通过完整保存基因组完整性,在细胞分裂之前的无差错DNA复制和通过正确的DNA损伤修复对于生物体的发育和维持是至关重要的。这不仅适用于蛋白质编码基因,但它也适用于重复的DNA元件,占人类基因组的一半以上。这里,我们专注于穿插和串联重复DNA元件的复制和修复动力学。
我们将基因组群体水平数据与单细胞免疫荧光原位杂交方法相结合,以同时标记复制/修复和重复DNA元件。我们发现:(1)正常的Alu元素在早期S期被复制;(2)LINE-1,它与富含AT的基因组区域相关,在整个S期重复,大多数根据其特定的组蛋白标记进行复制;(3)卫星III,构成着丝粒周围的异染色质,仅在S期中后期复制。至于DNA双链断裂修复过程,我们观察到Alu元素遵循全球基因组修复动力学,而LINE-1元件的修复速度较慢。最后,卫星III重复在稍后的时间点修复。
我们得出结论,特定重复元件中的组蛋白修饰主要决定其复制和修复时机。因此,Alu元素,其特征是常染色质特征,最早修复和复制,其次是LINE-1元素,包括更多杂色的欧盟/异色特征,最后,卫星串联重复,它们具有均匀的异色特征,并在兆碱基长的基因组区域上延伸。总之,这项工作再次强调了互补方法的必要性,以实现对基因组过程的综合和全面研究。
Preservation of genome integrity by complete, error-free DNA duplication prior to cell division and by correct DNA damage repair is paramount for the development and maintenance of an organism. This holds true not only for protein-encoding genes, but also it applies to repetitive DNA elements, which make up more than half of the human genome. Here, we focused on the replication and repair kinetics of interspersed and tandem repetitive DNA elements.
We integrated genomic population level data with a single cell immunofluorescence in situ hybridization approach to simultaneously label replication/repair and repetitive DNA elements. We found that: (1) the euchromatic Alu element was replicated during early S-phase; (2) LINE-1, which is associated with AT-rich genomic regions, was replicated throughout S-phase, with the majority being replicated according to their particular histone marks; (3) satellite III, which constitutes pericentromeric heterochromatin, was replicated exclusively during the mid-to-late S-phase. As for the DNA double-strand break repair process, we observed that Alu elements followed the global genome repair kinetics, while LINE-1 elements repaired at a slower rate. Finally, satellite III repeats were repaired at later time points.
We conclude that the histone modifications in the specific repeat element predominantly determine its replication and repair timing. Thus, Alu elements, which are characterized by euchromatic chromatin features, are repaired and replicated the earliest, followed by LINE-1 elements, including more variegated eu/heterochromatic features and, lastly, satellite tandem repeats, which are homogeneously characterized by heterochromatic features and extend over megabase-long genomic regions. Altogether, this work reemphasizes the need for complementary approaches to achieve an integrated and comprehensive investigation of genomic processes.