Nuclear pore association confers optimal expression levels for an inducible yeast gene

Abstract

The organization of the nucleus into subcompartments creates microenvironments that are thought to facilitate distinct nuclear functions. In budding yeast, regions of silent chromatin, such as those at telomeres and mating-type loci, cluster at the nuclear envelope creating zones that favour gene repression. Other reports indicate that gene transcription occurs at the nuclear periphery, apparently owing to association of the gene with nuclear pore complexes. Here we report that transcriptional activation of a subtelomeric gene, HXK1 (hexokinase isoenzyme 1), by growth on a non-glucose carbon source led to its relocalization to nuclear pores. This relocation required the 3' untranslated region (UTR), which is essential for efficient messenger RNA processing and export, consistent with an accompanying report. However, activation of HXK1 by an alternative pathway based on the transactivator VP16 moved the locus away from the nuclear periphery and abrogated the normal induction of HXK1 by galactose. Notably, when we interfered with HXK1 localization by either antagonizing or promoting association with the pore, transcript levels were reduced or enhanced, respectively. From this we conclude that nuclear position has an active role in determining optimal gene expression levels.

Co-transcriptional degradation by the 5′-3′ exonuclease Rat1p mediates quality control of HXK1 mRNP biogenesis in S. cerevisiae

“…Since the expression of HXK1 is known to be highly modulated by the level of glucose in the growth medium, 27 we wanted to verify if Rho exerts a similar effect under conditions where the HXK1 gene is at its highest expression. In agreement with previous measurements, 28 when the yeast cells were grown in 2% galactose instead of glucose, the steady-state level of HXK1 mRNA determined by RT-qPCR increased 16 to 17-fold. The expression of Rho in the galactosegrowth conditions leads to a 30% decrease of the HXK1 mRNA level (Fig.…”

“…HXK1 is a subtelomeric gene known to localize to the nuclear periphery and to form a gene loop between the promoter and the terminator region in interaction with the nuclear pore complex. 28,32,33 Although some of these properties have been observed under the highest expression (galactose growth) conditions that amplify the experimental detection, this does not rule out their existence under moderate expression (glucose growth) as in our case and as was observed by others. 34,35 Thus, an alternative hypothesis could be that the anchoring to the nuclear envelope and the formation of a gene loop structure could hinder the accessibility of the transcript 3 0 end to degradation by Rrp6p while leaving the 5 0 end accessible to Dcp2p and Rat1p.…”

Nuclear organization in genome stability: SUMO connections

“…Although there is no evidence yet showing that specific pores bind specific sets of genes, recent studies implicate nuclear pores in a range of cellular processes, well beyond their function in macromolecular transport. Notably, in budding yeast and Drosophila certain highly transcribed, and in some cases stress-induced, genes are associated with nuclear pores [11][12][13][14][15][16][17][18][19]. This association not only promotes efficient export of mRNAs through coupling of transcription with export [10,11,13,14], but also helps modulate transcript levels of some loci.…”

Chromatin organization at the nuclear periphery as revealed by image analysis of structured illumination microscopy data

“…The evidence for a functional relationship between active genes and NPCs has been mostly shown in yeast. Inducible yeast genes, such as INO1, are targeted to the NPC upon activation, and this association was proven to be functionally important (Light et al, 2010;Taddei et al, 2006). In metazoa, genome-wide studies have reported a role for nucleoporins during development (reviewed in Talamas and Capelson, 2015).…”