MUS81 is required for atypical recombination intermediate resolution but not crossover designation in rice

Microsatellite break-induced replication generates highly mutagenized extrachromosomal circular DNAs

Extrachromosomal circular DNAs (eccDNAs) are produced from all regions of the eucaryotic genome. We used inverse PCR of non-B microsatellites capable of forming hairpin, triplex, quadruplex and AT-rich structures integrated at a common ectopic chromosomal site to show that these non-B DNAs generate highly mutagenized eccDNAs by replication-dependent mechanisms. Mutagenesis occurs within the non-B DNAs and extends several kilobases bidirectionally into flanking and nonallelic DNA. Each non-B DNA exhibits a different pattern of mutagenesis, while sister clones containing the same non-B DNA also display distinct patterns of recombination, microhomology-mediated template switching and base substitutions. Mutations include mismatches, short duplications, long nontemplated insertions, large deletions and template switches to sister chromatids and nonallelic chromosomes. Drug-induced replication stress or the depletion of DNA repair factors Rad51, the COPS2 signalosome subunit or POLη change the pattern of template switching and alter the eccDNA mutagenic profiles. We propose an asynchronous capture model based on break-induced replication from microsatellite-induced DNA double strand breaks to account for the generation and circularization of mutagenized eccDNAs and the appearance of genomic homologous recombination deficiency (HRD) scars. These results may help to explain the appearance of tumor eccDNAS and their roles in neoantigen production, oncogenesis and resistance to chemotherapy.

Microsatellite break-induced replication generates highly mutagenized extrachromosomal circular DNAs

Extrachromosomal circular DNAs (eccDNAs) are produced from all regions of the eucaryotic genome. In tumors, highly transcribed eccDNAs have been implicated in oncogenesis, neoantigen production and resistance to chemotherapy. Here we show that unstable microsatellites capable of forming hairpin, triplex, quadruplex and AT-rich structures generate eccDNAs when integrated at a common ectopic site in human cells. These non-B DNA prone microsatellites form eccDNAs by replication-dependent mechanisms. The microsatellite-based eccDNAs are highly mutagenized and display template switches to sister chromatids and to nonallelic chromosomal sites. High frequency mutagenesis occurs within the eccDNA microsatellites and extends bidirectionally for several kilobases into flanking DNA and nonallelic DNA. Mutations include mismatches, short duplications, longer nontemplated insertions and large deletions. Template switching leads to recurrent deletions and recombination domains within the eccDNAs. Template switching events are microhomology-mediated, but do not occur at all potential sites of complementarity. Each microsatellite exhibits a distinct pattern of recombination, microhomology choice and base substitution signature. Depletion of Rad51, the COPS2 signalosome subunit or POLη alter the eccDNA mutagenic profiles. We propose an asynchronous capture model based on break-induced replication from microsatellite-induced DNA breaks for the generation and circularization of mutagenized eccDNAs and genomic homologous recombination deficiency (HRD) scars.

FANCM interacts with the MHF1-MHF2 complex to limit crossover frequency during rice meiosis

Crossovers (COs) are necessary for generating genetic diversity that breeders can select, but there are conserved mechanisms that regulate their frequency and distribution. Increasing CO frequency may raise the efficiency of selection by increasing the chance of integrating more desirable traits. In this study, we characterize rice FANCM and explore its functions in meiotic CO control. FANCM mutations do not affect fertility in rice, but they cause a great boost in the overall frequency of COs in both inbred and hybrid rice, according to genetic analysis of the complete set of fancm zmm (hei10, ptd, shoc1, mer3, zip4, msh4, msh5, and heip1) mutants. Although the early homologous recombination events proceed normally in fancm, the meiotic extra COs are not marked with HEI10 and require MUS81 resolvase for resolution. FANCM depends on PAIR1, COM1, DMC1, and HUS1 to perform its functions. Simultaneous disruption of FANCM and MEICA1 synergistically increases CO frequency, but it is accompanied by nonhomologous chromosome associations and fragmentations. FANCM interacts with the MHF complex, and ablation of rice MHF1 or MHF2 could restore the formation of 12 bivalents in the absence of the ZMM gene ZIP4. Our data indicate that unleashing meiotic COs by mutating any member of the FANCM-MHF complex could be an effective procedure to accelerate the efficiency of rice breeding.

Crossover interference mechanism: New lessons from plants

Plants are the source of our understanding of several fundamental biological principles. It is well known that Gregor Mendel discovered the laws of Genetics in peas and that maize was used for the discovery of transposons by Barbara McClintock. Plant models are still useful for the understanding of general key biological concepts. In this article, we will focus on discussing the recent plant studies that have shed new light on the mysterious mechanisms of meiotic crossover (CO) interference, heterochiasmy, obligatory CO, and CO homeostasis. Obligatory CO is necessary for the equilibrated segregation of homologous chromosomes during meiosis. The tight control of the different male and female CO rates (heterochiasmy) enables both the maximization and minimization of genome shuffling. An integrative model can now predict these observed aspects of CO patterning in plants. The mechanism proposed considers the Synaptonemal Complex as a canalizing structure that allows the diffusion of a class I CO limiting factor linearly on synapsed bivalents. The coarsening of this limiting factor along the SC explains the interfering spacing between COs. The model explains the observed coordinated processes between synapsis, CO interference, CO insurance, and CO homeostasis. It also easily explains heterochiasmy just considering the different male and female SC lengths. This mechanism is expected to be conserved in other species.