Distinct 'safe zones' at the nuclear envelope ensure robust replication of heterochromatic chromosome regions

Chromosome replication and transcription occur within a complex nuclear milieu whose functional subdomains are only beginning to be mapped out. The nuclear envelope (NE) generally interacts with heterochromatic regions of the genome that are inherently difficult to replicate. Here we delineate compositionally and functionally distict domains of the fission yeast NE, focusing on the NE regions specifically enriched for the inner NE protein, Bqt4, or the conserved lamin interacting domain protein, Lem2. Bqt4 is relatively mobile around the NE and acts in two capacities. First, Bqt4 is required for tethering two key heterochromatic regions, the chromosome termini and the mat locus, to the NE specifically while these regions are undergoing DNA replication. This positioning is required for robust replication and heterochromatin assembly in the wake of the replication fork. Second, Bqt4 mobilizes a subset of Lem2 molecules around the NE, where Lem2/Bqt4 promote pericentric heterochromatin maintenance. Opposing Bqt4-dependent Lem2 mobility are factors that stabilize Lem2 at its most abundant localization site beneath the centrosome, where Lem2 plays a crucial role in kinetochore maintenance. Our data prompt a model in which Bqt4-rich nuclear subdomains are 'safe zones' in which collisions between transcription and replication are averted and heterochromatin is reassembled faithfully following replication. Overall design: Examination of H3K9me histone modifications in 5 strains. Different strain numbers indicates that there could be unknown differences in genotypes of cells that should be otherwise similar. There are two types of replicates. One is by repeating the ChIP-Seq experiment on the same strain (e.g. JCT109 that is the parent). The second type of replicate is ''independent sister cells''; in this case the strain number is different but "relevant" genotype is the same. For example, JCF14512 and JCF14513 are sisters that come from the same parent with identical genotypes.