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Series GSE288633 Query DataSets for GSE288633
Status Public on Mar 24, 2025
Title thiol(SH)-linked alkylation for the metabolic sequencing (SLAM-seq) of RNA after Crm1 inhibition and Nup1/Nup2 degradation
Organism Saccharomyces cerevisiae
Experiment type Other
Summary Nuclear pore proteins (Nups) physically interact with hundreds of chromosomal sites, impacting transcription. In yeast, transcription factors mediate interactions between Nups and enhancers and promoters. To define the molecular basis of this mechanism, we exploited a separation-of-function mutation in the Gcn4 transcription factor that blocks its interaction with the nuclear pore complex (NPC). This mutation reduces the interaction of Gcn4 with the highly conserved nuclear export factor Crm1/Xpo1. Crm1 and Nups co-occupy enhancers and Crm1 inhibition blocks interaction of the nuclear pore protein Nup2 with the genome. In vivo, Crm1 interacts stably with the NPC. In vitro, Crm1 binds both Gcn4 and Nup2 directly. Importantly, the interaction between Crm1 and Gcn4 requires neither Ran-GTP nor the nuclear export sequence binding site. Finally, Crm1 and Ran-GTP stimulate DNA binding by Gcn4, suggesting that allosteric coupling between Crm1-Ran-GTP binding and DNA binding facilitates docking of transcription factor-bound enhancers at the NPC.
 
Overall design thiol(SH)-linked alkylation for the metabolic sequencing (SLAM-seq) was used to investigate the impact of Crm1 inhibition and degradation of Nup1 or Nup2 on the nascent and total transcriptome in budding yeast.
Web link https://doi.org/10.1016/j.molcel.2025.02.013
 
Contributor(s) Ge T, Marcou N, Brickner JH
Citation(s) 40068679
BioProject PRJNA1109460
Submission date Feb 03, 2025
Last update date Mar 25, 2025
Contact name Tiffany Ge
E-mail(s) tiffanyge@u.northwestern.edu
Organization name Northwestern University
Lab Brickner
Street address 2205 Tech Drive
City Evanston
State/province IL
ZIP/Postal code 60201
Country USA
 
Platforms (1)
GPL35358 Element AVITI (Saccharomyces cerevisiae)
Samples (35)
GSM8771584 Crm1(T539C), SDC LMB, Replicate 1
GSM8771585 Crm1(T539C), SDC LMB, Replicate 2
GSM8771586 Crm1(T539C), SDC LMB, Replicate 3
This SubSeries is part of SuperSeries:
GSE288820 Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex

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
GSE288633_RAW.tar 7.9 Mb (http)(custom) TAR (of TSV)
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Raw data are available in SRA
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