Maintaining genomic integrity and stability is particularly important for stem cells, which are at the top of the cell lineage origin. Here, we discovered that the plant-specific histone methyltransferase SUVR2 maintains the genome integrity of the root tip stem cells through chromatin remodeling and liquid–liquid phase separation (LLPS) when facing DNA double-strand breaks (DSBs). The histone methyltransferase SUVR2 (MtSUVR2) has histone methyltransferase activity and catalyzes the conversion of histone H3 lysine 9 monomethylation (H3K9me1) to H3K9me2/3 in vitro and in Medicago truncatula. Under DNA damage, the proportion of heterochromatin decreased and the level of DSB damage marker γ-H2AX increased in suvr2 mutants, indicating that MtSUVR2 promotes the compaction of the chromatin structure through H3K9 methylation modification to protect DNA from damage. Interestingly, MtSUVR2 was induced by DSBs to phase separate and form droplets to localize at the damage sites, and this was confirmed by immunofluorescence and fluorescence recovery after photobleaching experiments. The IDR1 and low-complexity domain regions of MtSUVR2 determined its phase separation in the nucleus, whereas the IDR2 region determined the interaction with the homologous recombinase MtRAD51. Furthermore, we found that MtSUVR2 drove the phase separation of MtRAD51 to form “DNA repair bodies,” which could enhance the stability of MtRAD51 proteins to facilitate error-free homologous recombination repair of stem cells. Taken together, our study reveals that chromatin remodeling-associated proteins participate in DNA repair through LLPS.

保持基因组的完整性和稳定性对于干细胞来说尤其重要，干细胞是细胞谱系起源的顶端。在这里，我们发现植物特异性组蛋白甲基转移酶 SUVR2 在面临 DNA 双链断裂 (DSB) 时通过染色质重塑和液-液相分离 (LLPS) 维持根尖干细胞的基因组完整性。组蛋白甲基转移酶 SUVR2 (MtSUVR2) 具有组蛋白甲基转移酶活性，可在体外和蒺藜苜蓿中催化组蛋白 H3 赖氨酸 9 单甲基化 (H3K9me1) 转化为 H3K9me2/3 。DNA损伤下， suvr2异染色质比例降低，DSB损伤标志物γ-H2AX水平升高突变体，表明 MtSUVR2 通过 H3K9 甲基化修饰促进染色质结构的压缩，以保护 DNA 免受损伤。有趣的是，DSBs 诱导 MtSUVR2 相分离并形成液滴以定位于损伤部位，这通过光漂白实验后的免疫荧光和荧光恢复得到证实。MtSUVR2 的 IDR1 和低复杂性结构域区域决定了其在细胞核中的相分离，而 IDR2 区域决定了与同源重组酶 MtRAD51 的相互作用。此外，我们发现MtSUVR2驱动MtRAD51的相分离形成“DNA修复体”，这可以增强MtRAD51蛋白的稳定性，从而促进干细胞的无错误同源重组修复。综合起来，