The Role of Transcription Factors and Nuclear Pore Proteins in Controlling the Spatial Organization of the Yeast Genome

Abstract

Loss of nuclear pore complex (NPC) proteins, transcription factors (TFs), histone modification enzymes, Mediator, and factors involved in mRNA export disrupts the physical interaction of chromosomal sites with NPCs. Conditional inactivation and ectopic tethering experiments support a direct role for the TFs Gcn4 and Nup2 in mediating interaction with the NPC but suggest an indirect role for factors involved in mRNA export or transcription. A conserved ''positioning domain'' within Gcn4 controls interaction with the NPC and inter-chromosomal clustering and promotes transcription of target genes. Such a function may be quite common; a comprehensive screen reveals that tethering of most yeast TFs is sufficient to promote targeting to the NPC. While some TFs require Nup100, others do not, suggesting two distinct targeting mechanisms. These results highlight an important and underappreciated function of TFs in controlling the spatial organization of the yeast genome through interaction with the NPC.

Recruitment of an Activated Gene to the Yeast Nuclear Pore Complex Requires Sumoylation

“…Two cis-acting DNA elements 5 to the INO1 ORF are involved in INO1 recruitment to NPCs following long-term repression (Ahmed et al, 2010;Light et al, 2010;. Both sites bind TFs, GRS-I binds Put3 and GRS-II binds Cbf1, and each TF is required for directing GRS-containing DNA elements to NPCs (Shetty and Lopes, 2010;Brickner and Brickner, 2012;Brickner et al, 2019). Notably, while TFs may be required for NPC association of activated genes Brickner et al, 2019), RNA polymerase II-mediated transcription is not necessarily required, as shown for both GAL1 and INO1 (Schmid et al, 2006;Brickner et al, 2007Brickner et al, , 2016.…”

“…Following their activation, numerous yeast genes are repositioned from the nuclear interior to the nuclear envelope (Brickner and Walter, 2004;Brickner et al, 2019). A wellstudied example is the INO1 gene.…”

“…The association of activated genes with NPCs is thought to occur through interactions between the transcriptional machinery and proteins located on the nuclear face of the NPC. Among these, Nup60 and the related proteins Mlp1/Mlp2 are required for INO1 association with NPCs (Brickner et al, 2007;Ahmed et al, 2010;Light et al, 2010;Brickner et al, 2019). These NPC proteins are also required for the association of the desumoylase Ulp1 with NPCs (Zhao et al, 2004;Palancade et al, 2007;Srikumar et al, 2013).…”

“…Among the various mechanisms by which NPCs can influence gene expression is their direct interactions with chromatin. NPCs interact with both transcriptionally repressed and active genes through interactions that appear to be mediated by transcription factors (TFs) of various types that bind specific chromatin sites and interact with different sets of Nups (Brickner et al, 2007;Ahmed et al, 2010;Light et al, 2010;Ruben et al, 2011;Van de Vosse et al, 2013;Brickner et al, 2019). These interactions influence both the spatial organization of associated genes and contribute to transcriptional state.…”

“…Following induction (inositol starvation), Opi1, presumably with Ume6 and Rpd3(L), dissociates from INO1. This is thought to be followed by the binding of TFs (Put3 and Cbf1) to cis-acting DNA elements (termed gene GRS1 and GRS2), which exhibit redundant functions in targeting INO1 to an NPC (Loewen et al, 2003;Brickner and Walter, 2004;Shetty and Lopes, 2010;Brickner and Brickner, 2012;Brickner et al, 2019). The SAGA complex (involved in transcription initiation) also appears to contribute to the association of active INO1 with the NPC (Lo et al, 2001(Lo et al, , 2005.…”