Co-expression network analysis revealing the potential regulatory roles of lncRNAs in atrial fibrillation

2019 ◽  
Vol 14 ◽  
Author(s):  
Lishui Shen ◽  
Guilin Shen ◽  
Xiaoli Lu ◽  
Guomin Ding ◽  
Xiaofeng Hu
Keyword(s):  
Atrial Fibrillation ◽  
Differentially Expressed ◽  
Biological Processes ◽  
Bioinformatics Analyses ◽  
The Public ◽  
Kegg Pathway Analysis ◽  
Novel Biomarkers ◽  
Non Coding Rnas ◽  
Public Datasets ◽  
Insight Into

Atrial fibrillation (AF) is one of the most common heart arrhythmic disorders all over the world. However, it is worth noting that the mechanism underlying AF is still dimness. In this study, we implemented a series of bioinformatics methods to explore the mechanisms of lncRNAs underlying AF pathogenesis. The present study analyzed the public datasets (GSE2240 and GSE115574) to identify differentially expressed long non-coding RNAs (lncRNAs) and mRNAs in the progression of AF. Totally, 71 differentially expressed lncRNAs and 390 DEGs were identified in AF.Next, we performed bioinformatics analyses to explore the functions of lncRNAs in AF. Gene Ontology (GO) analysis indicated that differentially expressed lncRNAs were involved in regulating multiple key biological processes, such as cell cycle and signal transduction. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated these lncRNAs were associated with the regulation of MAPK and Wnt signaling pathways. Eight lncRNAs (RP5-1154L15.2, RP11-339B21.15, RP11-448A19.1, RP11-676J12.4, LOC101930415, MALAT1, NEAT1, and PWAR6) were identified to be key lncRNAs and widely co-expressed with a series of differentially expressed genes (DEGs). Although further validation was still needed, our study may be helpful to elucidate the mechanisms of lncRNAs underlying AF pathogenesis and providing further insight into identifying novel biomarkers for AF.

scholarly journals Transcriptome analysis reveals potential function of long non-coding RNAs in 20-hydroxyecdysone regulated autophagy in Bombyx mori

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Huili Qiao ◽  
Jingya Wang ◽  
Yuanzhuo Wang ◽  
Juanjuan Yang ◽  
Bofan Wei ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Target Gene ◽  
Fat Body ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Differentially Expressed ◽  
Post Injection ◽  
Biological Processes ◽  
Potential Target ◽  
Non Coding Rnas

Abstract Background 20-hydroxyecdysone (20E) plays important roles in insect molting and metamorphosis. 20E-induced autophagy has been detected during the larval–pupal transition in different insects. In Bombyx mori, autophagy is induced by 20E in the larval fat body. Long non-coding RNAs (lncRNAs) function in various biological processes in many organisms, including insects. Many lncRNAs have been reported to be potential for autophagy occurrence in mammals, but it has not been investigated in insects. Results RNA libraries from the fat body of B. mori dissected at 2 and 6 h post-injection with 20E were constructed and sequenced, and comprehensive analysis of lncRNAs and mRNAs was performed. A total of 1035 lncRNAs were identified, including 905 lincRNAs and 130 antisense lncRNAs. Compared with mRNAs, lncRNAs had longer transcript length and fewer exons. 132 lncRNAs were found differentially expressed at 2 h post injection, compared with 64 lncRNAs at 6 h post injection. Thirty differentially expressed lncRNAs were common at 2 and 6 h post-injection, and were hypothesized to be associated with the 20E response. Target gene analysis predicted 6493 lncRNA-mRNA cis pairs and 42,797 lncRNA-mRNA trans pairs. The expression profiles of LNC_000560 were highly consistent with its potential target genes, Atg4B, and RNAi of LNC_000560 significantly decreased the expression of LNC_000560 and Atg4B. These results indicated that LNC_000560 was potentially involved in the 20E-induced autophagy of the fat body by regulating Atg4B. Conclusions This study provides the genome-wide identification and functional characterization of lncRNAs associated with 20E-induced autophagy in the fat body of B. mori. LNC_000560 and its potential target gene were identified to be related to 20-regulated autophagy in B. mori. These results will be helpful for further studying the regulatory mechanisms of lncRNAs in autophagy and other biological processes in this insect model.

scholarly journals Long non-coding RNAs as pan-cancer master gene regulators of associated protein-coding genes: a systems biology approach

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6388 ◽  
Author(s):  
Asanigari Saleembhasha ◽  
Seema Mishra
Keyword(s):  
Gene Expression ◽  
Gene Expression Pattern ◽  
Differentially Expressed ◽  
Regulation Of Transcription ◽  
Biological Processes ◽  
Lncrna Gene ◽  
Cancer Types ◽  
Non Coding Rnas ◽  
Rna Interaction ◽  
Pan Cancer

Despite years of research, we are still unraveling crucial stages of gene expression regulation in cancer. On the basis of major biological hallmarks, we hypothesized that there must be a uniform gene expression pattern and regulation across cancer types. Among non-coding genes, long non-coding RNAs (lncRNAs) are emerging as key gene regulators playing powerful roles in cancer. Using TCGA RNAseq data, we analyzed coding (mRNA) and non-coding (lncRNA) gene expression across 15 and 9 common cancer types, respectively. 70 significantly differentially expressed genes common to all 15 cancer types were enlisted. Correlating with protein expression levels from Human Protein Atlas, we observed 34 positively correlated gene sets which are enriched in gene expression, transcription from RNA Pol-II, regulation of transcription and mitotic cell cycle biological processes. Further, 24 lncRNAs were among common significantly differentially expressed non-coding genes. Using guilt-by-association method, we predicted lncRNAs to be involved in same biological processes. Combining RNA-RNA interaction prediction and transcription regulatory networks, we identified E2F1, FOXM1 and PVT1 regulatory path as recurring pan-cancer regulatory entity. PVT1 is predicted to interact with SYNE1 at 3′-UTR; DNAJC9, RNPS1 at 5′-UTR and ATXN2L, ALAD, FOXM1 and IRAK1 at CDS sites. The key findings are that through E2F1, FOXM1 and PVT1 regulatory axis and possible interactions with different coding genes, PVT1 may be playing a prominent role in pan-cancer development and progression.

scholarly journals Global Analyses of Expressed Piwi-Interacting RNAs in Gastric Cancer

2020 ◽  
Vol 21 (20) ◽  
pp. 7656
Author(s):  
Tatiana Vinasco-Sandoval ◽  
Fabiano Cordeiro Moreira ◽  
Amanda F. Vidal ◽  
Pablo Pinto ◽  
André M. Ribeiro-dos-Santos ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Gastric Carcinogenesis ◽  
Differentially Expressed ◽  
Small Rna Sequencing ◽  
Non Coding Rnas ◽  
Risk Biomarkers ◽  
Gastric Cancer Patients ◽  
Early Diagnose ◽  
Cancer Tissues ◽  
Insight Into

Gastric cancer (GC) represents a notable amount of morbidity and mortality worldwide. Understanding the molecular basis of CG will offer insight into its pathogenesis in an attempt to identify new molecular biomarkers to early diagnose this disease. Therefore, studies involving small non-coding RNAs have been widely explored. Among these, PIWI-interacting RNAs (piRNAs) are an emergent class that can play important roles in carcinogenesis. In this study, small-RNA sequencing was used to identify the global piRNAs expression profile (piRNome) of gastric cancer patients. We found 698 piRNAs in gastric tissues, 14 of which were differentially expressed (DE) between gastric cancer (GC), adjacent to gastric cancer (ADJ), and non-cancer tissues (NC). Moreover, three of these DE piRNAs (piR-48966*, piR-49145, piR-31335*) were differently expressed in both GC and ADJ samples in comparison to NC samples, indicating that the tumor-adjacent tissue was molecularly altered and should not be considered as a normal control. These three piRNAs are potential risk biomarkers for GC, especially piR-48966* and piR-31335*. Furthermore, an in-silico search for mRNAs targeted by the differentially expressed piRNAs revealed that these piRNAs may regulate genes that participate in cancer-related pathways, suggesting that these small non-coding RNAs may be directly and indirectly involved in gastric carcinogenesis.

scholarly journals Genome-wide analysis of tomato long non-coding RNAs and identification as endogenous target mimic for microRNA in response to TYLCV infection

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Jinyan Wang ◽  
Wengui Yu ◽  
Yuwen Yang ◽  
Xiao Li ◽  
Tianzi Chen ◽  
...  
Keyword(s):  
Post Inoculation ◽  
Biological Processes ◽  
Virus Induced Gene Silencing ◽  
Dna Virus ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Non Coding Rnas ◽  
Endogenous Target ◽  
Leaf Curl Virus ◽  
Insight Into

Abstract Recently, a large number of long noncoding RNAs (lncRNAs) have emerged as important regulators of many biological processes in animals and plants. However, how lncRNAs function during plant DNA virus infection is largely unknown. We performed strand-specific paired-end RNA sequencing of tomato samples infected with Tomato yellow leaf curl virus (TYLCV) with three biological replicates. Overall, we predicted 1565 lncRNAs including long intergenic ncRNAs (lincRNAs) and natural antisense transcripts (lncNATs) and definitively identified lnRNAs that are involved in TYLCV infection by virus-induced gene silencing (VIGS). We also verified the functions of a set of lncRNAs that were differentially expressed between 0 and 7 days post inoculation (dpi). More importantly, we found that several lncRNAs acted as competing endogenous target mimics (eTMs) for tomato microRNAs involved in the TYLCV infection. These results provide new insight into lncRNAs involved in the response to TYLCV infection that are important components of the TYLCV network in tomatoes.

scholarly journals Identification of differentially expressed microRNAs under imidacloprid exposure in Sitobion avenae Fabricius

2020 ◽  
Author(s):  
Baizhong Zhang ◽  
Shouping Zhang ◽  
Xu Su ◽  
Lanfen Xie ◽  
Wen-Yang Dong ◽  
...  
Keyword(s):  
Target Genes ◽  
De Novo ◽  
Sitobion Avenae ◽  
Differentially Expressed ◽  
Control Analysis ◽  
Sequencing Technology ◽  
Short Read Sequencing ◽  
Kegg Pathway Analysis ◽  
Candidate Target ◽  
Non Coding Rnas

Abstract Background: MicroRNAs (miRNAs), which are short single-stranded non-coding RNAs, regulate the expression of target genes, especially those involved in the regulation or metabolism of endogenous or xenobiotic compounds. Results: De novo assemblies of the transcriptome of Sitobion avenae Fabricius under control conditions and under imidacloprid treatment were obtained using Illumina short-read sequencing technology. Fifty-seven miRNAs, of which 36 were known and 21 were novel, were identified. Quantitative analysis of miRNA levels showed that 5 miRNAs were significantly up-regulated, and 11 miRNAs were significantly down-regulated in the nymphs of S. avenae treated with imidacloprid in comparison with those of the control. Analysis of the candidate target genes in S. avenae that could be regulated by these miRNAs were also carried out. The functions of the miRNAs, which could potentially regulate target genes that participate in metabolism, regulatory or detoxification pathways in S. avenae, were clarified based on Gene Ontology and KEGG pathway analysis. The effects of the miRNAs api-miR-1000, api-miR-316, and api-miR-iab-4 on susceptibility of S. avenae to imidacloprid was determined. Modulation of the abundances of api-miR-1000, api-miR-316, and api-miR-iab-4 by the addition of the correspondign inhibitors to the artificial diet significantly changed the susceptibility of S. avenae to imidacloprid, which further demonstrated the effect of these miRNAs on the regulation or metabolism of insecticides.Conclusion: The results of this study suggested that miRNAs differentially expressed in response to imidacloprid could play a critical regulatory role in the resistance of S. avenae to imidacloprid.

scholarly journals Genome-Wide Identification of Long Non-coding RNAs Responsive to Lasiodiplodia theobromae Infection in Grapevine

2019 ◽  
Vol 15 ◽  
pp. 117693431984136 ◽  
Author(s):  
Qikai Xing ◽  
Wei Zhang ◽  
Mei Liu ◽  
Lingxian Li ◽  
Xinghong Li ◽  
...  
Keyword(s):  
Biological Processes ◽  
Rna Seq ◽  
Lasiodiplodia Theobromae ◽  
Rna Molecules ◽  
Grapevine Trunk Diseases ◽  
Genome Wide ◽  
Botryosphaeria Dieback ◽  
Trunk Diseases ◽  
Non Coding Rnas ◽  
Insight Into

Long non-coding RNAs (lncRNAs) refer to a class of RNA molecules that are longer than 200 nucleotides and do not encode proteins. Numerous lncRNAs have recently emerged as important regulators of many biological processes in animals and plants, including responses to environmental stress and pathogens. Botryosphaeria dieback is one of the more severe grapevine trunk diseases worldwide. However, how lncRNAs function during Botryosphaeriaceae infection is largely unknown. We performed high-throughput RNA-sequencing (RNA-seq) of susceptible and more tolerant grapevine cultivars infected with Lasiodiplodia theobromae. Overall, we predicted 1826 novel candidate lncRNAs, including long intergenic non-coding RNAs (lincRNAs) and natural antisense transcripts (lncNATs). The data reveal the functions of a set of lncRNAs that were differentially expressed between the resistant cultivar Merlot and the susceptible cultivar Cabernet Franc. Several lncRNAs were predicted to be precursors for grape microRNAs involved in the L theobromae infection. These results provide new insight into the lncRNAs of grapevine that are involved in the response to L theobromae infection.

scholarly journals Integrated Genome-Wide Methylation and Expression Analyses Reveal Key Regulators in Osteosarcoma

2020 ◽  
Vol 2020 ◽  
pp. 1-11
Author(s):  
Fei Wang ◽  
Guoqing Qin ◽  
Junzhi Liu ◽  
Xiunan Wang ◽  
Baoguo Ye
Keyword(s):  
Molecular Mechanisms ◽  
Biological Processes ◽  
Free Survival ◽  
Primary Bone Tumors ◽  
Kegg Pathway Analysis ◽  
Genome Wide ◽  
Tumorigenesis And Progression ◽  
Novel Biomarkers ◽  
Primary Bone ◽  
Aberrant Dna Methylation

Osteosarcoma (OS) is one of the most common types of primary bone tumors in early adolescence with unsatisfied prognosis. Aberrant DNA methylation had been demonstrated to be related to tumorigenesis and progression of multiple cancers and could serve as the potential biomarkers for the prognosis of human cancers. In conclusion, this study identified 18 downregulated hypomethylation genes and 52 upregulated hypomethylation genes in OS by integrating the analysis the GSE97529 and GSE42572 datasets. Bioinformatics analysis revealed that OS-specific methylated genes were involved in regulating multiple biological processes, including chemical synaptic transmission, transcription, response to drug, and regulating immune response. KEGG pathway analysis showed that OS-specific methylated genes were associated with the regulation of Hippo, cAMP calcium, MAPK, and Wnt signaling pathways. By analyzing R2 datasets, this study showed that the dysregulation of these OS-specific methylated genes was associated with the metastasis-free survival time in patients with OS, including CBLN4, ANKMY1, BZW1, KRTCAP3, GZMB, KRTDAP, LY9, PFKFB2, PTPN22, and CLDN7. This study provided a better understanding of the molecular mechanisms underlying the progression and OS and novel biomarkers for the prognosis of OS.

scholarly journals Identification of differentially expressed microRNAs under imidacloprid exposure in Sitobion avenae Fabricius

2019 ◽  
Author(s):  
Baizhong Zhang ◽  
Xu Su ◽  
Lanfen Xie ◽  
Wen-Yang Dong ◽  
Fan-Bin Kong ◽  
...  
Keyword(s):  
Target Genes ◽  
De Novo ◽  
Sitobion Avenae ◽  
Differentially Expressed ◽  
Control Analysis ◽  
Sequencing Technology ◽  
Short Read Sequencing ◽  
Kegg Pathway Analysis ◽  
Candidate Target ◽  
Non Coding Rnas

Abstract Background MicroRNAs (miRNAs), which are short single-stranded non-coding RNAs, regulate the expression of target genes, especially those involved in the regulation or metabolism of endogenous or xenobiotic compounds.Results De novo assemblies of the transcriptome of Sitobion avenae Fabricius under control conditions and under imidacloprid treatment were obtained using Illumina short-read sequencing technology. Fifty-seven miRNAs, of which 36 were known and 21 were novel, were identified. Quantitative analysis of miRNA levels showed that five miRNAs were significantly up-regulated, and 11 miRNAs were significantly down-regulated in the nymphs of S. avenae treated with imidacloprid in comparison with those of the control. Analysis of the candidate target genes in S. avenae that could be regulated by these miRNAs were also carried out. The functions of the miRNAs, which could potentially regulate target genes that participate in metabolism, regulatory or detoxification pathways in S. avenae , were clarified based on Gene Ontology and KEGG pathway analysis. The effects of the miRNAs api-miR-1000, api-miR-316, and api-miR-iab-4 on susceptibility of S. avenae to imidacloprid was determined. Modulation of the abundances of api-miR-1000, api-miR-316, and api-miR-iab-4 by the addition of the correspondign inhibitors to the artificial diet significantly changed the susceptibility of S. avenae to imidacloprid, which further demonstrated the effect of these miRNAs on the regulation or metabolism of insecticides.Conclusion The results of this study suggested that miRNAs differentially expressed in response to imidacloprid could play a critical regulatory role in the resistance of S. avenae to imidacloprid.

scholarly journals Transcriptome Analysis Reveals Potential Function of Long Non-coding RNAs in 20-hydroxyecdysone Regulated Autophagy in Bombyx Mori

2021 ◽  
Author(s):  
Huili Qiao ◽  
Jingya Wang ◽  
Yuanzhuo Wang ◽  
Juanjuan Yang ◽  
Bofan Wei ◽  
...  
Keyword(s):  
Bombyx Mori ◽  
Target Gene ◽  
Fat Body ◽  
Expression Profiles ◽  
Functional Characterization ◽  
Differentially Expressed ◽  
Post Injection ◽  
Biological Processes ◽  
Potential Target ◽  
Non Coding Rnas

Abstract Background: 20-hydroxyecdysone (20E) plays important roles in insect molting and metamorphosis. 20E-induced autophagy has been detected during the larval–pupal transition in different insects. In Bombyx mori, autophagy is induced by 20E in the larval fat body. Long non-coding RNAs (lncRNAs) function in various biological processes in many organisms, including insects. Many lncRNAs have been reported to be potential for autophagy occurrence in mammals, but it has not been investigated in insects. Results: RNA libraries from the fat body of B. mori dissected at 2 and 6 h post-injection with 20E were sequenced, and comprehensive analysis of lncRNAs and mRNAs was performed. A total of 1035 lncRNAs were identified, including 905 lincRNAs and 130 antisense lncRNAs. Compared with mRNAs, lncRNAs had longer transcript length and fewer exons. 132 lncRNAs were found differentially expressed at 2 h post injection, compared with 64 lncRNAs at 6 h post injection. Thirty differentially expressed lncRNAs were common at 2 and 6 h post-injection, and were hypothesized to be associated with the 20E response. Target gene analysis predicted 6493 lncRNA-mRNA cis pairs and 42797 lncRNA-mRNA trans pairs. The expression profiles of LNC_000560 were highly consistent with its potential target genes, Atg4B, and RNAi of LNC_000560 significantly decreased the expression of Atg4B. These results indicated that LNC_000560 was potentially involved in the 20E-induced autophagy of the fat body by regulating Atg4B. Conclusions: This study provides the genome-wide identification and functional characterization of lncRNAs associated with 20E-induced autophagy in the fat body of B. mori. LNC_000560 and its potential target gene were identified to be related to 20-regulated autophagy in B. mori. These results will be helpful for further studying the regulatory mechanisms of lncRNAs in autophagy and other biological processes in this insect model.

scholarly journals A global profile of glucose-sensitive endothelial-expressed long non-coding RNAs

2016 ◽  
Vol 94 (9) ◽  
pp. 1007-1014 ◽  
Author(s):  
Krishna K. Singh ◽  
Laura-Eve Mantella ◽  
Yi Pan ◽  
Adrian Quan ◽  
Sandra Sabongui ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Endothelial Dysfunction ◽  
High Glucose ◽  
Umbilical Vein ◽  
Vascular Complications ◽  
Differentially Expressed ◽  
Bioinformatics Analyses ◽  
Glucose Levels ◽  
Elevated Glucose ◽  
Non Coding Rnas

Hyperglycemia-related endothelial dysfunction is believed to be the crux of diabetes-associated micro- and macro-vascular complications. We conducted a systematic transcriptional survey to screen for human endothelial long non-coding RNAs (lncRNAs) regulated by elevated glucose levels. lncRNAs and protein-coding transcripts from human umbilical vein endothelial cells (HUVECs) cultured under high (25 mmol/L) or normal (5 mmol/L) glucose conditions for 24 h were profiled with the Arraystar Human LncRNA Expression Microarray V3.0. Of the 30 586 lncRNAs screened, 100 were significantly upregulated and 186 appreciably downregulated (P < 0.05) in response to high-glucose exposure. In the same HUVEC samples, 133 of the 26 109 mRNAs screened were upregulated and 166 downregulated. Of these 299 differentially expressed mRNAs, 26 were significantly associated with 28 differentially expressed long intergenic non-coding RNAs (P < 0.05). Bioinformatics analyses indicated that the mRNAs most upregulated are primarily enriched in axon guidance signaling pathways; those most downregulated are notably involved in pathways targeting vascular smooth muscle cell contraction, dopaminergic signaling, ubiquitin-mediated proteolysis, and adrenergic signaling. This is the first lncRNA and mRNA transcriptome profile of high-glucose-mediated changes in human endothelial cells. These observations may prove novel insights into novel regulatory molecules and pathways of hyperglycemia-related endothelial dysfunction and, accordingly, diabetes-associated vascular disease.

Sign in / Sign up

Export Citation Format

Share Document