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| 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.
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| |
|
| Overall design |
ChIP-seq of FLAG pull down from HEK293T cells stabally transgenic for FLAG tagged Alyref, Chtop or Nxf1 fusion proteins.
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| |
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| 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 |
| E-mail(s) |
[email protected]
|
| 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)
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| This SubSeries is part of SuperSeries: |
| GSE113953 |
Co-transcriptional loading of RNA export factors shapes the human transcriptome |
|
| Relations |
| BioProject |
PRJNA542257 |
| SRA |
SRP197516 |
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