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Long noncoding RNA DICER1-AS1 functions in methylation regulation on the multi-drugresistance of osteosarcoma cells via miR-34a-5p and GADD45A

ABSTRACT: Long noncoding RNA DICER1-AS1 functions in methylation regulation on the multi-drugresistance of osteosarcoma cells via miR-34a-5p and GADD45A

PROVIDER: PRJNA658089 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR12476700_1.fastq.gz	Fastqsanger.gz
	SRR12476700_2.fastq.gz	Fastqsanger.gz
	SRR12476701.fastq.gz	Fastqsanger.gz
	SRR12476701_1.fastq.gz	Fastqsanger.gz
	SRR12476701_2.fastq.gz	Fastqsanger.gz

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Long noncoding RNA DICER1-AS1 functions in methylation regulation on the multi-drugresistance of osteosarcoma cells via miR-34a-5p and GADD45A (mRNA-seq)

Project description:Long noncoding RNA DICER1-AS1 functions in methylation regulation on the multi-drugresistance of osteosarcoma cells via miR-34a-5p and GADD45A (mRNA-seq)

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Long noncoding RNA DICER1-AS1 functions in methylation regulation on the multi-drugresistance of osteosarcoma cells via miR-34a-5p and GADD45A (lncRNA-seq)

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Long Noncoding RNA DICER1-AS1 Functions in Methylation Regulation on the Multi-Drugresistance of Osteosarcoma Cells <i>via</i> miR-34a-5p and GADD45A.

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Long noncoding RNA DICER1-AS1 functions in methylation regulation on the multi-drugresistance of osteosarcoma cells via miR-34a-5p and GADD45A

Project description:This SuperSeries is composed of the SubSeries listed below.

2020-08-20 | GSE153788 | GEO

Long noncoding RNA DICER1-AS1 functions in methylation regulation on the multi-drugresistance of osteosarcoma cells via miR-34a-5p and GADD45A (mRNA-seq)

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods: Total RNA was extracted by Trizol reagent, and DNA was produced by gene specific primers or random primers. Illumina-Hiseq 4000 system was used for RNA sequencing and Illumina-Hiseq 2000 system was used for library sequencing (BGI Technology Company). A single-ended library was prepared according to the Illumina-Truseq RNA sample preparation kit (Illumina) scheme 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 Results: Using an optimized data analysis workflow, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling. Conclusions: Our study represents the first detailed 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.

2020-08-20 | GSE153787 | GEO

Long noncoding RNA DICER1-AS1 functions in methylation regulation on the multi-drugresistance of osteosarcoma cells via miR-34a-5p and GADD45A (lncRNA-seq)

2020-08-20 | GSE153786 | GEO

Identification of SART3 as a pre-miR-34a–binding protein

Project description:MicroRNAs (miRNAs or miRs) are small, noncoding RNAs that are implicated in the regulation of nearly all biological processes. Global miRNA biogenesis is altered in many cancers and RNA-binding proteins (RBPs) have been shown to play a role in this process, presenting a promising avenue for targeting miRNA dysregulation in disease. miR-34a exhibits tumor-suppressive functions by targeting cell cycle regulators CDK4/6 and anti-apoptotic factor Bcl-2, among other regulatory pathways such as Wnt, TGF-, and Notch signaling. Many cancers show downregulation or loss of miR-34a, and synthetic miR-34a supplementation has been shown to inhibit tumor growth in vivo; however, the post-transcriptional mechanisms by which miR-34a is lost in cancer are not entirely understood. Here, we have used a proteomics-mediated approach to identify Squamous cell carcinoma antigen recognized by T-cells 3 (SART3) as a putative pre-miR-34a-binding protein. SART3 is a spliceosome recycling factor and nuclear RBP with no previously reported role in miRNA regulation. We demonstrate that SART3 binds pre-miR-34a with specificity over pre-let-7d and begin to elucidate a new functional role for this protein in non-small lung cancer cells. Overexpression of SART3 led to increased miR-34a levels, downregulation of the miR-34a target genes CDK4 and CDK6, and cell cycle arrest in the G1 phase. In vitro binding studies showed that the RNA-recognition motifs within the SART3 sequence are responsible for selective pre-miR-34a binding. Collectively, our results present evidence for an influential role of SART3 in miR-34a biogenesis and cell cycle progression.

2019-10-14 | PXD015278 | Pride

Gadd45a promotes DNA demethylation through TDG

Project description:Growth arrest and DNA-damage-inducible protein 45 (Gadd45) family members have been implicated in DNA demethylation in vertebrates. However, it remained unclear how they contribute to the demethylation process. Here, we demonstrate that Gadd45a promotes active DNA demethylation through thymine DNA glycosylase (TDG) which has recently been shown to excise 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) generated in Ten-eleven-translocation (Tet) -initiated oxidative demethylation. The connection of Gadd45a with oxidative demethylation is evidenced by the enhanced activation of a methylated reporter gene in HEK293T cells expressing Gadd45a in combination with catalytically active TDG and Tet. Gadd45a interacts with TDG physically and increases the removal of 5fC and 5caC from genomic and transfected plasmid DNA by TDG. Knockout of both Gadd45a and Gadd45b from mouse ES cells leads to hypermethylation of specific genomic loci most of which are also targets of TDG and show 5fC enrichment in TDG-deficient cells. These observations indicate that the demethylation effect of Gadd45a is mediated by TDG activity. This finding thus unites Gadd45a with the recently defined Tet-initiated demethylation pathway.

2015-05-07 | GSE62496 | GEO

miRNAs regulated by Gadd45a during somatic cell reprogramming

Project description:Gadd45a can enhance somatic cell reprogramming significantly. To explore the roles of Gadd45a playing in reprogramming, we performed miRNA microarray to identify miRNAs and signals pathways that regulated by Gadd45a.

2014-04-22 | GSE56942 | GEO

Genes regulated by Gadd45a during somatic cell reprogramming

Project description:Gadd45a can enhance somatic cell reprogramming significantly. To explore the roles of Gadd45a playing in reprogramming, we performed whole genome microarray to identify genes and signals pathways that regulated by Gadd45a.

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