Characterization of lncRNA–miRNA–mRNA Network to Reveal Potential Functional ceRNAs in Bovine Skeletal Muscle

Yue, Binglin; Li, Hui; Liu, Mei; Li, Mingxun; Lei, Chuzhao; Huang, Bizhi

doi:10.3389/fgene.2019.00091

Cited by 43 publications

(40 citation statements)

References 63 publications

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“…lncRNAs can be either single-exonic or multi-exonic, while it is a challenge to distinguish true lncRNAs from the abundant one exon, low expression fragments and expression noise assembled from RNA-Seq data (Cabili et al 2011;Derrien et al 2012). Thus, we only chose multi-exonic lncRNAs for further analysis, as was done in other studies (Tong et al 2017;Kern et al 2018;Yang et al 2018;Yue et al 2019), and depends on a highly stringent filtering pipeline to minimise the number of false-positive lncRNAs. Consequently, 4155 non-protein coding transcripts were considered as highly reliable lncRNAs, which was less than previous studies due to our stringent criteria (Billerey et al 2014;Liu et al 2017;Choi et al 2019;Yue et al 2019).…”

Section: Discussionmentioning

confidence: 99%

“…Thus, we only chose multi-exonic lncRNAs for further analysis, as was done in other studies (Tong et al 2017;Kern et al 2018;Yang et al 2018;Yue et al 2019), and depends on a highly stringent filtering pipeline to minimise the number of false-positive lncRNAs. Consequently, 4155 non-protein coding transcripts were considered as highly reliable lncRNAs, which was less than previous studies due to our stringent criteria (Billerey et al 2014;Liu et al 2017;Choi et al 2019;Yue et al 2019). These lncRNAs have different expression distribution in different chromosomes.…”

Section: Discussionmentioning

confidence: 99%

“…With the development of genetic array and high throughput sequencing technology, more and more lncRNAs have been discovered in human, rat and mouse (Zhao et al 2016). Recently, lncRNAs have also been identified in pig (Yang et al 2017;Jin et al 2018;Kern et al 2018), chicken (Muret et al 2017;Kern et al 2018;Li et al 2019), sheep (Ren et al 2016;Ling et al 2017;Bush et al 2018;Sulayman et al 2019) and cattle (Billerey et al 2014;Koufariotis et al 2015;Tong et al 2017;Bush et al 2018;Kern et al 2018;Weikard et al 2018;Yang et al 2018;Choi et al 2019;Wang et al 2019;Yue et al 2019).…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification and characterisation of long non-coding RNAs in two Chinese cattle breeds

Jia

Chen

et al. 2020

Italian Journal of Animal Science

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Long non-coding RNAs (lncRNAs) have been essentially involved in all kinds of important biological processes, such as cell differentiation and development. In this study, we comprehensively profiled genome-wide lncRNAs of bovine skeletal muscle in two Chinese cattle breeds using RNAseq approach. The longissimus dorsi samples were collected from three Charolais (CH) and three Tongjiang (TJ) adult cattle, respectively. Approximately 80 million reads were obtained per library, and by which we assembled 31,009 unique transcripts. We successfully identified a total of 4155 different lncRNAs in six muscle samples, consisting of 3204 intronic lncRNAs, 737 intergenic lncRNAs, 113 sense lncRNAs and 101 antisense lncRNAs. Among them, 32 lncRNAs were differentially expressed (Fold Change >1.0, FDR < 0.05) between CH and TJ. Among these lncRNAs, 1744 identified bovine lncRNAs were located adjacent to 1146 protein-coding genes (<100 kb upstream and downstream) and functionally enriched in organ development, gene regulation and signal transduction. Our results provide a catalogue of bovine skeletal muscle-related lncRNAs, which will complement the list of bovine lncRNAs and contribute to understanding of the molecular mechanism of underpinning muscle development in cattle. HIGHLIGHTS The first study to compare specialised beef cattle breed with Chinese local beef cattle breed on long non-coding RNA (lncRNA). The 4155 different lncRNAs in beef cattle genome were identified to complement the list of bovine lncRNAs. The 1146 protein-coding genes were found maybe in cis-regulatory relationships with lncRNAs to understand the molecular mechanism underpinning muscle development in cattle.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification and characterisation of long non-coding RNAs in two Chinese cattle breeds

Jia

Chen

et al. 2020

Italian Journal of Animal Science

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“…ceRNA theory indicates that lncRNAs act as sponge for miRNA to manipulate the expression of coding gene. 16 Therefore, identifying miRNA/mRNA that has a connection with DGCR5 will advance our understanding of the DGCR5 roles in NSCLC. Growing evidence has revealed that miRNAs play crucial roles in tumor development.…”

Section: Discussionmentioning

confidence: 99%

LncRNA DGCR5 regulates the non‐small cell lung cancer cell growth, migration, and invasion through regulating miR‐211‐5p/EPHB6 axis

Kang

Shi

et al. 2019

BioFactors

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Non‐small cell lung cancer (NSCLC) accounts for about 80% of lung cancers worldwide. In recent years, importance of noncoding RNAs including long noncoding RNA and microRNA in regulating tumor progression has been appreciated. Abnormally expression of DiGeorge syndrome critical region gene 5 (DGCR5) was found in multiple human cancers but its function in NSCLC is largely unknown. Reverse transcription quantitative polymerase chain reaction (RT‐qPCR) was conducted to explore DGCR5 expression level in NSCLC. Bioinformatic analyses were conducted to explore the targets of DGCR5. Cell counting kit‐8 assay, wound‐healing assay, and transwell invasion assay were performed to analyze functions of DGCR5. RT‐qPCR revealed that DGCR5 expression in NSCLC cells was significantly lower than in normal cell. DGCR5 overexpression suppresses NSCLC cell growth, migration, and invasion. Online algorithms found EPH receptor B6 (EPHB6) and DGCR5 contains same miR‐211‐5p binding region. The predicted connections were further validated by luciferase activity reporter assay. Recue experiments showed DGCR5 regulates NSCLC cell behaviors via targeting miR‐211‐5p/EPHB6. These findings collectively identified DGCR5/miR‐211‐5p/EPHB6 triple axis in NSCLC, which may novel understanding regarding the tumorigenesis of NSCLC.

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“…This ceRNA network was visualized using Cytoscape software (Version 3.6.0). [18] In this network, nodes and edges represented biological data in a direct manner in which each node represented a biological molecule, and the edges represented interactions between nodes. [19] LncRNAs, mRNAs, and miRNAs in the ceRNA network were presented as blue diamonds, green ellipses, and red triangles, respectively.…”

Section: Construction Of the Lncrna-mediated Cerna Networkmentioning

confidence: 99%

Identification of lncRNA–miRNA–mRNA regulatory network associated with Primary Open Angle Glaucoma

Zhou

Tan

et al. 2020

Preprint

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Background Primary open angle glaucoma (POAG) is a complicated disorder characterized by a progressive permanent degeneration of retinal ganglion cell (RGCs) death. An increasing number of studies have suggested that long noncoding RNAs (lncRNAs) have the ability to regulate gene expression; however, thus far, the mechanisms and functions of lncRNAs in the development of POAG are still unclear. Methods Using the data from Gene Expression Omnibus (GEO), differentially expressed lncRNAs and differentially expressed mRNAs between POAG patients and controls were identified. Then, the lncRNA–miRNA–mRNA competing endogenous RNA (ceRNA) network was constructed, and the key lncRNAs in POAG were identified. A Gene Ontology (GO) analysis and a Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed to assess the enriched biological functions of mRNA in the ceRNA network. Results During this study, a POAG-related ceRNA network with 37 miRNA nodes, 248 lncRNA nodes, 178 mRNA nodes, and 1985 edges was constructed. In addition, four lncRNAs (DNAJC27-AS1, AF121898, OIP5-AS1, and SNX29P2) were established as hub RNAs in this ceRNA network. The functional assay showed that 18 GO terms and 17 pathways were enriched. Conclusion This study provides novel insights into the lncRNA-related ceRNA network in POAG, and the four lncRNAs were identified in the development of POAG.

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Characterization of lncRNA–miRNA–mRNA Network to Reveal Potential Functional ceRNAs in Bovine Skeletal Muscle

Cited by 43 publications

References 63 publications

Genome-wide identification and characterisation of long non-coding RNAs in two Chinese cattle breeds

Genome-wide identification and characterisation of long non-coding RNAs in two Chinese cattle breeds

LncRNA DGCR5 regulates the non‐small cell lung cancer cell growth, migration, and invasion through regulating miR‐211‐5p/EPHB6 axis

Identification of lncRNA–miRNA–mRNA regulatory network associated with Primary Open Angle Glaucoma

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