Hes1 is Associated with Long Non-Coding RNAs in Colorectal Cancer
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PROVIDER: PRJNA555748 | ENA |
REPOSITORIES: ENA
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Project description:Previous studies have documented that long non-coding RNAs participate in a wide-spectrum of biological processes. We hypothesized that long non-coding RNAs may promote glycolysis and tumorigenesis in colorectal cancer by manipulating of target genes. To test this hypothesis, we performed a global non-coding RNA expression profiling in 10 CRC tissues.
2021-02-23 | GSE139402 | GEO
Project description:Background:Long noncoding RNAs (lncRNAs) play important roles in the development and pathophysiology of colorectal cancer (CRC). Our previous study showed that Hes1 was involved in the self-renewal and tumorigenicity of stem-like cancer cells in CRC. Methods:ArrayStar Human LncRNA/mRNA Expression Microarray Version 3.0 was used to detect lncRNA expression in CRC tissues compared with their matched non-tumoral tissues. RNA-binding protein immunoprecipitation and sequencing (RIP-seq) assay was used to detect lncRNAs binding to Hes1. Real-time qPCR was used to detect expression of specific lncRNAs in CRC tissues. Results:We found significantly up-regulated as well as down-regulated lncRNAs in CRC tissues compared with their matched non-tumoral tissues. We also screened a number of lncRNAs interacting with Hes1 in CRC cells. Interestingly, we found several lncRNAs binding to Hes1 (such as, GNAS-AS1, RP11-89K10.1, and RP11-465L10.10) were up-regulated in CRC tissues showed by the tissue microarray. Next, we confirmed that Hes1 directly interacted with these lncRNAs using RIP-qPCR and RNA pulldown assay. Finally, we verified the expression of these lncRNAs in 32 CRC samples as well as the adjacent non-tumoral tissues using real-time qPCR. Conclusions:Based on these, we speculate that Hes1 interacts with one or more lncRNAs which contribute to the development and progression of CRC.
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Project description:Long non-coding RNAs in B cells
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Project description:The Arraystar Human LncRNA Array v2.0 was designed for researchers who were interested in profiling both LncRNAs and protein-coding RNAs in human genome. 33,045 LncRNAs were collected from the authoritative data sources including RefSeq, UCSC knowngenes, Ensembl and many related literatures. This experiment is to profile lncRNAs and protein-coding RNAs using Arraystar Human LncRNA Array v2.0. Identification of coding RNAs and lncRNAs that are diffrentially expressed in colorectal cancer by comparing sample A-E (normal colorectal cells) vs sample F-J (colorectal tumor cells) and c-MYC-regulating lncRNAs by comparing sample 1-3 (triplicate of HCT116 cells treated with control siRNA) vs sample 4-6 (triplicate of HCT116 cells treated with siRNA targeting MYC) and sample 7-9 (triplicate of RKO cells treated with control siRNA) vs sample 10-12 (triplicate of RKO cells treated with siRNA targeting MYC) .
2013-09-20 | E-GEOD-39846 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the SubSeries listed below.
2019-07-21 | GSE134552 | GEO
Project description:Long non-coding RNAs are involved in the activation of glycolysis in colorectal cancer
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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:Using RNA CaptureSeq we annotated non-coding RNAs transcribed from genome intervals surrounding breast cancer risk signals in a range of mammary-derived tissue and cell lines.
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Project description:Colorectal cancer (CRC) is one of the leading causes of cancer-related death worldwide. Despite substantial progress in understanding the molecular mechanisms and treatment of CRC in recent years, the overall survival rate of CRC patients has not improved dramatically. The development of CRC is multifactor and multistep processes, in which abnormal gene expression may play an important role. With the advance of human tumor molecular biology, a series of studies have highlighted the role of long non-coding RNAs (lncRNAs) in the development of CRC. CRC-related lncRNAs have been demonstrated to regulate the genes by various mechanisms, including epigenetic modifications, lncRNA-miRNA and lncRNA-protein interactions, and by their actions as miRNA precursors or pseudogenes. Since some lncRNAs can be detected in human body fluid and have good specificity and accessibility, they have been suggested to be used as novel potential biomarkers for CRC diagnosis and prognosis as well as in the prediction of the response to therapy. Therefore, in this review, we will focus on lncRNAs in CRC development, the mechanisms and biomarkers of lncRNAs in CRC.
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Project description:Leishmania major is a kinetoplastid protozoan parasite which causes the debilitating infectious disease cutaneous leishmaniasis (CL). This disease results in scars and disfiguration of the infected individuals. The L. major genome was the first leishmanial genome to be sequenced in 2005 and this study resulted in the identification of 8,300 protein coding genes. This landmark study paved the way for further sequencing of other leishmanial parasites (L. infantum, L. braziliensis and L. donovani). A recent study provided the glimpse of the global transcriptome of L. major promastigotes. This study identified 1,884 uniquely expressed non-coding RNAs (ncRNA) in L. major. Additionally, we had previously mapped the global proteome of L. major promastigote using a proteogenomic approach which resulted in identification of 3,613 proteins in L. major promastigotes which covered 43% of its proteome. In the present study, we have carried out extensive analysis of the 1,884 novel ncRNAs using a proteogenomic approach to identify their protein coding potential. Our analysis resulted in identification of 10 novel protein coding genes based on peptide data and additional hundreds of proteins coding genes based on homology searches of previously classified ncRNA genes. We have analyzed each of these novel protein coding genes and in the process have improved the genome annotation of L. major on the basis of mass spectrometry derived peptide data and also based on homology.
2016-05-11 | PXD002465 | Pride