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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and CANT1 Overexpression Retinoblastoma Transcriptomes

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and CANT1 Overexpression Retinoblastoma Transcriptomes

PROVIDER: PRJNA593183 | ENA |

REPOSITORIES: ENA

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Next Generation Sequencing Facilitates Quantitative Analysis of Retinoblastoma Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Retinoblastoma Transcriptomes

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and CANT1 Overexpression Retinoblastoma Transcriptomes

Project description:PURPOSE: Retinoblastoma (RB) is the most common malignant intraocular tumor of childhood. Recent studies have shown that long non-coding RNAs (lncRNAs), which are longer than 200 bp and without protein-coding ability, are key regulators of tumorigenesis. However, the role of lncRNAs in retinoblastoma remains to be elucidated. METHODS: LncRNA CASC15-New-Transcript 1 (CANT1) expression was determined by real-time PCR in RB cells. Tumor characteristics in CANT1-overexpressing RB cells were determined through CCK8 cell viability assay, soft agar assay and mouse xenograft experiment. RNA transcriptome-sequencing was performed to find downstream target genes of CANT1. CANT1's interactions with phosphoinositide 3-kinase gamma (PI3Kγ) were studied through chromatin oligonucleotide precipitation (ChOP) and chromatin immunoprecipitation (ChIP) assays. RESULTS: In this study, we found that the expression of lncRNA CANT1 was significantly downregulated in RB. Notably, CANT1 overexpression significantly inhibited RB growth both in vitro and in vivo. Furthermore, lncRNA CANT1, which was mainly located in the nucleus, occupied the promoter of PI3Kγ and blocked histone methyltransferase hSET1 from binding to the PI3Kγ promoter, thus abolishing hSET1-mediated histone H3K4 trimethylation of the PI3Kγ promoter and inhibiting PI3Kγ expression. Furthermore, we found that silencing PI3Kγ either by CANT1 overexpression or by PI3Kγ siRNA, reduced the activity of PI3K/Akt signaling and suppressed RB tumorigenesis. CONCLUSIONS: LncRNA CANT1 acts as a suppressor of RB progression by blocking gene-specific histone methyltransferase recruitment. These findings outline a new CANT1 modulation mechanism and provide an alternative option for RB treatment.

2020-02-05 | GSE141327 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Retinoblastoma Transcriptomes

Project description:Methods: mRNA profiles of retinoblastoma samples and para-tumor were generated by deep sequencing, in triplicate, using Illumina. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and OsAFB6 overexpression mutant Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transgene-derived OsAFB6 overexpression mutant transcriptome profiling (RNA-seq) to microarray Methods: young panicle(<1mm) mRNA profiles of 80 individual plants of OsAFB6 overexpression mutants and the correspondinng negative plants during the same transgenic event as control were generated by deep sequencing, in two replicate, using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. Results: Using an optimized data analysis workflow, we found 59 genes were upregulated and 229 genes were down regulated in OsAFB6 overexpression mutant. Conclusions: Our study represents the first detailed analysis of young panicle transcriptomes of OsAFB6 overexpression mutant, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and IRX5-overexpression hMSCs Transcriptomes

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Next Generation Sequencing Facilitates Quantitative Analysis of ISL1 Regulated Transcriptomes

Project description:The goals of this study are to analyze the transcriptome profiling (RNA-seq) after ISL1 overexpression in Huh7 cells.

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