Biology subjects

Tock, A. J.

Publications and source records attributed to Tock, A. J..

5 recordsLinked to original sources

bioRxiv2023

Structural variation and DNA methylation shape the centromere-proximal meiotic crossover landscape in Arabidopsis

BackgroundCentromeres load kinetochore complexes onto chromosomes, which mediate spindle attachment and allow segregation during cell division. Although centromeres perform a conserved cellular function, their underlying DNA sequences are highly divergent within and between species. Despite variability in DNA sequence, centromeres are also universally suppressed for meiotic crossover recombination, across eukaryotes. However, the genetic and epigenetic factors responsible for suppression of centromeric crossovers remain to be completely defined. ResultsTo explore the centromere-proximal recombination landscape, we mapped 14,397 crossovers against fully assembled Arabidopsis thaliana genomes. A. thaliana centromeres comprise megabase-scale satellite repeat arrays that load nucleosomes containing the CENH3 histone variant. Each chromosome possesses a structurally polymorphic 3-4 megabase region where crossovers were absent, that includes the satellite arrays, flanked by 1-2 megabase low-recombination zones. The recombination-suppressed regions are enriched for Gypsy/Ty3 retrotransposons, and additionally contain expressed genes with high genetic diversity that initiate meiotic recombination, yet do not crossover. We mapped crossovers at high-resolution in proximity to CEN3, which resolved punctate centromere-proximal hotspots that overlapped gene islands embedded in heterochromatin. Centromeres are densely DNA methylated and the recombination landscape was remodelled in DNA methylation mutants. We observed that the centromeric low-recombining zones decreased and increased crossovers in CG (met1) and non-CG (cmt3) mutants, respectively, whereas the core non recombining zones remained suppressed. ConclusionOur work relates the genetic and epigenetic organisation of the A. thaliana centromeres and flanking pericentromeric heterochromatin to the zones of crossover suppression that surround the CENH3-occupied satellite repeat arrays.

genomics↗

bioRxiv2021

The genetic and epigenetic landscape of the Arabidopsis centromeres

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. One-sentence summaryLong read sequencing and assembly of the Arabidopsis centromeres reveals their genetic and epigenetic topography.

genomics↗

bioRxiv2019

An ultra high-density Arabidopsis thaliana crossover map that refines the influences of structural variation and epigenetic features

Many environmental, genetic, and epigenetic factors are known to affect the frequency and positioning of meiotic crossovers (COs). Suppression of COs by large, cytologically visible inversions and translocations has long been recognized, but relatively little is known about how smaller structural variants (SVs) affect COs. To examine fine-scale determinants of the CO landscape, including SVs, we used a rapid, cost-effective method for high-throughput sequencing to generate a precise map of over 17,000 COs between the Col-0 and Ler accessions of Arabidopsis thaliana. COs were generally suppressed in regions with SVs, but this effect did not depend on the size of the variant region, and was only marginally affected by the variant type. CO suppression did not extend far beyond the SV borders, and CO rates were slightly elevated in the flanking regions. Disease resistance gene clusters, which often exist as SVs, exhibited high CO rates at some loci, but there was a tendency toward depressed CO rates at loci where large structural differences exist between the two parents. Our high-density map also revealed in fine detail how CO positioning relates to genetic (DNA motifs) and epigenetic (chromatin structure) features of the genome. We conclude that suppression of COs occurs over a narrow region spanning large and small-scale SVs, representing influence on the CO landscape in addition to sequence and epigenetic variation along chromosomes.

genetics↗

bioRxiv2019

REC8-cohesin, chromatin and transcription orchestrate meiotic recombination in the Arabidopsis genome

During meiosis chromosomes undergo DNA double-strand breaks (DSBs) that can be repaired using a homolog to produce crossovers, which creates genetic diversity. Meiotic recombination occurs coincident with homolog pairing and polymerization of the meiotic axis and synaptonemal complex (SC). REC8-cohesin is required to connect chromosomes to the axis and to organize axis polymerization. However, control of REC8 loading along chromosomes, in relation to chromatin, transcription and recombination, is not yet fully understood. Therefore, we performed REC8 ChIP-seq in Arabidopsis, which revealed strong enrichment in centromeric heterochromatin. REC8 abundance correlates with suppression of meiotic DSBs and crossovers, despite axis loading of SPO11-1 in these regions. Loss of the heterochromatic marks H3K9me2 and non-CG DNA methylation in kyp/suvh4 suvh5 suvh6 mutants causes remodeling of REC8 and gain of meiotic recombination locally in repeated sequences, although centromere cohesion is maintained. In the chromosome arms, REC8 is enriched within gene bodies, exons and GC-rich sequences, and anti-correlates with transcription. Highest REC8 occupancy occurred in facultatively silent, H3K27me3-modified genes. Using immunocytology we show that axis polycomplexes form in rec8 mutants that recruit recombination foci with altered stoichiometry, leading to catastrophic non-homologous recombination. Therefore, REC8 plays a key role organizing meiotic chromosome architecture and promoting high-fidelity interhomolog recombination. Despite this pro-recombination role, local REC8 enrichment associates with DSB repression at the fine scale, which is consistent with the tethered-loop/axis model. Coincident with its organizational role during meiosis, REC8-cohesin occupancy along the chromosomes is shaped by multiple chromatin states and transcription.

genomics↗

bioRxiv2017

Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis transposons and gene regulatory regions

Meiotic recombination initiates via DNA double strand breaks (DSBs) generated by SPO11 topoisomerase-like complexes. Recombination frequency varies extensively along eukaryotic chromosomes, with hotspots controlled by chromatin and DNA sequence. To map meiotic DSBs throughout a plant genome, we purified and sequenced Arabidopsis SPO11-1-oligonucleotides. DSB hotspots occurred in gene promoters, terminators and introns, driven by AT-sequence richness, which excludes nucleosomes and allows SPO11-1 access. A strong positive relationship was observed between SPO11-1 DSBs and final crossover levels. Euchromatic marks promote recombination in fungi and mammals, and consistently we observe H3K4me3 enrichment in proximity to DSB hotspots at gene 5-ends. Repetitive transposons are thought to be recombination-silenced during meiosis, in order to prevent non-allelic interactions and genome instability. Unexpectedly, we found strong DSB hotspots in nucleosome-depleted Helitron/Pogo/Tc1/Mariner DNA transposons, whereas retrotransposons were coldspots. Hotspot transposons are enriched within gene regulatory regions and in proximity to immunity genes, suggesting a role as recombination-enhancers. As transposon mobility in plant genomes is restricted by DNA methylation, we used the met1 DNA methyltransferase mutant to investigate the role of heterochromatin on the DSB landscape. Epigenetic activation of transposon meiotic DSBs occurred in met1 mutants, coincident with reduced nucleosome occupancy, gain of transcription and H3K4me3. Increased met1 SPO11-1 DSBs occurred most strongly within centromeres and Gypsy and CACTA/EnSpm coldspot transposons. Together, our work reveals complex interactions between chromatin and meiotic DSBs within genes and transposons, with significance for the diversity and evolution of plant genomes.

genomics↗