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Co-transcriptional loading of RNA export factors shapes the human transcriptome

ABSTRACT: Co-transcriptional loading of RNA export factors shapes the human transcriptome

PROVIDER: PRJNA454664 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7087900.fastq.gz	Fastqsanger.gz
	SRR7087910.fastq.gz	Fastqsanger.gz
	SRR7087920.fastq.gz	Fastqsanger.gz
	SRR7087930.fastq.gz	Fastqsanger.gz
	SRR7087901.fastq.gz	Fastqsanger.gz

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piRNA-guided co-transcriptional silencing coopts nuclear export factors

Project description:piRNA-guided co-transcriptional silencing coopts nuclear export factors

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Co-transcriptional Loading of RNA Export Factors Shapes the Human Transcriptome.

Project description:During gene expression, RNA export factors are mainly known for driving nucleo-cytoplasmic transport. While early studies suggested that the exon junction complex (EJC) provides a binding platform for them, subsequent work proposed that they are only recruited by the cap binding complex to the 5' end of RNAs, as part of TREX. Using iCLIP, we show that the export receptor Nxf1 and two TREX subunits, Alyref and Chtop, are recruited to the whole mRNA co-transcriptionally via splicing but before 3' end processing. Consequently, Alyref alters splicing decisions and Chtop regulates alternative polyadenylation. Alyref is recruited to the 5' end of RNAs by CBC, and our data reveal subsequent binding to RNAs near EJCs. We demonstrate that eIF4A3 stimulates Alyref deposition not only on spliced RNAs close to EJC sites but also on single-exon transcripts. Our study reveals mechanistic insights into the co-transcriptional recruitment of mRNA export factors and how this shapes the human transcriptome.

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Co-transcriptional loading of RNA export factors shapes the human transcriptome

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

2019-05-01 | GSE113953 | GEO

Budding yeast mRNA export and processing factors

Project description:Budding yeast mRNA export and processing factors

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piRNA-guided co-transcriptional silencing coopts nuclear export factors

Project description:The PIWI-interacting RNA (piRNA) pathway is a small RNA-based immune system that controls the expression of transposons and maintains genome integrity in animal germlines1,2. In Drosophila, piRNA-guided silencing is achieved, in part, via co-transcriptional repression of transposons by Piwi. This depends on Panoramix (Panx)3,4; however, precisely how an RNA binding event silences transcription remains to be determined. Here we show that Nuclear Export Factor 2 (Nxf2) and its co-factor, Nxt1, form a complex with Panx, and are required for co-transcriptional silencing of transposons in somatic and germline cells of the ovary. Tethering of Nxf2 to either RNA or DNA results in silencing of target loci and the concomitant accumulation of repressive chromatin marks. Nxf2 and Panx proteins are mutually required for proper localization and stability. We mapped the protein domains crucial for the Nxf2/Panx complex formation and show that the amino-terminal portion of Panx is sufficient to induce transcriptional silencing. Loss of Nxf2 or Panx results in nuclear accumulation of transposon transcripts, which is for some transposons Piwi-dependent. We propose a model whereby Piwi binding to nascent transposon RNAs can provide a fail-safe mechanism, by promoting their nuclear retention, for those few transcripts that might be generated during the process of recognition and co-transcriptional repression.

2019-06-20 | GSE121661 | GEO

RNAi knock down of export factors in Drosphila Schneider cell lines

Project description:Six different endogenous Drosophila proteins (all potential export factors) have been inactivated using RNAi and leptomycin B (LMB) treatments. Five different endogenous Drosophila proteins (all potential export factors) have been targeted by RNAi. The effect on mRNA export is analyzed by monitoring the levels of mRNAs in cytoplasmic and total samples. Samples from knock-downs are compared to samples obtained from (GFP transfected) control cells processed in parallel. [The two samples compared have the same name, but the suffix _KD for knock down and _ctrl for the control]. The potential export factors targeted by RNAi are: NXF1, NXF2, NXF3, p15 and UAP56. In an additional control experiment the translation initiation factor eIF4G was targeted by RNAi (to control for the specificity of the observed effects). The samples were taken 2 (nxf1_d2), 4 (nxf1_d4, p15_d4, uap56_d4), 5 (nxf2_d5, nxf3_d5) or 6 (IF_d6) days after transfecting with dsRNA. Crm1, a transport factor responsible for protein export and the export of UsnRNAs and ribosomal subunits, has been specifically inactivated using LMB (instead of RNAi).

2003-05-15 | E-MEXP-4 | biostudies-arrayexpress

piRNA-guided co-transcriptional silencing coopts nuclear export factors

2019-06-20 | PXD011415 | Pride

Genome-wide CRISPR screen for export factors of NORAD lncRNA

Project description:Genome-wide CRISPR screen for export factors of NORAD lncRNA

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Trypanosomes can initiate nuclear export co-transcriptionally

Project description:The nuclear envelope serves as important mRNA surveillance system. In yeast and human, several control systems act in parallel to prevent nuclear export of unprocessed mRNAs. Trypanosomes lack homologues to most of the involved proteins and their nuclear mRNA metabolism is non-conventional exemplified by polycistronic transcription and mRNA processing by trans-splicing. We here visualised nuclear export in trypanosomes by probing large, endogenous mRNA by intramolecular multi-colour single molecule FISH (smFISH). In addition, unspliced mRNAs were visualised by co-probing two adjacent introns or intergenic regions. We found that the initation of nuclear export requires neither the completion of transcription nor trans-splicing. Nevertheless, the inhibition of trans-splicing blocked cytoplasmic transport of the of unspliced mRNAs and only a small fraction reached the nucleus-distant cytoplasm. Most of the unspliced transcripts remained at the nuclear periphery, within transport and in nuclear periphery granules (NPGs) localised at the cytoplasmic site of nuclear pores that resemble stress granules in composition. Our work shows that, in striking contrast to other eukaryotes, trypanosomes can start nuclear export while the mRNA is still transcribed, but unspliced transcripts remain ‘stuck’ in nuclear pores, probably awaiting processing or decay. Our data indicate that trypanosomes regulate the completion of nuclear export rather than the start.

2018-10-26 | PXD010143 | Pride

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