Long non-coding RNA RP11-820 promotes extracellular matrix production via regulating miR-3178/MYOD1 in human trabecular meshwork cells
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
PROVIDER: GSE126170 | GEO | 2019/02/07
REPOSITORIES: GEO
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Project description:Methods and Materials The high throughput RNA sequencing (RNA-seq) data from kidney biopsies of LN patients and controls was applied studied to screen for candidate lncRNAs. Quantitative real-time polymerase chain reaction(RT-qPCR) was used to detect the expression of lncRNAs and individual IFN-stimulated genes (ISGs). Western blotting and dual-luciferace luciferase reporter assay was adopted to explore the specific function of the candidate lncRNA. Results The expression of lncRNA RP11-2B6.2 was significantly increased in the kidney tissues from LN patients compared with those from healthy controls, and positive correlated with the degree of disease activity and renal injuryinjuries. Additionally, expression of LncRNA RP11-2B6.2 could be stimulated by type I IFN. Silencing it RP11-2B6.2 significantly reduced the expression of a group of interferon-stimulating genes(ISGs) including IFIT1, OAS1, etc., Furthermore, it lncRNA RP11-2B6.2 affected the expression of IFN alpha and beta receptor subunit 1 (IFNAR1), phosphorylation of Jak1 and Stat1, and the luciferase activity induced by interferon stimulated response element(ISRE). Conclusion Long noncoding RNA RP11-2B6.2 is a positive regulator of the type I IFN signaling pathway in LN. It LncRNA RP11-2B6.2 may contribute to the pathogenesis of LN and provide served as a potentially therapeutic target.
2019-05-01 | GSE98422 | GEO
Project description:Long non-coding RNAs (lncRNAs) play important roles in numerous diseases and represent an emerging layer of cancer biology. However, the role that lncRNAs play in the pathogenesis of pediatric B-cell leukemia (B-ALL) with t(12;21) (ETV6-RUNX1) translocation is largely unknown. In this study, we assessed the lncRNA expression profiles of 42 pediatric B-ALL (24 with and 18 without the t(12;21) translocation) and 4 bone marrows from healthy donors. We identified 117 lncRNAs that were differentially expressed (fold change> 1.5 and FDR > 0.05) between the B-ALL subgroups (ETV6-RUNX1-positive and ETV6-RUNX1-negative). The most upregulated lncRNAs in ETV6-RUNX1 positive B-ALL were TCL6, RP4-697K14.3, LOC100292680, RP11-345I18.1, LINC00599 and TRAF3IP2-AS1, while the most downregulated were RP11-135F9.1, RP11-561B11.1, AK095221, RP11-463H12.1, AC007283.4 and CCDC26. Coding-non-coding gene co-expression networks were constructed to identify lncRNAs with potential functions in ETV6-RUNX1 translocation. Levels of representative lncRNA-mRNA pairs were further detected by RT-qPCR in patients with pediatric B-ALL. Importantly, pediatric B-ALL patients who expressed low levels of the lncRNA TCL6 had lower disease-free survival than patients with high levels of TCL6. Thus, these findings provide the first detailed description of lncRNA expression profiles related to t(12;21) translocation in pediatric B-ALL. Such lncRNAs profiles might play important roles in driving normal cells to leukemic cells. These lncRNAs may provide novel molecular biomarkers and offer new basis for combating pediatric B-ALL.
2019-12-10 | GSE128254 | GEO
Project description:The challenge of oligohydramnios study is multiple causes of oligohydramnios. Long noncoding RNAs (lncRNAs) is a set of RNAs that has been proved to function in multiple biological process. Currently, little is know about their expression and possible role in oligohydramnios. Total RNA was isolated from fetal membranes ressected from oligohydramnios pregnant women (OR) and normal amniotic fluid control (Normal).RNA-sequencing (RNA-seq) obtain that a total of 801 lncRNAs and 367 mRNAs were differentially expressed in OR. Of which, 638 lncRNAs and 189 mRNAs were upregulated, and 163 lncRNAs and 178 mRNAs were downregulated. Of these lncRNAs, 566 of them were intergenic lncRNA, 351 were intronic antisense lncRNA，and 300 natural antisense. The differentially expressed lncRNA were primary located in chromosome 2, 1 and 11. KEGG enrichment pathways revealed the differential expressed mRNAs were enriched in pathway in cancer, Ras signaling pathway, TNF signaling pathway, focal adhesion, and chemokine signaling pathway. The qRT-PCR result confirmed that LINC00515 and RP11-388P9.2 were upregulated in OR. Furthermore, the constructed lncRNA-miRNA-mRNA regulatory network revealed TNR, CFTR, ABCC2, ABCA12, and COL9A2 as the candidate targets of LINC00515 and RP11-388P9.2. A wide range of lncRNAs were alert in OR, in particularly, LINC00515 and RP11-388P9.2 were confirmed to be uprgulated in OR, and their predicted downstream targets were transport and tissue growth and development associated. Further study focused on the role of differential expressed lncRNAs such as LINC00515 and RP11-388P9.2 would provide more insight into the pathophysiology in OR
2019-12-30 | GSE142701 | GEO
Project description:Long non-coding RNAs (lncRNAs) are defined as non-protein-coding transcripts that are at least 200 nucleotides long. They are known to play pivotal roles in regulating gene expression, especially during stress responses in plants. We used a large collection of in-house transcriptome data from various soybean (Glycine max and Glycine soja) tissues treated under different conditions to perform a comprehensive identification of soybean lncRNAs. We also retrieved publicly available soybean transcriptome data that were of sufficient quality and sequencing depth to enrich our analysis. In total, RNA-seq data of 332 samples were used for this analysis. An integrated reference-based, de novo transcript assembly was developed that identified ~69,000 lncRNA gene loci. We showed that lncRNAs are distinct from both protein-coding transcripts and genomic background noise in terms of length, number of exons, transposable element composition, and sequence conservation level across legume species. The tissue-specific and time-specific transcriptional responses of the lncRNA genes under some stress conditions may suggest their biological relevance. The transcription start sites of lncRNA gene loci tend to be close to their nearest protein-coding genes, and they may be transcriptionally related to the protein-coding genes, particularly for antisense and intronic lncRNAs. A previously unreported subset of small peptide-coding transcripts was identified from these lncRNA loci via tandem mass spectrometry, which paved the way for investigating their functional roles. Our results also highlight the current inadequacy of the bioinformatic definition of lncRNA, which excludes those lncRNA gene loci with small open reading frames (ORFs) from being regarded as protein-coding.
2020-01-09 | PXD014553 | Pride
Project description:Downregulations of TCAM1P-004 and RP11-598D14.1 were frequently observed in HCC tumors as compared to adjacent non-tumor tissues. To further study the molecular functions of TCAM1P-004 and RP11-598D14.1, we attempted to identify the gene targets regulated by either lncRNAs. Knockdown of TCAM1P-004 or RP11-598D14.1 were achieved by transduction of lentivirus carrying respective shRNAs in non-tumor hepatocyte MIHA cells. Diffferentially expressed genes after knockdown of the lncRNAs were compared to cells tranduced with lentivirus carrying scramble shRNAs.
2018-10-24 | E-MTAB-7280 | biostudies-arrayexpress
Project description:Pericytes are essential for vessel maturation and endothelial barrier function. Long non-coding RNAs (lncRNAs) regulate endothelial cell function, but their role in pericyte biology remains unexplored. Here we characterize the human pericyte transcriptome following knockdown of lncRNA HypERrlnc (RP11-65J21.3).
2017-08-10 | GSE92887 | GEO
Project description:Objective: To analysis lncRNAs expression profiles and identify differentially expressed lncRNAs in CD4+ T cells response to T. pallidum infection in neurosyphilis patients. Methods: CD4+ T cells were isolated from peripheral blood mononuclear cells. RNA extraction was performed to conduct further experiments. Expression profiles of mRNAs and lncRNAs in CD4+ T cells isolated from neurosyphilis patients and healthy controls were analyzed by using microarray assay. Four lncRNAs were selected to conduct validation by using real time-quantitative polymerase chain reaction and the expression levels of those above mentioned lncRNAs in neurosyphilis patients and healthy controls were compared. Results: In total, 17, 278 lncRNAs and 15, 840 mRNA were found to be differentially expressed when comparing the CD4+ T cells between neurosyphilis patients and healthy control individuals. Of these transcripts, 2258 lncRNAs and 1728 mRNAs were significantly over or under expressed, respectively. Compared with healthy controls, AC068282.3 (fold change: 21.90) and CTD-3064M3.3 (fold change: 23.93) were the most over-expressed and under-expressed lncRNAs in neurosyphilis patients. The majority of differentially expressed lncRNAs are from intergenic regions (~ 57.5%), intronic antisense to protein-coding loci (~ 15.0%), natural antisense to protein-coding loci (~12.1%). It is worth noting that 59 lncRNAs were significant difference along with significantly different mRNA. Among the 59 pairs of genes, LOC7999 mRNA was positively correlated with lncRNA RP11-160E2.16, RP11-160E2.11, RP11-160E2.19, respectively; NKX1-1 mRNA was positively correlated with lncRNA RP11-1398P2.1, RP11-160E2.19, XLOC_003422, respectively. The following five mRNAs were correlated with two differential lncRNAs, namely DUSP16, AP000349.1, FAM115C, TIMM8A, SMCHD1. GO analysis revealed that the differentially expressed coding genes were mainly involved in the biological processes, and among them, the most significant association was observed in defense response to fungus, defense response to bacterium, killing cells of other organism and disruption of cells of other organism. Subsequent pathway analysis was also conducted, and T cell receptor signaling pathway, MAPK signaling pathway, TGF-beta signaling pathway, etc. were found out to be associated with differentially expressed mRNAs. Conclusion: The present study revealed the differential expression profiles of lncRNAs in CD4+ T cells response to T. pallidum infection in neurosyphilis patients. LncRNAs are involved in the key biological process in CD4+ T cell response to T. pallidum infection.
2017-09-08 | GSE103599 | GEO
Project description:Long non-coding RNA RP11-820 promotes extracellular matrix production via regulating miR-3178/MYOD1 in human trabecular meshwork cells
| PRJNA521227 | ENA
Project description:Many lncRNAs have been discovered using transcriptomic data, however, it is unclear what fraction of lncRNAs is functional and what structural properties affect their phenotype. MUNC lncRNA (also known as DRReRNA) acts as an enhancer RNA for the Myod1 gene in cis and stimulates the expression of other promyogenic genes in trans by recruiting the cohesin complex. Here, experimental probing of the RNA structure revealed that MUNC contains multiple structural domains not detected by prediction algorithms in the absence of experimental information. We show that these specific and structurally distinct domains are required for induction of promyogenic genes, for binding genomic sites and gene expression regulation, and for binding the cohesin complex. Myod1 induction and cohesin interaction comprise only a subset of MUNC phenotype. Our study reveals unexpectedly complex, structure-driven functions for the MUNC lncRNA and emphasizes the importance of experimentally determined structures for understanding structure-function relationships in lncRNAs.
2022-01-21 | GSE174217 | GEO
Project description:Many lncRNAs have been discovered using transcriptomic data, however, it is unclear what fraction of lncRNAs is functional and what structural properties affect their phenotype. MUNC lncRNA (also known as DRReRNA) acts as an enhancer RNA for the Myod1 gene in cis and stimulates the expression of other promyogenic genes in trans by recruiting the cohesin complex. Here, experimental probing of the RNA structure revealed that MUNC contains multiple structural domains not detected by prediction algorithms in the absence of experimental information. We show that these specific and structurally distinct domains are required for induction of promyogenic genes, for binding genomic sites and gene expression regulation, and for binding the cohesin complex. Myod1 induction and cohesin interaction comprise only a subset of MUNC phenotype. Our study reveals unexpectedly complex, structure-driven functions for the MUNC lncRNA and emphasizes the importance of experimentally determined structures for understanding structure-function relationships in lncRNAs.
2022-01-21 | GSE174203 | GEO