Exportin-1 functions as an adaptor for transcription factor-mediated docking of chromatin at the nuclear pore complex

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.

This dataset contains processed aligned reads (.bam files) from four main questions we addressed in our paper:
1) Where do Crm1, Nups, and RNA Pol II bind in the genome? [ChEC-seq2]
2) What is the relationship between Crm1 and Nup2? Are they interdependent or does the binding of one factor depend on the other? [ChEC-seq2]
3) Does loss of Crm1 or Nups (Nup1/Nup2) affect nascent transcription? If so, how? [SLAM-seq]
4) How does Leptomycin B (LMB, inhibitor of Crm1) affect binding of Crm1 and transcription factor Gcn4 to the genome? [ChEC-seq2]

ChEC-seq2 data was obtained and processed as described in VanBelzen et al. 2024, with reads trimmed with Trimmomatic and mapped to the Saccharomyces cerevisiae genome (sacCer3) using Bowtie2. For peak calling analyses, we processed the bam files by trimming them to the first base pair and called peaks using DoubleChEC (VanBelzen et al. 2024). SLAM-seq was performed as described in Herzog et al. 2017 and Alalam et al., 2022, using 0.2 mM 4-thiouracil (4sU) for 6 min at 30°C prior to harvesting, and processed using SLAM-DUNK (Herzog et al. 2017), which generated the read counts (.tsv files). Differential expression was analyzed using DESeq2 (Love et al., 2014). All sample information (BioProject, Biosample, SRA, GEO) is included in the Sample information spreadsheet.