Topic
NcRNA processing
About: NcRNA processing is a research topic. Over the lifetime, 10 publications have been published within this topic receiving 271 citations.
Papers
TL;DR: It is found that most abundant exosomal RNA species are the fragments of 28S and 18S rRNA subunits, which limits the number of reads from other RNAs, and protocols allowing depletion of fragmented rRNA should be utilized in the future RNA-seq analyses on exosomes.
Abstract: Exosomes are nanosized (30–100 nm) membrane vesicles secreted by most cell types. Exosomes have been found to contain various RNA species including miRNA, mRNA and long non-protein coding RNAs. A number of cancer cells produce elevated levels of exosomes. Because exosomes have been isolated from most body fluids they may provide a source for non-invasive cancer diagnostics. Transcriptome profiling that uses deep-sequencing technologies (RNA-Seq) offers enormous amount of data that can be used for biomarkers discovery, however, in case of exosomes this approach was applied only for the analysis of small RNAs. In this study, we utilized RNA-Seq technology to analyze RNAs present in microvesicles secreted by human breast cancer cell lines.
Exosomes were isolated from the media conditioned by two human breast cancer cell lines, MDA-MB-231 and MDA-MB-436. Exosomal RNA was profiled using the Ion Torrent semiconductor chip-based technology. Exosomes were found to contain various classes of RNA with the major class represented by fragmented ribosomal RNA (rRNA), in particular 28S and 18S rRNA subunits. Analysis of exosomal RNA content revealed that it reflects RNA content of the donor cells. Although exosomes produced by the two cancer cell lines shared most of the RNA species, there was a number of non-coding transcripts unique to MDA-MB-231 and MDA-MB-436 cells. This suggests that RNA analysis might distinguish exosomes produced by low metastatic breast cancer cell line (MDA-MB-436) from that produced by highly metastatic breast cancer cell line (MDA-MB-231). The analysis of gene ontologies (GOs) associated with the most abundant transcripts present in exosomes revealed significant enrichment in genes encoding proteins involved in translation and rRNA and ncRNA processing. These GO terms indicate most expressed genes for both, cellular and exosomal RNA.
For the first time, using RNA-seq, we examined the transcriptomes of exosomes secreted by human breast cancer cells. We found that most abundant exosomal RNA species are the fragments of 28S and 18S rRNA subunits. This limits the number of reads from other RNAs. To increase the number of detectable transcripts and improve the accuracy of their expression level the protocols allowing depletion of fragmented rRNA should be utilized in the future RNA-seq analyses on exosomes. Present data revealed that exosomal transcripts are representative of their cells of origin and thus could form basis for detection of tumor specific markers.
213 citations
TL;DR: A microarray containing probes that tile all known yeast noncoding RNAs found a general loss of Box C/D snoRNAs in the TetO7-BCD1 mutant and identified a relationship between tRNA 5′ end processing and tRNA splicing, processes that were previously thought to be independent.
Abstract: We used a microarray containing probes that tile all known yeast noncoding RNAs (ncRNAs) to investigate RNA biogenesis on a global scale The microarray verified a general loss of Box C/D snoRNAs in the TetO7-BCD1 mutant, which had previously been shown for only a handful of snoRNAs We also monitored the accumulation of improperly processed flank sequences of pre-RNAs in strains depleted for known RNA nucleases, including RNase III, Dbr1p, Xrn1p, Rat1p and components of the exosome and RNase P complexes Among the hundreds of aberrant RNA processing events detected, two novel substrates of Rnt1p (the RUF1 and RUF3 snoRNAs) were identified We also identified a relationship between tRNA 5′ end processing and tRNA splicing, processes that were previously thought to be independent This analysis demonstrates the applicability of microarray technology to the study of global analysis of ncRNA synthesis and provides an extensive directory of processing events mediated by yeast ncRNA processing enzymes
30 citations
TL;DR: For example, plantDario as mentioned in this paper is an extension of DARIO to plant short non-coding RNAs (sncRNAs), which includes modifications to cope with plant-specific ncRNA processing.
Abstract: High-throughput sequencing techniques have made it possible to assay an organism’s entire repertoire of small non-coding RNAs (ncRNAs) in an efficient and cost-effective manner. The moderate size of small RNAseq datasets makes it feasible to provide free web services to the research community that provide many basic features of a small RNA-seq analysis including quality control, read normalization, ncRNA quantification, and the prediction of putative novel ncRNAs. DARIO is one such system that so far has been focussed on animals. Here we report on the extension of this system to plant short non-coding RNAs (sncRNAs), which includes modifications to cope with plant-specific ncRNA processing. The current version of plantDARIO covers analyses of mapping files, RNA-seq quality control, expression analyses of annotated ncRNAs, prediction of miRNAs and snoRNAs from unknown expressed loci, and expression analyses of user-defined loci for Arabidopsis thaliana, Beta vulgaris, and Solanum lycopersicum. It links to a visualization browser for custom track display. The easy-to-use platform of plantDARIO quantifies RNA expression based on annotated ncRNAs from different ncRNA databases and also some ncRNA annotations validated by our group. The plantDARIO web site can be accessed at http://plantdario.bioinf.uni-leipzig.de/.
24 citations
TL;DR: This study aimed to investigate potential gene and signal pathway associated with tumour progression and its role in disease progression.
Abstract: Objectives This study aimed to investigate potential gene and signal pathway associated with tumour progression. Methods Related microarray data set of breast cancer was obtained from Gene Expression Omnibus database, and differential-expressed genes (DEGs) between two control samples and two treated samples were analysed using statistical software R. We collected 50 epigallocatechin-3-gallate(EGCG)-related genes and 119 breast cancer-related genes to create a knowledge base for following pathway analysis. Key findings A total of 502 mRNAs were identified as DEGs based on microarray analysis. Upregulated DEGs mainly enriched in nuclear nucleosome, cell adhesion, DNA packaging complex, Wnt-activated receptor activity, etc., while the downregulated DEGs significantly enriched in ncRNA processing, mitotic nuclear division, DNA helicase activity, etc. DEGs mostly enriched in gap junction, cell cycle, oxidative phosphorylation, focal adhesion, etc. EGCG suppressed FAK signalling pathway. Furthermore, EGCG could inhibit breast cancer cell proliferation and promote apoptosis by modulating CCND1. Conclusions Epigallocatechin 3-gallate might exert influence on breast cancer progression through inhibiting focal adhesion kinase (FAK) signalling pathway.
20 citations
TL;DR: In this article, the authors analyzed the TIMP gene family in gastric cancer, and the prognostic and diagnostic value was assessed by gene set enrichment analysis (GSEA), further functions of gene were verified by cell proliferation, migration and invasion assays in human Gastric cancer cell line.
Abstract: Background: Tissue inhibitor of metalloproteinases (TIMP) gene family, including TIMP1, TIMP2, TIMP3 and TIMP4, was found to be correlated with serval cancers. Still the diagnostic and prognostic study of it in gastric cancer (GC) have few reports. Methods and materials: In this study, the gene expression and clinical data were acquired from the Cancer Gene Atlas (TCGA), function enrichment was used by several databases for verifying known function. Operating characteristic (ROC) curves with area under the curve (AUC) used to assess diagnostic value. Survival analysis and joint-effects survival analysis was performed by the Kaplan-Meier curve. The results were adjusted by cox-regression model. Nomogram is used to directly predict the survival rate for individual GC patient. The potential mechanism for diagnostic and prognostic value was assessed by gene set enrichment analysis (GSEA). Further functions of gene were verified by cell proliferation, migration and invasion assays in human gastric cancer cell line. Results: TIMP1 was expressed in GC tissue was higher than normal gastric tissue. TIMP3 and TIMP4 have expressed in normal gastric tissue were higher than GC tissue. TIMP1, TIMP3 and TIMP4 have potential diagnostic value (AUC=0.842, 0.729, 0.786 respectively; all P<0.01). Low expression of TIMP2 and TIMP3 associated with favorable overall survival (all P<0.05). TIMP2 and TIMP3, which had significantly affection of prognosis were found having some function such as tRNA processing, cell cycle pathway ncRNA processing. The silencing of TIMP3 could inhibit the migration and invasion of gastric cancer cell. Conclusion: We analyzed the TIMP gene family in GC, and the prognostic and diagnostic value. TIMP1 and TIMP2 could be used as diagnostic biomarkers in GC. TIMP2 and TIMP3 could be used as potential biomarkers for GC's prognosis.
9 citations
Related Topics (5)
Performance Metrics
| Year | Papers |
|---|---|
| 2021 | 1 |
| 2020 | 1 |
| 2019 | 1 |
| 2018 | 1 |
| 2017 | 1 |
| 2014 | 2 |