A closer look at centromeres Centromeres are key for anchoring chromosomes to the mitotic spindle, but they have been difficult to sequence because they can contain many repeating DNA elements. These repeats, however, carry regularly spaced, distinctive sequence markers because of sequence heterogeneity between the mostly, but not completely, identical DNA sequence repeats. Such differences aid sequence assembly. Naish et al . used ultra-long-read DNA sequencing to establish a reference assembly that resolves all five centromeres in the small mustard plant Arabidopsis . Their view into the subtly homogenized world of centromeres reveals retrotransposons that interrupt centromere organization and repressive DNA methylation that excludes centromeres from meiotic crossover repair. Thus, Arabidopsis centromeres evolve under the opposing forces of sequence homogenization and retrotransposon disruption. —PJH

One-sentence summary: REC8 association with the genome correlates with multiple chromatin states and is required to organize meiotic chromosome architecture and interhomolog recombination.

During meiosis, interhomolog recombination produces crossovers and noncrossovers to create genetic diversity. Meiotic recombination frequency varies at multiple scales, with high subtelomeric recombination and suppressed centromeric recombination typical in many eukaryotes. During recombination, sister chromatids are tethered as loops to a polymerized chromosome axis, which, in plants, includes the ASY1 HORMA domain protein and REC8–cohesin complexes. Using chromatin immunoprecipitation, we show an ascending telomere-to-centromere gradient of ASY1 enrichment, which correlates strongly with REC8–cohesin ChIP-seq data. We mapped crossovers genome-wide in the absence of ASY1 and observe that telomere-led recombination becomes dominant. Surprisingly,asy1/+heterozygotes also remodel crossovers toward subtelomeric regions at the expense of the pericentromeres. Telomeric recombination increases inasy1/+occur in distal regions where ASY1 and REC8 ChIP enrichment are lowest in wild type. In wild type, the majority of crossovers show interference, meaning that they are more widely spaced along the chromosomes than expected by chance. To measure interference, we analyzed double crossover distances, MLH1 foci, and fluorescent pollen tetrads. Interestingly, while crossover interference is normal inasy1/+, it is undetectable inasy1mutants, indicating that ASY1 is required to mediate crossover interference. Together, this is consistent with ASY1 antagonizing telomere-led recombination and promoting spaced crossover formation along the chromosomes via interference. These findings provide insight into the role of the meiotic axis in patterning recombination frequency within plant genomes.

Centromeres attach chromosomes to spindle microtubules during cell division and, despite this conserved role, show paradoxically rapid evolution and are typified by complex repeats. We used ultra-long-read sequencing to generate the Col-CEN Arabidopsis thaliana genome assembly that resolves all five centromeres. The centromeres consist of megabase-scale tandemly repeated satellite arrays, which support high CENH3 occupancy and are densely DNA methylated, with satellite variants private to each chromosome. CENH3 preferentially occupies satellites with least divergence and greatest higher-order repetition. The centromeres are invaded by ATHILA retrotransposons, which disrupt genetic and epigenetic organization of the centromeres. Crossover recombination is suppressed within the centromeres, yet low levels of meiotic DSBs occur that are regulated by DNA methylation. We propose that Arabidopsis centromeres are evolving via cycles of satellite homogenization and retrotransposon-driven diversification.

Meiotic crossovers are tightly restricted in most eukaryotes, despite an excess of initiating DNA double-strand breaks. The majority of plant crossovers are dependent on Class I interfering repair, with a minority formed via the Class II pathway. Class II repair is limited by anti-recombination pathways, however similar pathways repressing Class I crossovers are unknown. We performed a forward genetic screen in Arabidopsis using fluorescent crossover reporters, to identify mutants with increased or decreased recombination frequency. We identified HIGH CROSSOVER RATE1 ( HCR1 ) as repressing crossovers and encoding PROTEIN PHOSPHATASE X1. Genome-wide analysis showed that hcr1 crossovers are increased in the distal chromosome arms. MLH1 foci significantly increase in hcr1 and crossover interference decreases, demonstrating an effect on Class I repair. Consistently, yeast two-hybrid and in planta assays show interaction between HCR1 and Class I proteins, including HEI10, PTD, MSH5, and MLH1. We propose that HCR1 plays a major role in opposition to pro-recombination kinases to restrict crossovers in Arabidopsis.

Meiosis is a specialized cell division that contributes to halve the genome content and reshuffle allelic combinations between generations in sexually reproducing eukaryotes. During meiosis, a large number of programmed DNA double-strand breaks (DSBs) are formed throughout the genome. Repair of meiotic DSBs facilitates the pairing of homologs and forms crossovers which are the reciprocal exchange of genetic information between chromosomes. Meiotic recombination also influences centromere organization and is essential for proper chromosome segregation. Accordingly, meiotic recombination drives genome evolution and is a powerful tool for breeders to create new varieties important to food security. Modifying meiotic recombination has the potential to accelerate plant breeding but it can also have detrimental effects on plant performance by breaking beneficial genetic linkages. Therefore, it is essential to gain a better understanding of these processes in order to develop novel strategies to facilitate plant breeding. Recent progress in targeted recombination technologies, chromosome engineering, and an increasing knowledge in the control of meiotic chromosome segregation has significantly increased our ability to manipulate meiosis. In this review, we summarize the latest findings and technologies on meiosis in plants. We also highlight recent attempts and future directions to manipulate crossover events and control the meiotic division process in a breeding perspective.

During meiosis, DNA double-strand breaks (DSBs) occur throughout the genome, a subset of which are repaired to form reciprocal crossovers between chromosomes. Crossovers are essential to ensure balanced chromosome segregation and to create new combinations of genetic variation. Meiotic DSBs are formed by a topoisomerase-VI-like complex, containing catalytic (e.g. SPO11) proteins and auxiliary (e.g. PRD3) proteins. Meiotic DSBs are formed in chromatin loops tethered to a linear chromosome axis, but the interrelationship between DSB-promoting factors and the axis is not fully understood. Here, we study the localisation of SPO11-1 and PRD3 during meiosis, and investigate their respective functions in relation to the chromosome axis. Using immunocytogenetics, we observed that the localisation of SPO11-1 overlaps relatively weakly with the chromosome axis and RAD51, a marker of meiotic DSBs, and that SPO11-1 recruitment to chromatin is genetically independent of the axis. In contrast, PRD3 localisation correlates more strongly with RAD51 and the chromosome axis. This indicates that PRD3 likely forms a functional link between SPO11-1 and the chromosome axis to promote meiotic DSB formation. We also uncovered a new function of SPO11-1 in the nucleation of the synaptonemal complex protein ZYP1. We demonstrate that chromosome co-alignment associated with ZYP1 deposition can occur in the absence of DSBs, and is dependent on SPO11-1, but not PRD3. Lastly, we show that the progression of meiosis is influenced by the presence of aberrant chromosomal connections, but not by the absence of DSBs or synapsis. Altogether, our study provides mechanistic insights into the control of meiotic DSB formation and reveals diverse functional interactions between SPO11-1, PRD3 and the chromosome axis.

18During meiosis chromosomes undergo DNA double-strand breaks (DSBs) that can be 19 repaired using a homolog to produce crossovers, which creates genetic diversity. 20Meiotic recombination occurs coincident with homolog pairing and polymerization of 21 the meiotic axis and synaptonemal complex (SC). REC8-cohesin is required to connect 22 chromosomes to the axis and to organize axis polymerization. However, control of 23 REC8 loading along chromosomes, in relation to chromatin, transcription and 24 recombination, is not yet fully understood. Therefore, we performed REC8 ChIP-seq in 25 Arabidopsis, which revealed strong enrichment in centromeric heterochromatin. REC8 26 abundance correlates with suppression of meiotic DSBs and crossovers, despite axis 27 loading of SPO11-1 in these regions. Loss of the heterochromatic marks H3K9me2 28 and non-CG DNA methylation in kyp/suvh4 suvh5 suvh6 mutants causes remodeling of 29 REC8 and gain of meiotic recombination locally in repeated sequences, although 30 centromere cohesion is maintained. In the chromosome arms, REC8 is enriched within 31 gene bodies, exons and GC-rich sequences, and anti-correlates with transcription. 32Highest REC8 occupancy occurred in facultatively silent, H3K27me3-modified genes. 33Using immunocytology we show that axis polycomplexes form in rec8 mutants that 34 recruit recombination foci with altered stoichiometry, leading to catastrophic non-35 homologous recombination. Therefore, REC8 plays a key role organizing meiotic 36 chromosome architecture and promoting high-fidelity interhomolog recombination. 37Despite this pro-recombination role, local REC8 enrichment associates with DSB 38 repression at the fine scale, which is consistent with the tethered-loop/axis model. 39Coincident with its organizational role during meiosis, REC8-cohesin occupancy along 40 the chromosomes is shaped by multiple chromatin states and transcription. 42Keywords: 44Cohesin, REC8, meiosis, recombination, crossover, H3K9me2, DNA methylation. 45 46 47 48 49 50 51 52 2 Introduction: 53 54 Cohesin complexes form ~35-50 nm rings that can topologically embrace one or more 55 DNA helices (Uhlmann 2016; Nasmyth and Haering 2009; Peters et al. 2008). Cohesin 56 rings consist of paired structural maintenance of chromosomes (SMC) proteins that 57 interact at hinge and ATPase head domains, with the head regions clamped by an α-58 kleisin (Gligoris and Löwe 2016). DNA can enter and exit cohesin rings at the subunit 59 interfaces, and the rings undergo dynamic cycles of association and disassociation 60 with chromosomes (