Spatio-temporal chromosomal arrangements by late-replicating heterochromatin

Abstract

Fungal centromeres are clustered near microtubule organizing centers to help adopt the Rabl chromosomal organization. The role of centromere clustering in driving large-scale changes in structural and functional chromatin assembly remains unclear. Here, using Hi-C and super-resolution microscopy, we show that cell cycle-dependent centromere declustering and clustering states in Cryptococcus neoformans drive global changes in the 3D genome architecture. Centromeres and telomeres are scattered around the nuclear periphery at interphaseG1, and this arrangement constrains the inter-arm interactions within a chromosome, providing a unique interphaseG1 chromosome organization. Moreover, centromeres and telomeres are organized as compartments, segregating them from active euchromatic regions. Polymer modeling reveals that the transition from the unclustered to clustered centromere state during the cell cycle involves changes from a globular to an elongated chromosome architecture. Strikingly, while clustered centromeres replicate early in most yeasts, C. neoformans centromeres replicate late in S-phase, hinting a possible link between centromere clustering dynamics and CEN DNA replication timing. Overall, our study uncovers several unique organizational principles governing the dynamic genome architecture in an evolutionarily diverged basidiomycete yeast. SignificanceChromosomes occupy the nuclear space in many ways. Primary chromosomal arrangements are such that centromere regions of different chromosomes either form a cluster, as in yeasts, or are scattered around the nuclear periphery, more common in metazoans. Exceptionally, centromeres show cell cycle stage-specific clustering in the basidiomycete fungus Cryptococcus neoformans. We show that the spatial positioning and the refractory nature of centromeres and telomeres shape the arrangement and large-scale organization of chromosomes in C. neoformans. Metazoan-like late-replicating centromeres in C. neoformans possibly favor the unclustered/scattered centromere state in S-phase, not commonly found in fungi. Our results not only highlight the remarkable genome plasticity of C. neoformans but also raise the possibility that centromere replication timing determines genome organization principles.