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Series GSE130992 Query DataSets for GSE130992
Status Public on May 10, 2019
Title ChIP-seq of TREX complex proteins in HEK293T cells
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary 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.
Overall design ChIP-seq of FLAG pull down from HEK293T cells stabally transgenic for FLAG tagged Alyref, Chtop or Nxf1 fusion proteins.
Contributor(s) Sudbery I, Viphakone N, Heath C, Sims D, Wilson S
Citation(s) 31104896
Submission date May 10, 2019
Last update date Aug 01, 2019
Contact name Ian Sudbery
Organization name University of Sheffield
Department Molecular Biology and Biotechnology
Lab Sudbery Lab for Computational Genomics
Street address Firth Court, Western Bank
City Sheffield
ZIP/Postal code S11 8HG
Country United Kingdom
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (10)
GSM3759262 Alyref ChIP rep 1
GSM3759263 Alyref ChIP rep 2
GSM3759264 Alyref Input rep 1
This SubSeries is part of SuperSeries:
GSE113953 Co-transcriptional loading of RNA export factors shapes the human transcriptome
BioProject PRJNA542257
SRA SRP197516

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE130992_RAW.tar 3.1 Gb (http)(custom) TAR (of BW)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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