Interspecies conservation of organisation and function between nonhomologous regional centromeres

Pin Tong,Carolin A Müller,Alison L Pidoux,Conrad A Nieduszynski,Manu Shukla,Robin C Allshire,Ryan Ard,Jesus Torres-Garcia,Harald Berger,Nicholas R T Toda

doi:10.1038/s41467-019-09824-4

Abstract

Despite the conserved essential function of centromeres, centromeric DNA itself is not conserved. The histone-H3 variant, CENP-A, is the epigenetic mark that specifies centromere identity. Paradoxically, CENP-A normally assembles on particular sequences at specific genomic locations. To gain insight into the specification of complex centromeres, here we take an evolutionary approach, fully assembling genomes and centromeres of related fission yeasts. Centromere domain organization, but not sequence, is conserved between Schizosaccharomyces pombe, S. octosporus and S. cryophilus with a central CENP-ACnp1 domain flanked by heterochromatic outer-repeat regions. Conserved syntenic clusters of tRNA genes and 5S rRNA genes occur across the centromeres of S. octosporus and S. cryophilus, suggesting conserved function. Interestingly, nonhomologous centromere central-core sequences from S. octosporus and S. cryophilus are recognized in S. pombe, resulting in cross-species establishment of CENP-ACnp1 chromatin and functional kinetochores. Therefore, despite the lack of sequence conservation, Schizosaccharomyces centromere DNA possesses intrinsic conserved properties that promote assembly of CENP-A chromatin.

Highlights

Introduction ofS. pombe central-core (S.pom-cnt) DNA on minichromosomes into S. pombe results in the establishment and maintenance of CENP-ACnp[1] chromatin if S.pom-cnt is adjacent to heterochromatin, or if CENP-A is overexpressed[6,17,18,36]
We show that Schizosaccharomyces centromeres are not conserved in sequence, those of Schizosaccharomyces octosporus and Schizosaccharomyces cryophilus share with S. pombe a conserved organization of a central domain assembled in CENP-ACnp[1] chromatin, flanked by outer repeats assembled in heterochromatin
Despite the lack of sequence conservation, S. octosporus and S. cryophilus centromere organization is strongly conserved with that of S. pombe, having CENP-ACnp1-assembled central domains separated by clusters of tRNA genes from outer repeats assembled in heterochromatin[13,14] (Supplementary Fig. 5, Supplementary Table 3, Supplementary Data 5)

Summary

Introduction

Introduction ofS. pombe central-core (S.pom-cnt) DNA on minichromosomes into S. pombe results in the establishment and maintenance of CENP-ACnp[1] chromatin if S.pom-cnt is adjacent to heterochromatin, or if CENP-A is overexpressed[6,17,18,36]. Centromere function was established on S.oct-cnt-containing minichromosomes in hi-CENP-ACnp[1] cells (Fig. 6b, c and Table 1). CENP-ACnp[1] ChIP-quantitative PCR (ChIP-qPCR) indicated that, for minichromosomes with established centromere function, CENP-ACnp[1] chromatin was assembled on nonhomologous S.oct-cnt DNA, to levels similar to those at endogenous S. pombe centromeres and to S.pom-cnt[2] on a minichromosome (Fig. 6d). Minichromosomes containing S. cryophilus central-core regions (S.cry-cnt) were able to establish functional centromeres and segregation function in S. pombe. These S.cry-cnt-bearing minichromosomes assembled CENP-ACnp[1] chromatin to high levels, similar to those at endogenous S. pombe centromeres (Supplementary Fig. 8). Our analyses indicate that S.oct-cnt and S.cry-cnt DNAs are competent to establish CENP-A chromatin and centromere function in S. pombe when CENPACnp[1] is overexpressed, suggesting that S. octosporus and S. cryophilus central-core DNA have intrinsic properties that promote the establishment of CENP-A chromatin despite lacking sequence homology

Methods

Results

Conclusion