Biased removal and loading of centromeric histone H3 during reproduction underlies uniparental genome elimination

Abstract

Uniparental genome elimination is a dramatic case of centromeric failure, resulting in the postzygotic loss of a parental chromosome set. Genome partitioning during cell division relies on centromere attachment to spindle fibers through kinetochores. Centromeres are epigenetically specified by CENP-A (CENH3), a conserved centromeric specific histone H3 variant. In Arabidopsis, CENH3 modification results in haploid inducers, whose genome is eliminated frequently when crossed to the wild type. To investigate the underlying mechanism, we dissected the timing and molecular features of genome elimination. In zygotes and early embryos from genome elimination crosses, CENH3 occupied only the centromeres contributed by the wild-type parent. Haploid inducer chromosomes had defective kinetochores and missegregated, often forming micronuclei. This uniparental loss of centromere identity is initiated by the removal of altered CENH3 at fertilization, while wild-type CENH3 persists and maintains strong centromeric identity. Weak centromeres were capable of rebuilding functional kinetochores, but often failed when in competition with normal ones. We induced a similar weak state by mitotic dilution of wild-type CENH3. Furthermore, weakness was suppressed by crosses of haploid inducers to other variants of haploid inducers, and enhanced by mutations in ​VIM1,​ a ubiquitin ligase known to modify CENH3 and centromeric DNA methylation.. The differential stability of altered CENH3 during reproduction has important genetic and evolutionary implications.

A CENH3 mutation promotes meiotic exit and restores fertility in SMG7-deficient Arabidopsis

“…However, the substantially reduced level of CENH3 that, according to the immunocytological data, results in smaller centromeres and impaired mitotic spindles, was not efficient in haploid induction, at least in Arabidopsis cenh3-4 mutants. Notably, a comparably low frequency of Arabidopsis haploids was found after reducing the amount of wild-type CENH3 through female gametogenesis in plants heterozygous for the cenh3-1 null mutation [ 61 ]. Also in wheat, multiple knock-outs of homeologous CENH3 genes are insufficient to induce haploid plants unless combined with a hypomorphic mutation containing a short deletion in the CENH3 N-terminal domain [ 62 ].…”

Chromoanagenesis from radiation-induced genome damage in Populus

“…In plants, there are multiple cases of extensive genomic rearrangements [ 10 , 13 ], but when applying the important criterion of highly frequent and clustered (at least 10) rearrangements within a single chromosome, only haploid induction crosses in Arabidopsis thaliana display catastrophic chromosomal reconstructing patterns [ 14 ]. In these haploid induction crosses, both chromothripsis and chromoanasynthesis were detected, and the early zygotic divisions are often also accompanied by the formation of micronuclei [ 15 ], another diagnostic feature of chromothripsis [ 1 , 12 ].…”

A CENH3 mutation promotes meiotic exit and restores fertility in SMG7-deficient Arabidopsis

“…However, the substantially reduced level of CENH3 that, according to the immunocytological data, results in smaller centromeres and impaired mitotic spindles, was not efficient in haploid induction, at least in Arabidopsis cenh3-2 mutants. Notably, a comparably low frequency of Arabidopsis haploids was found after reducing the amount of wild-type CENH3 through female gametogenesis in plants heterozygous for the cenh3-1 null mutation [60]. Also in wheat, multiple knockouts of homeologous CENH3 genes are insufficient to induce haploid plants unless combined with a hypomorphic mutation containing a short deletion in the CENH3 N-terminal domain [61].…”