Nuclear Basket Proteins Mlp1 and Nup2 Drive Heat Shock–Induced 3D Genome Restructuring

The nuclear pore complex (NPC), a multisubunit complex located within the nuclear envelope, regulates RNA export and the import and export of proteins. Here we address the role of the NPC in driving thermal stress-induced 3D genome repositioning of _Heat Shock Responsive_ (_HSR_) genes in yeast. We found that two nuclear basket proteins, Mlp1 and Nup2, although dispensable for NPC integrity, are required for driving _HSR_ genes into coalesced chromatin clusters, consistent with their strong, heat shock-dependent recruitment to _HSR_ gene regulatory and coding regions. _HSR_ gene clustering occurs predominantly within the nucleoplasm and is independent of the essential scaffold-associated proteins Nup1 and Nup145. Notably, double depletion of Mlp1 and Nup2 has little effect on the formation of Heat Shock Factor 1 (Hsf1)-containing transcriptional condensates, Hsf1 and Pol II recruitment to _HSR_ genes, or _HSR_ mRNA abundance. Our results define a 3D genome restructuring role for nuclear basket proteins extrinsic to the NPC and downstream of _HSR_ gene activation.