Estrem Brandon, Davis Richard E, Wang Jianbin
Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.
Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, 80045, USA.
bioRxiv. 2024 Mar 16:2024.03.15.585292. doi: 10.1101/2024.03.15.585292.
Most DNA double-strand breaks (DSBs) are harmful to genome integrity. However, some forms of DSBs are essential to biological processes, such as meiotic recombination and V(D)J recombination. DSBs are also required for programmed DNA elimination (PDE) in ciliates and nematodes. In nematodes, the DSBs are healed with telomere addition. While telomere addition sites have been well-characterized, little is known regarding the DSBs that fragment nematode chromosomes. Here, we used embryos from the nematode to study the timing of PDE breaks and examine the DSBs and their end processing. Using END-seq, we characterize the DSB ends and demonstrate that DNA breaks are introduced before mitosis, followed by extensive end resection. The resection profile is unique for each break site, and the resection generates 3' overhangs before the addition of telomeres. Interestingly, telomere healing occurs much more frequently on retained DSB ends than on eliminated ends. This biased repair of the DSB ends in may be due to the sequestration of the eliminated DNA into micronuclei, preventing their ends from telomere healing. Additional DNA breaks occur within the eliminated DNA in both and , ensuring chromosomal breakage and providing a fail-safe mechanism for nematode PDE.
大多数DNA双链断裂（DSB）对基因组完整性有害。然而，某些形式的DSB对于生物过程至关重要，例如减数分裂重组和V（D）J重组。纤毛虫和线虫中的程序性DNA消除（PDE）也需要DSB。在线虫中，DSB通过添加端粒来修复。虽然端粒添加位点已得到充分表征，但关于使线虫染色体断裂的DSB却知之甚少。在这里，我们使用线虫的胚胎来研究PDE断裂的时间，并检查DSB及其末端加工。使用END-seq，我们对DSB末端进行了表征，并证明DNA断裂在有丝分裂之前引入，随后进行广泛的末端切除。每个断裂位点的切除图谱都是独特的，并且在添加端粒之前，切除会产生3'突出端。有趣的是，端粒修复在保留的DSB末端比在消除的末端更频繁地发生。线虫中DSB末端的这种偏向性修复可能是由于消除的DNA被隔离到微核中，阻止了它们的末端进行端粒修复。在秀丽隐杆线虫和嗜热栖热放线菌中，额外的DNA断裂都发生在消除的DNA内，确保染色体断裂，并为线虫的PDE提供一种故障安全机制。
