Extrachromosomal DNA (microDNA) in Human, Mouse and Chicken

MicroDNAs are <400-base long extrachromosomal circles found in mammalian cells. Tens of thousands of microDNAs were found in all tissue types, including sperm. MicroDNAs arose preferentially from areas with high gene density, high GC content, high exon density, promoters with activating chromatin modifications and in sperm from the 5''UTR of full-length LINE-1 elements, but were depleted from lamin-associated heterochromatin. Furthermore, analysis of microDNAs from a set of human cancer cell lines revealed lineage-specific patterns of microDNA origins. A survey of microDNAs from chicken cell lines defective in various DNA repair proteins revealed that homologous recombination repair and non-homologous end joining repair pathways are not required for microDNA production. A deletion of the MSH3 protein, involved in DNA mismatch repair, resulted in a significant decrease in microDNA abundance specifically from non-CpG areas of the genome. Thus microDNAs arise as part of normal cellular physiology, either from DNA breaks associated with RNA metabolism or from replication slippage followed by mismatch repair. Overall design: Circular DNA profiling by high throughput sequencing. Five human, ten mouse and nine chicken samples are analyzed

微DNA（MicroDNAs）是一类长度小于400个碱基的染色体外环状DNA，广泛存在于哺乳动物细胞中。研究人员在包括精子在内的所有组织类型中均检出数以万计的微DNA。微DNA的起源具有显著偏好性：富集于基因密度高、GC含量高、外显子密度高的区域，以及带有激活型染色质修饰的启动子区域；在精子中则多起源于全长长散在核元件1（LINE-1）的5'非翻译区（5'UTR），但在核纤层相关异染色质区域中微DNA的丰度显著降低。此外，对多株人类癌细胞系的微DNA进行分析后发现，其起源模式具有细胞谱系特异性。对多种DNA修复蛋白缺陷的鸡细胞系的微DNA进行检测后发现，微DNA的生成并不依赖于同源重组修复（homologous recombination repair）与非同源末端连接修复（non-homologous end joining repair）通路。敲除参与DNA错配修复的MSH3蛋白后，基因组非CpG区域来源的微DNA丰度出现显著下降。由此可见，微DNA的生成是正常细胞生理过程的一部分，其来源可分为两类：与RNA代谢相关的DNA断裂，或是复制滑移后经错配修复介导的过程。实验整体设计：采用高通量测序开展环状DNA图谱分析，共纳入5份人类样本、10份小鼠样本及9份鸡样本进行检测。