Similar Datasets
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
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
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
Project description:To examine whether the competition between hMTR4 with ALYREF is important for the specific exosome recruitment, we performed stranded RNA-seq using rRNA-depleted nuclear RNAs isolated from ALYREF and control overexpression cells.
2017-12-06 | GSE100982 | GEO
Project description:During gene expression, RNA export factors are mainly known for driving nucleocytoplasmic transport. While early studies suggested that the Exon Junction Complex (EJC) may provide a binding platform for them, subsequent work proposed that they are only recruited by the Cap-Binding Complex (CBC) to the 5’ end of RNAs, as part of the TREX complex. Using iCLIP, we show that the export receptor Nxf1 and two TREX subunits, Alyref and Chtop, are actually recruited to the whole mRNA co-transcriptionally via splicing but before 3’-end processing. Consequently, Alyref can alter splicing decisions and Chtop regulates alternative polyadenylation. Surprisingly, we observe that eIF4A3 stimulates Alyref deposition on single exon or spliced RNAs close to EJC sites. Additional experiments suggest that Alyref is recruited to the 5’-end of RNAs by CBC before binding RNAs near EJCs. Our study reveals mechanical insights into the co-transcriptional recruitment of mRNA export factors and how this shapes the human transcriptome.
2019-05-01 | GSE113896 | GEO
Project description:During gene expression, RNA export factors are mainly known for driving nucleocytoplasmic transport. While early studies suggested that the Exon Junction Complex (EJC) may provide a binding platform for them, subsequent work proposed that they are only recruited by the Cap-Binding Complex (CBC) to the 5’ end of RNAs, as part of the TREX complex. Using iCLIP, we show that the export receptor Nxf1 and two TREX subunits, Alyref and Chtop, are actually recruited to the whole mRNA co-transcriptionally via splicing but before 3’-end processing. Consequently, Alyref can alter splicing decisions and Chtop regulates alternative polyadenylation. Surprisingly, we observe that eIF4A3 stimulates Alyref deposition on single exon or spliced RNAs close to EJC sites. Additional experiments suggest that Alyref is recruited to the 5’-end of RNAs by CBC before binding RNAs near EJCs. Our study reveals mechanical insights into the co-transcriptional recruitment of mRNA export factors and how this shapes the human transcriptome.
2019-05-10 | GSE130992 | GEO
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
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
Project description:Through deep RNA-seq of human monocyte-derived macrophages, we identified RP11-184M15.1, a human macrophage-specific lincRNA, to be highly induced in the cytoplasm of IL-4-stimulated macrophage. Preliminary data showed that treatment of IL-4-stimulated THP1 human macrophages with RP11-184M15.1 small interfering RNA (siRNA) repressed apoptosis of resolving macrophages, as shown by decreased Annexin V+ macrophages, and reduced protein expression of cleaved PARP. Biotinylated RP11-184M15.1 pulldown coupled with mass spectrometry indicated an interaction between RP11-184M15.1 and zinc finger RNA-binding protein (ZFR). RIP corroborated the proposed interaction between RP11-184M15.1 and ZFR. RNAInter revealed mRNAs predicted to interact with ZFR, and some of those genes (e.g., ALYREF, CCNYL1) were also differentially expressed in RNA-seq data of control versus RP11-184M15.1 knockdown in IL-4-stimulated THP1 macrophages. qPCR validated that ALYREF and CCNYL1 expression are reduced with RP11-184M15.1 knockdown. In contrast, with ZFR siRNA, ALYREF and CCNYL1 mRNA expressions were elevated. Thus, a hypothesis to be further tested is that RP11-184M15.1 interacts with ZFR to regulate mRNA stability in IL-4-stimulated macrophages. Nuclear RNA export factor 1 (NXF1) was also validated by RIP to interact with RP11-184M15.1. NXF1 is a known interacting partner of ALYREF in the transcription-export (TREX) complex. With RP11-184M15.1 knockdown, the protein level of ALYREF decreased, and Ingenuity Pathway Analysis (IPA) of RNA-seq data of control versus RP11-184M15.1 knockdown revealed that THO complex subunit 5 homolog (THOC5), another component of the TREX complex, may be an upstream regulator. In addition, past studies have revealed that ALYREF and NXF1 are involved in nuclear export of inflammatory mRNAs and proinflammatory macrophage phenotype, respectively. With RP11-184M15.1 knockdown, there was decreased expression of inflammatory macrophage-associated genes. It may be possible that RP11-184M15.1 functions in mRNA export, along with NXF1 and ALYREF.
2022-11-23 | GSE218308 | GEO