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Evaluation of the consequences of ALYREF silencing on gene expression patterns in colorectal cancer cells

ABSTRACT: Evaluation of the consequences of ALYREF silencing on gene expression patterns in colorectal cancer cells

PROVIDER: PRJNA786774 | ENA |

REPOSITORIES: ENA

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Evaluation of the consequences of ALYREF silencing on gene expression patterns in colorectal cancer cells

Project description:In order to uncover the underlying mechanisms behind the observed oncogenic phenotype of ALYREF in colorectal cancer in vitro and in vivo, we applied a whole transcriptome analysis to find deregulated genes upon ALYREF silencing.

2021-12-08 | GSE190340 | GEO

ALYREF Mediates RNA m5C Modification to Promote Hepatocellular Carcinoma Progression

Project description:The RNA methyltransferase Aly/REF export factor (ALYREF) is considered one type of “reader” protein located in the nucleus that recognizes and binds directly with m5C sites in RNA and facilitates the export of RNA from the nucleus to the cytoplasm. Notably, ALYREF is considered a promising target for diagnosis and prognosis prediction. However, until now, the low number of related studies has limited the understanding of the mechanism of the HCC-promoting effects of ALYREF. To further elucidate the oncogenic roles of ALYREF in hepatocellular carcinoma (HCC), we assessed the expression levels of ALYREF in clinical samples and HCC cell lines and explored the effects of ALYREF deficiency by both in vitro experiments and m5C-methylated RNA immunoprecipitation sequencing (m5C-MeRIP-Seq)

2023-03-22 | GSE221793 | GEO

RNA-seq analysis of Alyref and Gabpb1 knockout embryos

Project description:We have identified Alyref and Gabpb1 as developmentally important genes by siRNA screening. Gene knockout (KO) of Alyref and Gabpb1 by the CRISPR/Cas9 system resulted in early developmental arrest in mice. To gain mechanistic insight into the developmental role of Alyref and Gabpb1, we performed RNA sequencing (RNA-seq) analysis of the KO embryos.

2023-08-11 | GSE199874 | GEO

Global RNA-binding profile of the mRNA export adaptor ALYREF

Project description:The TREX complex (TREX) plays key roles in nuclear export of mRNAs. However, little is known about its transcriptome-wide binding targets. We used individual cross-linking and immunoprecipitation (iCLIP) to identify the binding sites of ALYREF, an mRNA export adaptor in TREX, in human cells. As expected, iCLIP reads are mainly mapped to exons of mRNAs. Globally, ALYREF binding shows two apparent enrichments on the mRNA, one is near the 5’ end and the other is very close to the 3’ end. In addition, numerous middle exons harbor ALYREF binding sites. CBP80 and PABPN1 mainly affect ALYREF binding at the 5’ and the 3’ region, respectively. Interestingly, we found that the 3’ processing factor CstF64 directly interacts with ALYREF and is required for the overall binding of ALYREF on the mRNA. Sequence analysis led to the identification of multiple

2017-05-19 | GSE99069 | GEO

Functional Enrichment Analysis of ALYREF

Project description:We investigated the biological function and mechanism of ALYREF based on RIP and RNA-seq in C42 cell

2022-02-05 | GSE195701 | GEO

ALYREF links 3'processing and nuclear export of histone mRNAs

Project description:To examine whether ALYREF can facilitate the 3'processing of RD histone mRNA,we isolated and sequenced the polyadenylated and nonpolyadenylated RNAs from control and ALYREF KD cells

2019-02-27 | GSE113422 | GEO

ALYREF is shared by polyadenylated and nonpolyadenylated mRNA processing and export pathways [iCLIP-seq]

Project description:we try to investigate the binding of ALYREF and NXF1 on histone mRNA when the cell treated with indicated siRNAs. ALYREF plays key roles in nuclear export of polyadenylated mRNAs and also modulates their 3' processing, but whether it is involved in regulating RNAs beyond polyadenylated mRNAs is unknown. The replication-dependent (RD) histone mRNAs are not polyadenylated, but end in a stem-loop (SL) structure. Here we demonstrate that ALYREF prevalently binds a region next to the SL on RD histone mRNAs. SL-binding protein (SLBP) directly interacts with ALYREF and ensures this binding. To examine how SLBP KD impact ALYREF distribution on the histone mRNA, we carried out ALYREF iCLIP in control and SLBP KD cells. To investigate the functional consequence for ALYREF binding on histone mRNAs, we isolated polyA+ and polyA- RNAs from control and ALYREF KD cells, and carried out RNA-seq separately.

2019-02-27 | GSE124735 | GEO

Functional Enrichment Analysis of ALYREF

Project description:Functional Enrichment Analysis of ALYREF

| PRJNA801860 | ENA

An ALYREF-MYCN coactivator complex drives neuroblastoma tumorigenesis through effects on USP3 and MYCN stability

Project description:To achieve the very high oncoprotein levels required to drive the malignant state, cancer cells utilise the ubiquitin proteasome system to regulate proteins involved in growth signalling pathways. Here we identify a transcriptional coactivator, ALYREF, expressed from the most common genetic copy number variation in childhood neuroblastoma, chromosome 17q21-ter gain. We show strong co-operativity between ALYREF and MYCN from transgenic models of neuroblastoma in vitro and in vivo. MYCN induced ALYREF transcription, and the two proteins formed a nuclear coactivator complex which stimulated transcription of the ubiquitin specific peptidase 3, USP3. We found that increased USP3 levels markedly reduced K-48- and K-63-linked ubiquitination of MYCN, thus driving up MYCN protein stability. In the MYCN-ALYREF-USP3 signal, ALYREF was required for MYCN effects on the malignant phenotype in vitro and that of USP3 on MYCN stability. Our data define a novel MYCN oncoprotein dependency state which provides rationale for future pharmacological studies.

2020-05-12 | GSE150303 | GEO

5-methylcytosine modification and the ALYREF reader protein promote retrovirus replication

Project description:The 5-methylcytosine (m5C) modification is present at appreciable amounts in the mammalian transcriptome, but its precise location and function is still poorly understood. Here, we identify high m5C levels and map their locations in a model retrovirus, the murine leukemia virus, and show that the ALYREF m5C reader protein regulates viral replication. Our results reveal a single-nucleotide m5C profile in a virus and its function in a eukaryotic mRNA.

2020-04-14 | GSE139606 | GEO

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