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ALYREF is shared by polyadenylated and nonpolyadenylated mRNA processing and export pathways

ABSTRACT: ALYREF is shared by polyadenylated and nonpolyadenylated mRNA processing and export pathways

PROVIDER: PRJNA514865 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7047430.fastq.gz	Fastqsanger.gz
	SRR7047440.fastq.gz	Fastqsanger.gz
	SRR7047431.fastq.gz	Fastqsanger.gz
	SRR7047441.fastq.gz	Fastqsanger.gz
	SRR7047432.fastq.gz	Fastqsanger.gz

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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

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

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

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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 links 3'processing and nuclear export of histone mRNAs

Project description:ALYREF links 3'processing and nuclear export of histone mRNAs

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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

ALYREF is shared by polyadenylated and nonpolyadenylated mRNA processing and export pathways

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

2019-02-27 | GSE125005 | GEO

ALYREF links 3'-end processing to nuclear export of non-polyadenylated mRNAs.

Project description:The RNA-binding protein ALYREF plays key roles in nuclear export and also 3'-end processing of polyadenylated mRNAs, but whether such regulation also extends to non-polyadenylated RNAs is unknown. Replication-dependent (RD)-histone mRNAs are not polyadenylated, but instead 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 promotes its recruitment. ALYREF promotes histone pre-mRNA 3'-end processing by facilitating U7-snRNP recruitment through physical interaction with the U7-snRNP-specific component Lsm11. Furthermore, ALYREF, together with other components of the TREX complex, enhances histone mRNA export. Moreover, we show that 3'-end processing promotes ALYREF recruitment and histone mRNA export. Together, our results point to an important role of ALYREF in coordinating 3'-end processing and nuclear export of non-polyadenylated mRNAs.

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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)

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Project description:This SuperSeries is composed of the following subset Series: GSE30703: Budding yeast mRNA poly( A) site mapping GSE30705: Budding yeast mRNA export and processing factor localization Refer to individual Series

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Budding yeast mRNA export and processing factors

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