Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA291503 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR2135570.fastq.gz | Fastqsanger.gz | |||
| SRR2135571.fastq.gz | Fastqsanger.gz | |||
| SRR2135572.fastq.gz | Fastqsanger.gz | |||
| SRR2135564.fastq.gz | Fastqsanger.gz | |||
| SRR2135565.fastq.gz | Fastqsanger.gz |
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Project description:The flow of genetic information from DNA to protein requires polymerase-II transcribed RNA characterized by the presence of a 5’cap. The cap-binding complex (CBC), consisting of the nuclear cap-binding protein (NCBP) 2 and its adaptor NCBP1, is believed to bind all capped RNA and to be necessary for its processing and intracellular localization. Here, we show that NCBP1 but not NCBP2 is required for cell viability and poly(A) RNA export. We identify C17orf85 (here named NCBP3) as cap-binding protein that together with NCBP1 forms an alternative CBC in higher eukaryotes. NCBP3 binds mRNA, associates with components of the mRNA processing machinery and contributes to poly(A) RNA export. Loss of NCBP3 can be compensated by NCBP2 under steady state conditions. However, NCBP3 becomes pivotal under stress conditions such as virus infection. We propose the existence of an alternative CBC involving NCBP1 and -3 that plays a key role in mRNA biogenesis.
2015-10-01 | GSE71552 | GEO
Project description:ARS2 is a highly conserved metazoan protein involved in numerous aspects of nuclear RNA metabolism. As a direct partner of the nuclear cap-binding complex (CBC) it mediates interactions with diverse RNA processing and transport machineries in a transcript-dependent manner. Here we present the human ARS2 crystal structure, which exhibits similarities and metazoan-specific differences to the plant homologue SERRATE, most notably an additional RRM domain. We present biochemical, biophysical and cellular interactome data comparing wild type and mutant ARS2 that identify regions critical for interactions with FLASH (involved in histone mRNA biogenesis), NCBP3 (a putative cap-binding protein involved in mRNA export) and single-stranded RNA. We show that FLASH and NCBP3 have overlapping binding sites on ARS2 and that CBC-ARS2-NCBP3 form a ternary complex that is mutually exclusive with CBC-ARS-PHAX (involved in snRNA export). Our results support that mutually exclusive higher order CBC-ARS2 complexes are critical in determining Pol II transcript fate.
2018-09-03 | PXD009035 | Pride
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: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 | GSE113952 | 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:hCLE/RTRAF-HSPC117-DDX1-FAM98B: A new cap-binding complex that activates mRNA translation
| PRJNA331206 | ENA
Project description:A 5′, 7-methylguanosine cap is a quintessential feature of RNA polymerase II-transcribed RNAs, and thus a textbook aspect of co-transcriptional pre-mRNA processing. The cap is bound by the cap-binding complex (CBC), canonically consisting of nuclear cap-binding proteins 1 and 2 (NCBP1/2). Recently, NCBP3 has been proposed to form an alternative, non-canonical CBC, together with NCBP1. NCBP3 has also been shown to interact with the canonical CBC along with the protein SRRT (aka ARS2), in a manner that is mutually exclusive with the RNA export factor, PHAX. Taken together, ambiguities and missing information in the bona fide physiological protein-protein associations of NCBP3 persist. In an effort to clarify the compositions of NCBP1-, 2-, and 3-related macromolecular assemblies, including their intersections and differences, we have applied our recently developed interactome screening platform (PMID: 25938370). Here the experimental design and data processing have been modified and updated to identify interactome differences between targets of affinity capture under a wide range of experimental conditions, followed by label-free quantitative mass spectrometry.
2020-11-09 | PXD016038 | Pride
Project description:The nuclear cap-binding complex (CBC) stimulates multiple steps in several RNA maturation pathways, but how it functions in humans is incompletely understood. For small capped RNAs like pre-snRNAs, the CBC recruits PHAX. Here, we identify the CBCAP complex, composed of CBC, Ars2 and PHAX, and show that both CBCAP and CBC-Ars2 complexes can be reconstituted from recombinant proteins. Ars2 stimulates PHAX binding to the CBC as well as snRNAs 3'-end processing, hereby coupling maturation with export. In vivo, CBC and Ars2 bind similar capped non-coding and coding RNAs, and stimulate their 3M-bM-^@M-^Y-end processing. Strongest effects are displayed for cap-proximal polyadenylation sites, thereby favoring premature transcription termination. Ars2 functions in part through the mRNA 3M-bM-^@M-^Y-end cleavage factor CLP1, which binds RNA Polymerase II through PCF11. Ars2 is thus a major CBC effector that stimulates functional and cryptic 3'-end processing sites. In total 12 samples; 4 control IP, 2 Flag- Ars2 IP and 2 Flag-CBP20 IP; 2 control FFL siRNA and 2 siRNA Ars2
2013-11-08 | E-GEOD-52131 | biostudies-arrayexpress
Project description:Gene expression results from mRNA - RNA-binding protein (RBP) interactions within messenger ribonucleoprotein (mRNP) particles. We identified heterogeniety of nuclear mRNP composition involved in mRNA biogenesis and export with different occupancy and stoichiometry of RNA-binding proteins. Especially, mRNA export adopter protein Yra1 showed large variation of its stoichiometry on single mRNPs. We identified stoichiometry of Yra1 in the nuclear cap binding complex (Cbp80) bound mRNPs and it can be dissected into two categories (one and multiple Yra1 bound mRNPs). Multiple Yra1 containing mRNPs specifically co-occupied with THO complex (Hpr1). To investigate gene dependency to form different Yra1 stoichiometry mRNPs, we performed RNA-IP experiment for Yra1 with two step purification by Cbp80/Yra1 and Hpr1/Yra1.
2024-02-14 | GSE226972 | GEO
Project description:Global RNA-binding profile of the mRNA export adaptor ALYREF
| PRJNA387174 | ENA