Structure and Function in the Budding Yeast Nucleus

Abstract

Budding yeast, like other eukaryotes, carries its genetic information on chromosomes that are sequestered from other cellular constituents by a double membrane, which forms the nucleus. An elaborate molecular machinery forms large pores that span the double membrane and regulate the traffic of macromolecules into and out of the nucleus. In multicellular eukaryotes, an intermediate filament meshwork formed of lamin proteins bridges from pore to pore and helps the nucleus reform after mitosis. Yeast, however, lacks lamins, and the nuclear envelope is not disrupted during yeast mitosis. The mitotic spindle nucleates from the nucleoplasmic face of the spindle pole body, which is embedded in the nuclear envelope. Surprisingly, the kinetochores remain attached to short microtubules throughout interphase, influencing the position of centromeres in the interphase nucleus, and telomeres are found clustered in foci at the nuclear periphery. In addition to this chromosomal organization, the yeast nucleus is functionally compartmentalized to allow efficient gene expression, repression, RNA processing, genomic replication, and repair. The formation of functional subcompartments is achieved in the nucleus without intranuclear membranes and depends instead on sequence elements, protein-protein interactions, specific anchorage sites at the nuclear envelope or at pores, and long-range contacts between specific chromosomal loci, such as telomeres. Here we review the spatial organization of the budding yeast nucleus, the proteins involved in forming nuclear subcompartments, and evidence suggesting that the spatial organization of the nucleus is important for nuclear function. TABLE OF CONTENTS Abstract 107Introduction 108

Perinuclear tethers license telomeric DSBs for a broad kinesin- and NPC-dependent DNA repair process

“…Deletion of the Nup84 subcomplex components Nup84 or Nup145, or of the perinuclear telomere-tethering protein Esc1, significantly decreased survival of the subtelomeric DSB, as expected ( Fig. 1b; Supplementary Table 1) 21,22,28 . Disruption of the telomere-tethering complex cohibin (composed of Lrs4 and Csm1 proteins) alone or in combination with Esc1 deletion, similarly compromised subtelomeric DSB survival (Fig.…”

“…It will be important to determine whether error-prone DNA repair processes similar to the one uncovered here play a role in secondary or resistant cancers. In addition, perinuclear telomere tethers have been viewed as guardians of chromosome ends 4,21 . However, our findings suggest that in the presence of a DSB, perinuclear tethers can help propagate compromised genomes through engagement of the BIR pathway.…”

“…These telomeric clusters do not co-localize with nuclear pore complexes 17 . Intriguingly, the ability to survive a subtelomeric DSB is dependent on Nup84 as well as a number of factors known to anchor telomere clusters to the nuclear envelope 12,13,[18][19][20][21][22] . However, the relationship between perinuclear telomere tethers and nuclear pore subcomplexes in subtelomeric DNA repair remains unknown 12,23 .…”

Cohesins and condensins orchestrate the 4D dynamics of yeast chromosomes during the cell cycle

“…The chromosomes of prokaryotes and eukaryotes display multiple levels of hierarchical organization, whose dynamic changes influence or regulate metabolic processes including gene expression and DNA replication and repair (Taddei & Gasser, 2012; Wang et al , 2013; Dekker & Mirny, 2016). The improper coordination of chromosome condensation and segregation during the cell cycle can lead to important structural abnormalities and result in cell death or diseases such as cancer (Valton & Dekker, 2016).…”

“…The genome of budding yeast Saccharomyces cerevisiae presents a Rabl organization driven by (i) centromeres clustering at the spindle pole body (SPB, S. cerevisiae microtubule organizing center), (ii) telomeres tethering to the nuclear envelope, (iii) the nucleolus where the rDNA is sequestered opposite to the SPB, and (iv) chromosome arm length (Burgess & Kleckner, 1999; Taddei & Gasser, 2012). Hi‐C experiments have confirmed this Rabl organization, but the existence of sub‐megabase structures within yeast chromosomes similar to mammalian topological associated domains or their bacterial equivalent is still controversial (Duan et al , 2010; Hsieh et al , 2015; Eser et al , 2017).…”