Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis transposons and gene regulatory regions
Nucleosomes and DNA methylation shape meiotic DSB frequency in Arabidopsis transposons and gene regulatory regions
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DOI：
10.1101/160911
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发表时间：
2017-07
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通讯作者：
Kyuha Choi;Xiaohui Zhao;Christophe Lambing;C. Underwood;Thomas J. Hardcastle;Heïdi Serra;Andrew J. Tock;Piotr A. Ziolkowski;Nataliya E. Yelina;R. Martienssen;I. Henderson
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作者：
Kyuha Choi;Xiaohui Zhao;Christophe Lambing;C. Underwood;Thomas J. Hardcastle;Heïdi Serra;Andrew J. Tock;Piotr A. Ziolkowski;Nataliya E. Yelina;R. Martienssen;I. Henderson
减数分裂重组通过SPO 11拓扑异构酶样复合物产生的DNA双链断裂（DSB）启动。真核生物染色体上的突变频率沿着变化很大，热点受染色质和DNA序列控制。为了在整个植物基因组中定位减数分裂DSB，我们纯化并测序了拟南芥SPO 11 -1-寡核苷酸。DSB热点发生在基因启动子、终止子和内含子中，由AT序列丰富性驱动，其排除核小体并允许SPO 11 -1进入。在SPO 11 -1 DSB和最终交叉水平之间观察到强正相关。常染色质标记促进真菌和哺乳动物中的重组，并且我们一致地观察到H3 K4 me 3在基因5 '端的DSB热点附近富集。重复转座子被认为在减数分裂期间重组沉默，以防止非等位基因相互作用和基因组不稳定性。出乎意料的是，我们在核小体缺失的Helitron/Pogo/Tc 1/Mariner DNA转座子中发现了强DSB热点，而反转录转座子是冷点。热点转座子富集在基因调控区域内并靠近免疫基因，表明其作为重组增强子的作用。由于转座子在植物基因组中的移动性受到DNA甲基化的限制，我们使用met 1 DNA甲基转移酶突变体来研究异染色质对DSB景观的作用。转座子减数分裂DSB的表观遗传激活发生在met 1突变体中，与核小体占用率降低、转录增益和H3 K4 me 3一致。增加的met 1 SPO 11 -1 DSB在着丝粒和Gypsy和CACTA/EnSpm冷点转座子内发生得最强烈。总之，我们的工作揭示了基因和转座子内染色质和减数分裂DSB之间的复杂相互作用，对植物基因组的多样性和进化具有重要意义。
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.