3390/ani11113053 - 26 Oct 2021

Cited by 1 | Viewed by 1653

Abstract

MicroRNAs (miRNAs) constitute small regulatory molecules for a wide array of biological activities (18~24 nucleotides in length), including adipogenesis and adipose deposition. Their effect is, however, incompletely defined in inducing fat accumulation in castrated male pigs. Based on our study, four nine-times miRNAs were selected to examine their functions in adipose formation activities. In 3T3-L1 cells and backfat tissues of castrated and intact male pigs, miR-F4-C12 was identified as a factor in adipose development utilizing quantitative real-time PCR (qRT-PCR). Further, miR-F4-C12 was identified to promote fat development, suggesting that miR-F4-C12 was involved in adipogenesis. Moreover, phosphoinositide-3-kinase regulatory subunit 1 (PIK3R1) was proposed by the TargetScan, miRDB and starBase as a target of miR-F4-C12 and verified through a two-luciferase reporter assay. The over-expression of miR-F4-C12 dramatically decreases the PIK3R1 protein level in 3T3-L1 cells. The mRNA and protein levels of PIK3R1 in castrated pigs are reduced relative to intact pigs, providing further evidence that PIK3R1 is involved in regulating adipose accumulation. These results suggest that miR-F4-C12 involves adipose development and may regulate subcutaneous adipose tissue accumulation by targeting PIK3R1 in castrated male pigs. Full article

(This article belongs to the Special Issue Non-Coding RNAs Roles in Animals)

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13 pages, 4775 KiB

Open AccessArticle

Analysis of mRNA and Long Non-Coding RNA Expression Profiles in Developing Yorkshire Pig Spleens

by Xinjian Li, Xuelei Han, Caixia Sun, Gaiying Li, Kejun Wang, Xiuling Li and Ruimin Qiao

Animals 2021, 11(10), 2768; https://doi.org/10.3390/ani11102768 - 23 Sep 2021

Cited by 5 | Viewed by 2096

Abstract

Epidemic diseases cause great economic loss in pig farms each year; some of these diseases are characterized mainly in the spleen, but mRNA and lncRNA (long non-coding RNA) expression networks in developing Yorkshire pig spleens remain obscure. Here, we profiled the systematic characters of mRNA and lncRNA repertoires in three groups of spleens from nine Yorkshire pigs, each three aged at seven days, 90 days, and 180 days. By using a precise mRNA and lncRNA identification pipeline, we identified 19,647 genes and 219 known and 3219 putative lncRNA transcripts; 1729 genes and 64 lncRNAs therein were found to express differentially. The gene expression characteristics of genes and lncRNAs were found to be basically fixed before 90 days after birth. Three large gene expression modules were detected. The enrichment analyses of differentially expressed genes and the potential target genes of differentially expressed lncRNAs both displayed the crucial roles of up-regulation in immune activation and hematopoiesis, and down-regulation in cell replication and division in 90 days and 180 days compared to seven days. ENSSSCT00000001325 was the only lncRNA transcript that existed in the three groups. CDK1, PCNA, and PLK were detected to be node genes that varied with age. This study contributes to a further understanding of mRNA and lncRNA expression in different developmental pig spleens. Full article

(This article belongs to the Special Issue Non-Coding RNAs Roles in Animals)

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14 pages, 3649 KiB

Open AccessArticle

Circular PPP1R13B RNA Promotes Chicken Skeletal Muscle Satellite Cell Proliferation and Differentiation via Targeting miR-9-5p

by Xiaoxu Shen, Yuanhang Wei, Guishuang You, Wei Liu, Felix Kwame Amevor, Yao Zhang, Haorong He, Menggen Ma, Yun Zhang, Diyan Li, Qing Zhu and Huadong Yin

Animals 2021, 11(8), 2396; https://doi.org/10.3390/ani11082396 - 13 Aug 2021

Cited by 19 | Viewed by 3473

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 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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13 pages, 3068 KiB

Open AccessArticle

Expression Characteristics of microRNA in Pig Umbilical Venous Blood and Umbilical Arterial Blood

by Mailin Gan, Lin Liu, Shunhua Zhang, Zongyi Guo, Ya Tan, Jia Luo, Qiong Yang, Hongmei Pan, Xuewei Li, Jinyong Wang, Linyuan Shen and Li Zhu

Animals 2021, 11(6), 1563; https://doi.org/10.3390/ani11061563 - 27 May 2021

Cited by 4 | Viewed by 3602

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 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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24 pages, 7005 KiB

Open AccessArticle

RNA-Seq Reveals Function of Bta-miR-149-5p in the Regulation of Bovine Adipocyte Differentiation

by Hongfang Guo, Rajwali Khan, Sayed Haidar Abbas Raza, Syed Muhammad Suhail, Hamayun Khan, Sher Bahadar Khan, Ayman Hassan Abd El-Aziz and Linsen Zan

Animals 2021, 11(5), 1207; https://doi.org/10.3390/ani11051207 - 22 Apr 2021

Cited by 16 | Viewed by 3115

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 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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17 pages, 6937 KiB

Open AccessArticle

MicroRNA-148a Regulates the Proliferation and Differentiation of Ovine Preadipocytes by Targeting PTEN

by Xiayang Jin, Zhiyun Hao, Mengli Zhao, Jiyuan Shen, Na Ke, Yize Song, Lirong Qiao, Yujie Lu, Liyan Hu, Xinmiao Wu, Jiqing Wang and Yuzhu Luo

Animals 2021, 11(3), 820; https://doi.org/10.3390/ani11030820 - 15 Mar 2021

Cited by 11 | Viewed by 2034

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 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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19 pages, 6735 KiB

Open AccessArticle

RNA-Seq Implies Divergent Regulation Patterns of LincRNA on Spermatogenesis and Testis Growth in Goats

by Dongdong Bo, Xunping Jiang, Guiqiong Liu, Ruixue Hu and Yuqing Chong

Animals 2021, 11(3), 625; https://doi.org/10.3390/ani11030625 - 26 Feb 2021

Cited by 9 | Viewed by 1846

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 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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13 pages, 2174 KiB

Open AccessArticle

Long Noncoding RNA LncPGCR Mediated by TCF7L2 Regulates Primordial Germ Cell Formation in Chickens

by Jingyi Jiang, Chen Chen, Shaoze Cheng, Xia Yuan, Jing Jin, Chen Zhang, Xiaolin Sun, Jiuzhou Song, Qisheng Zuo, Yani Zhang, Guohong Chen and Bichun Li

Animals 2021, 11(2), 292; https://doi.org/10.3390/ani11020292 - 24 Jan 2021

Cited by 5 | Viewed by 2237

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 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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18 pages, 4732 KiB

Open AccessArticle

Analysis of lncRNA Expression Profile during the Formation of Male Germ Cells in Chickens

by Wen Gao, Chen Zhang, Kai Jin, Yani Zhang, Qisheng Zuo and Bichun Li

Animals 2020, 10(10), 1850; https://doi.org/10.3390/ani10101850 - 11 Oct 2020

Cited by 11 | Viewed by 2274

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 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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12 pages, 1154 KiB

Open AccessArticle

RNA-Seq Reveals the Expression Profiles of Long Non-Coding RNAs in Lactating Mammary Gland from Two Sheep Breeds with Divergent Milk Phenotype

by Zhiyun Hao, Yuzhu Luo, Jiqing Wang, Jiang Hu, Xiu Liu, Shaobin Li, Xiayang Jin, Na Ke, Mengli Zhao, Liyan Hu, Yujie Lu, Xinmiao Wu and Lirong Qiao

Animals 2020, 10(9), 1565; https://doi.org/10.3390/ani10091565 - 3 Sep 2020

Cited by 7 | Viewed by 3059

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 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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20 pages, 1846 KiB

Open AccessReview

Long Non-Coding RNAs in Insects

by Chhavi Choudhary, Shivasmi Sharma, Keshav Kumar Meghwanshi, Smit Patel, Prachi Mehta, Nidhi Shukla, Duy Ngoc Do, Subhash Rajpurohit, Prashanth Suravajhala and Jayendra Nath Shukla

Animals 2021, 11(4), 1118; https://doi.org/10.3390/ani11041118 - 14 Apr 2021

Cited by 24 | Viewed by 7115

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 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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