scholarly journals Circular RNA Expression Profiles and Features in NAFLD Mice: A Study Using RNA-Seq Data

2020 ◽  
Author(s):  
Xinlu Yuan ◽  
Jianjun Diao ◽  
Anqing Du ◽  
Song Wen ◽  
Ligang Zhou ◽  
...  
Keyword(s):  
Expression Profile ◽  
Noncoding Rna ◽  
Expression Profiles ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Mice Model ◽  
Specific Expression ◽  
Nonalcoholic Fatty Liver ◽  
Sequencing Method

Abstract Background: Nonalcoholic fatty liver disease (NAFLD) is primarily characterized by the hepatic cholesterol accumulation. Circular RNA (circRNA), one of noncoding RNA, involves in many liver diseases progression. However, no recent studies on circRNA expression profiles in NAFLD have been reported previously.Methods: A NAFLD mouse model was constructed by providing high-fat diet (HFD) for 32 weeks. The circRNAs expression profile in normal mice and NAFLD mice were determined using high-output RNA sequencing method and bioinformatics methods, while the differentially expressed circRNAs were confirmed using Sanger sequencing and qRT-PCR. The circRNA-miRNA network was also predicted. The biological functions of circRNAs were annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG).Results: The results demonstrated the successful construction of NAFLD mice model by immunohistology and serology assay. In total, 93 dysregulated circRNAs were observed, including 57 upregulated circRNAs and 36 downregulated circRNAs, in the NAFLD group. The circRNA-miRNA network revealed the complex interaction between circRNAs and its potential miRNA targets in NAFLD. The characteristic of tissue-specific expression in circRNA was demonstrated. The differentially expressed circRNAs with important biological function were also annotated using GO and KEGG. Both DDAH1 and VAV3 genes were found to be associated with the NAFLD development.Conclusions: Taken together, this study demonstrated the circRNAs expression profile and features in NAFLD, which may provide potential biological markers for the pathogenesis of NAFLD.

scholarly journals Circular RNA expression profiles and features in NAFLD mice: a study using RNA-seq data

2020 ◽  
Author(s):  
Xinlu Yuan ◽  
Jianjun Diao ◽  
Anqing Du ◽  
Song Wen ◽  
Ligang Zhou ◽  
...  
Keyword(s):  
Expression Profile ◽  
Noncoding Rna ◽  
Expression Profiles ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Mice Model ◽  
Specific Expression ◽  
Nonalcoholic Fatty Liver ◽  
Sequencing Method

Abstract Background: Nonalcoholic fatty liver disease (NAFLD) is primarily characterized by the hepatic cholesterol accumulation. Circular RNA (circRNA), one of noncoding RNA, involves in many liver diseases progression. However, no recent studies on circRNA expression profiles in NAFLD have been reported previously. Methods: A NAFLD mouse model was constructed by providing high-fat diet (HFD) for 32 weeks. The circRNAs expression profile in normal mice and NAFLD mice were determined using high-output RNA sequencing method and bioinformatics methods, while the differentially expressed circRNAs were confirmed using Sanger sequencing and qRT-PCR. The circRNA-miRNA network was also predicted. The biological functions of circRNAs were annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Results: The results demonstrated the successful construction of NAFLD mice model by immunohistology and serology assay. In total, 93 dysregulated circRNAs were observed, including 57 upregulated circRNAs and 36 downregulated circRNAs, in the NAFLD group. The circRNA-miRNA network revealed the complex interaction between circRNAs and its potential miRNA targets in NAFLD. The characteristic of tissue-specific expression in circRNA was demonstrated. The differentially expressed circRNAs with important biological function were also annotated using GO and KEGG. Both DDAH1 and VAV3 genes were found to be associated with the NAFLD development. Conclusions: Taken together, this study demonstrated the circRNAs expression profile and features in NAFLD, which may provide potential biological markers for the pathogenesis of NAFLD.

scholarly journals Circular RNA expression profiles and features in NAFLD mice: a study using RNA-seq data

2020 ◽  
Vol 18 (1) ◽  
Author(s):  
Xinlu Yuan ◽  
Jianjun Diao ◽  
Anqing Du ◽  
Song Wen ◽  
Ligang Zhou ◽  
...  
Keyword(s):  
Expression Profile ◽  
Noncoding Rna ◽  
Expression Profiles ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Mice Model ◽  
Specific Expression ◽  
Nonalcoholic Fatty Liver ◽  
Sequencing Method

Abstract Background Nonalcoholic fatty liver disease (NAFLD) is primarily characterized by the hepatic cholesterol accumulation. Circular RNA (circRNA), one of noncoding RNA, involves in many liver diseases progression. However, no recent studies on circRNA expression profiles in NAFLD have been reported previously. Methods A NAFLD mouse model was constructed by providing high-fat diet (HFD) for 32 weeks. The circRNAs expression profile in normal mice and NAFLD mice were determined using high-output RNA sequencing method and bioinformatics methods, while the differentially expressed circRNAs were confirmed using Sanger sequencing and qRT-PCR. The circRNA-miRNA network was also predicted. The biological functions of circRNAs were annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Results The results demonstrated the successful construction of NAFLD mice model by immunohistology and serology assay. In total, 93 dysregulated circRNAs were observed, including 57 upregulated circRNAs and 36 downregulated circRNAs, in the NAFLD group. The circRNA-miRNA network revealed the complex interaction between circRNAs and its potential miRNA targets in NAFLD. The characteristic of tissue-specific expression in circRNA was demonstrated. The differentially expressed circRNAs with important biological function were also annotated using GO and KEGG. Both DDAH1 and VAV3 genes were found to be associated with the NAFLD development. Conclusions Taken together, this study demonstrated the circRNAs expression profile and features in NAFLD, which may provide potential biological markers for the pathogenesis of NAFLD.

scholarly journals Long noncoding RNA expression profile of mouse cementoblasts under compressive force

2019 ◽  
Vol 89 (3) ◽  
pp. 455-463 ◽  
Author(s):  
Hao Liu ◽  
Yiping Huang ◽  
Yingying Zhang ◽  
Yineng Han ◽  
Yixin Zhang ◽  
...  
Keyword(s):  
Expression Profile ◽  
Long Noncoding Rna ◽  
Functional Annotation ◽  
Noncoding Rna ◽  
Compressive Loading ◽  
Compressive Force ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Lncrna Expression ◽  
Qrt Pcr

ABSTRACT Objectives: To investigate the long noncoding RNA (lncRNA) expression profile of cementoblasts under compressive force. Materials and Methods: Mouse cementoblasts were exposed to compression (1.5 g/cm2) for 8 hours. RNA sequencing (RNA-seq) was performed to compare the transcriptomes of the compressed and control cells. Quantitative real-time polymerase chain reaction (qRT-PCR) was used to validate five of the differentially expressed lncRNAs of interest. Gene Ontology (GO) functional annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were also performed. Results: A total of 70 lncRNAs and 521 mRNAs were differentially regulated in cementoblasts subjected to compressive loading. Among the differentially expressed lncRNAs, 57 were upregulated and 13 downregulated. The expression levels of the five selected lncRNAs (Prkcz2, Hklos, Trp53cor1, Gdap10, and Ak312-ps) were validated by qRT-PCR and consistent with the RNA-seq results. GO functional annotation demonstrated upregulation of genes associated with cellular response to hypoxia and apoptotic processes during compressive loading. KEGG analysis identified the crucial pathways involving the hypoxia-inducing factor-1α, forkhead box O, and mammalian target of rapamycin signaling pathways. Conclusions: Mechanical compression changes the lncRNA expression profile of cementoblasts, providing important references for further investigation into the role and regulation of lncRNAs in compressed cementoblasts and root resorption during orthodontic treatment.

scholarly journals Comprehensive Expression Profiling Analysis of Pituitary Indicates that circRNA Participates in the Regulation of Sheep Estrus

Genes ◽  
2019 ◽  
Vol 10 (2) ◽  
pp. 90 ◽  
Author(s):  
Xiaoyue Li ◽  
Cunyuan Li ◽  
Junchang Wei ◽  
Wei Ni ◽  
Yueren Xu ◽  
...  
Keyword(s):  
Expression Profiles ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Rna Seq ◽  
Endocrine Organ ◽  
Reverse Transcription Quantitative Pcr ◽  
Significant Difference ◽  
Profiling Analysis

The pituitary gland is the most important endocrine organ that mainly regulates animal estrus by controlling the hormones synthesis. There is a significant difference between the estrus state and anestrus state of sheep pituitary system. Here, we studied the circular RNA (circRNA) expression profiles of the anterior pituitary of estrus and anestrus sheep using RNA-seq technology. Through this study, we identified a total of 12,468 circRNAs and 9,231 differentially expressed circRNAs in the estrus and anestrus pituitary system of sheep. We analyzed some differentially expressed circRNAs by reverse transcription quantitative-PCR (RT-qPCR), and some circRNAs were demonstrated using RNase-R+ resistance experiments. CircRNAs involving the regulation of estrus-related terms and pathways are enriched by using gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. In addition, we also predicted partial microRNA-circRNA interaction network for circRNAs that regulate sheep estrus. Overall, this study explored a potential substantial role played by circRNAs involved in pituitary regulation on sheep estrus and proposed new questions for further study.

scholarly journals Identification of Circular RNA-MicroRNA-Messenger RNA Regulatory Network in Atrial Fibrillation by Integrated Analysis

2020 ◽  
Vol 2020 ◽  
pp. 1-13
Author(s):  
Tao Liu ◽  
Guoru Zhang ◽  
Yaling Wang ◽  
Mingyue Rao ◽  
Yang Zhang ◽  
...  
Keyword(s):  
Atrial Fibrillation ◽  
Regulatory Network ◽  
Messenger Rna ◽  
Noncoding Rna ◽  
Expression Profiles ◽  
Arrhythmogenic Right Ventricular Cardiomyopathy ◽  
Circular Rna ◽  
Host Gene ◽  
Differentially Expressed ◽  
Integrated Analysis

Background. Circular RNA (circRNA) is a noncoding RNA that forms a closed-loop structure, and its abnormal expression may cause disease. We aimed to find potential network for circRNA-related competitive endogenous RNA (ceRNA) in atrial fibrillation (AF). Methods. The circRNA, miRNA, and mRNA expression profiles in the heart tissue from AF patients were retrieved from the Gene Expression Omnibus database and analyzed comprehensively. Differentially expressed circRNAs (DEcircRNAs), differentially expressed miRNAs (DEmiRNAs), and differentially expressed mRNAs (DEmRNAs) were identified, followed by the establishment of DEcircRNA-DEmiRNA-DEmRNA regulatory network. Functional annotation analysis of host gene of DEcircRNAs and DEmRNAs in ceRNA regulatory network was performed. In vitro experiment and electronic validation were used to validate the expression of DEcircRNAs, DEmiRNAs, and DEmRNAs. Results. A total of 1611 DEcircRNAs, 51 DEmiRNAs, and 1250 DEmRNAs were identified in AF. The DEcircRNA-DEmiRNA-DEmRNA network contained 62 circRNAs, 14 miRNAs, and 728 mRNAs. Among which, two ceRNA regulatory pairs of hsa-circRNA-100053-hsa-miR-455-5p-TRPV1 and hsa-circRNA-005843-hsa-miR-188-5p-SPON1 were identified. In addition, six miRNA-mRNA regulatory pairs including hsa-miR-34c-5p-INMT, hsa-miR-1253-DDIT4L, hsa-miR-508-5p-SMOC2, hsa-miR-943-ACTA1, hsa-miR-338-3p-WIPI1, and hsa-miR-199a-3p-RAP1GAP2 were also obtained. MTOR was a significantly enriched signaling pathway of host gene of DEcircRNAs. In addition, arrhythmogenic right ventricular cardiomyopathy, dilated cardiomyopathy, and hypertrophic cardiomyopathy were remarkably enriched signaling pathways of DEmRNAs in DEcircRNA-DEmiRNA-DEmRNA regulatory network. The expression validation of hsa-circRNA-402565, hsa-miR-34c-5p, hsa-miR-188-5p, SPON1, DDIT4L, SMOC2, and WIPI1 was consistent with the integrated analysis. Conclusion. We speculated that hsa-circRNA-100053-hsa-miR-455-5p-TRPV1 and hsa-circRNA-005843-hsa-miR-188-5p-SPON1 interaction pairs may be involved in AF.

scholarly journals Comprehensive circular RNA expression profiles in intermuscular fat from lean and obese pigs

2019 ◽  
Author(s):  
Zhiguo Miao ◽  
Jinzhou Zhang ◽  
Shan Wang ◽  
Paneng Wei
Keyword(s):  
Expression Profile ◽  
High Throughput Sequencing ◽  
Target Genes ◽  
Expression Profiles ◽  
Circular Rna ◽  
Differentially Expressed ◽  
Real Time Quantitative Pcr ◽  
Significant Difference ◽  
Intermuscular Fat ◽  
Fattening Period

AbstractCircular RNA (circRNA) plays an important regulatory role in development and differentiation. Intermuscular fat in pork affects the tenderness and juiciness of the meat. In this study, we investigated the performances of Landrace (lean) and Jinhua (obese) pigs at the fattening period and explored the expression profile of circRNAs in intermuscular fat from the two breeds by Illumina high-throughput sequencing. we identified 5 548 circRNAs, specifically 2 651 (47.78%) in the Jinhua pigs, and 2 897 (52.22%) in the Landrace pigs. A totale of 809 differentially expressed circRNAs were observed between the the Jinhua and Landrace pigs, but only 29 of these circRNAs showed significant difference (19 upregulated and 10 downregulated). All 1 306 unigenes and 27 differentially expressed unigenesinvolved in lipid transport and metabolism; replication, recombination and repair; and signaling pathway were annotated. A total of 550 target miRNAs were perfect seed matches and 20 522 target genes were foundBy RNAhybrid and miRanda software prediction. Results from real-time quantitative PCR also confirmed the differential expression of 13 mRNAs between the two pig breeds. This study provides comprehensive expression profiles of circRNAs in Sus scrofa adipose metabolism and development, which can be used to clarify their functions.Summary statementThe paper explored the expression profile of circRNAs in intermuscular fat from Landrace and Jinhua pigs at the fattening period, to provide insights into circRNAregulation in animal adipose metabolism.

scholarly journals Long Noncoding RNA and Circular RNA Expression Profiles of Monocyte-Derived Dendritic Cells in Autoimmune Hepatitis

2021 ◽  
Vol 12 ◽  
Author(s):  
Fan Yang ◽  
Xiaoli Fan ◽  
Yifeng Liu ◽  
Yi Shen ◽  
Shenglan Zhao ◽  
...  
Keyword(s):  
Dendritic Cells ◽  
Autoimmune Hepatitis ◽  
Peripheral Blood ◽  
Noncoding Rna ◽  
Cell Function ◽  
Expression Profiles ◽  
Circular Rna ◽  
Circular Rnas ◽  
Rna Seq ◽  
Pathway Analyses

Autoimmune hepatitis (AIH) is a chronic liver disease caused by disruption of liver immune homeostasis. The effect of dendritic cells (DCs) on the pathogenesis of AIH is not fully understood. Long noncoding RNAs (lncRNAs), circular RNAs (circRNAs), and microRNAs (miRNAs) have been shown to play critical roles in the regulation of cell function. In this study, we analyzed the immunophenotypic characteristics of DCs in the peripheral blood. The percentage of mature DCs was higher in AIH patients than in healthy controls (HCs), and the proportion of mature DCs decreased after treatment. We isolated monocyte-derived DCs (moDCs) from the peripheral blood, obtained whole RNA-sequencing (RNA-seq) data for the moDCs from the two groups, and identified differentially expressed (DE) lncRNAs, circRNAs, miRNAs and mRNAs. In addition, we performed Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses for the DE mRNAs and constructed competing endogenous RNA (ceRNA) networks. ENST00000543334, hsa_circ_0000279, and hsa_circ_0005076 were selected and validated by RT-qPCR. These results provide a possible molecular mechanism of DCs in the pathogenesis of AIH and identify some potential therapeutic targets.

scholarly journals Cerebellar Long Noncoding RNA Expression Profile in a Niemann-Pick C Disease Mouse Model

2021 ◽  
Author(s):  
Shiqian Han ◽  
Meng Ren ◽  
Tianyin Kuang ◽  
Mao Pang ◽  
Dongwei Guan ◽  
...  
Keyword(s):  
Expression Profile ◽  
Noncoding Rna ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Rna Seq ◽  
Lysosomal Storage ◽  
Lncrna Expression ◽  
Type C ◽  
Niemann Pick

AbstractNiemann-Pick type C (NP-C) disease is a neurodegenerative lysosomal storage disorder primarily caused by mutations in NPC1. However, its pathogenesis remains poorly understood. While mounting evidence has demonstrated the involvement of long noncoding RNAs (lncRNAs) in the pathogenesis of neurodegenerative disorders, the lncRNA expression profile in NP-C has not been determined. Here, we used RNA-seq analysis to determine lncRNA and mRNA expression profiles of the cerebella of NPC1−/− mice. We found that 272 lncRNAs and 856 mRNAs were significantly dysregulated in NPC1−/− mice relative to controls (≥ 2.0-fold, p < 0.05). Quantitative real-time PCR (qRT‐PCR) was utilized to validate the expression of selected lncRNAs and mRNAs. Next, a lncRNA-mRNA coexpression network was employed to examine the potential roles of the differentially expressed (DE) lncRNAs. Functional analysis revealed that mRNAs coexpressed with lncRNAs are mainly linked to immune system–related processes and neuroinflammation. Moreover, knockdown of the lncRNA H19 ameliorated changes in ROS levels and cell viability and suppressed the lipopolysaccharide (LPS)–induced inflammatory response in vitro. Our findings indicate that dysregulated lncRNA expression patterns are associated with NP-C pathogenesis and offer insight into the development of novel therapeutics based on lncRNAs.

scholarly journals Comprehensive circRNA-microRNA-mRNA network analysis revealed the novel regulatory mechanism of Trichosporon asahii infection

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Ming-Wang Zhang ◽  
Zhi-Hong Zhu ◽  
Zhi-Kuan Xia ◽  
Xin Yang ◽  
Wan-Ting Luo ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Noncoding Rna ◽  
Expression Profiles ◽  
Differentially Expressed ◽  
Luciferase Reporter ◽  
Circular Rnas ◽  
Rna Seq ◽  
Trichosporon Asahii ◽  
Cerna Network ◽  
Pathway Analyses

Abstract Background Invasive Trichosporon asahii (T. asahii) infection frequently occurs with a high mortality in immunodeficient hosts, but the pathogenesis of T. asahii infection remains elusive. Circular RNAs (circRNAs) are a type of endogenous noncoding RNA that participate in various disease processes. However, the mechanism of circRNAs in T. asahii infection remains completely unknown. Methods RNA sequencing (RNA-seq) was performed to analyze the expression profiles of circRNAs, microRNAs (miRNAs), and mRNAs in THP-1 cells infected with T. asahii or uninfected samples. Some of the RNA-seq results were verified by RT-qPCR. Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were used to analyze the differentially expressed mRNAs. A circRNA-miRNA-mRNA network was constructed and verified by dual-luciferase reporter assay and overexpression experiments. Results A total of 46 circRNAs, 412 mRNAs and 47 miRNAs were differentially expressed at 12 h after T. asahii infection. GO and KEGG analyses showed that the differentially expressed mRNAs were primarily linked to the leukocyte migration involved in the inflammatory response, the Toll-like receptor signaling pathway, and the TNF signaling pathway. A competing endogenous RNA (ceRNA) network was constructed with 5 differentially expressed circRNAs, 5 differentially expressed miRNAs and 42 differentially expressed mRNAs. Among them, hsa_circ_0065336 was found to indirectly regulate PTPN11 expression by sponging miR-505-3p. Conclusions These data revealed a comprehensive circRNA-associated ceRNA network during T. asahii infection, thus providing new insights into the pathogenesis of the T. asahii-host interactions.

Genome-Wide Identification of differently expressed lncRNAs, mRNAs, and circRNAs in patients with osteoarthritis

2020 ◽  
Vol 15 ◽  
Author(s):  
Yeqing Sun ◽  
Lei Chen ◽  
Yingqi Zhang ◽  
Jincheng Zhang ◽  
Shashi Ranjan Tiwari
Keyword(s):  
Regulatory Networks ◽  
Expression Profiles ◽  
Interleukin 1 ◽  
Interaction Network ◽  
Circular Rna ◽  
Negative Regulation ◽  
Differentially Expressed ◽  
Positive Regulation ◽  
Proteinprotein Interaction ◽  
Differently Expressed Genes

Background: Osteoarthritis (OA), one of the most important causes leading to joint disability, was considered as an untreatable disease. A series of genes were reported to regulate the pathogenesis of OA, including microRNAs, Long non-coding RNAs and Circular RNA. So far, the expression profiles and functions of lncRNAs, mRNAs, and circRNAs in OA are not fully understood. Objective: The present study aimed to identify differently expressed genes in OA. Methods: The present study conducted RNA-seq to identify differently expressed genes in OA. Ontology (GO) analysis was used to analysis the Molecular Function and Biological Process. KEGG pathway analysis was used to perform the differentially expressed lncRNAs in biological pathways. Results: Hierarchical clustering revealed a total of 943 mRNAs, 518 lncRNAs, and 300 circRNAs were dysregulated in OA compared to normal samples. Furthermore, we constructed differentially expressed mRNAs mediated proteinprotein interaction network, differentially expressed lncRNAs mediated trans regulatory networks, and competitive endogenous RNA (ceRNA) to reveal the interaction among these genes in OA. Bioinformatics analysis revealed these dysregulated genes were involved in regulating multiple biological processes, such as wound healing, negative regulation of ossification, sister chromatid cohesion, positive regulation of interleukin-1 alpha production, sodium ion transmembrane transport, positive regulation of cell migration, and negative regulation of inflammatory response. To the best of our knowledge, this study for the first time revealed the expression pattern of mRNAs, lncRNAs and circRNAs in OA. Conclusion: This study provided novel information to validate these differentially expressed RNAs may be as possible biomarkers and targets in OA.

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