程序化DNA消除(PDE)是基因组完整性范例的显著例外。在后生,PDE通常与种系向体细胞分化同时发生。在PDE期间,部分基因组DNA丢失,导致体细胞基因组减少。先前的研究已经描述了丢失的序列,以及染色体行为,在后生动物PDE期间。然而,缺乏研究后生动物PDE机制和后果的系统。这里,我们提出了自由生活的Rhabditidae线虫Oscheiustipulae中PDE的功能和遗传模型,一个还包括秀丽隐杆线虫的家庭。最近有人建议O.tipulae消除DNA。使用分期胚胎和DNAFISH,我们表明O.tipulaePDE发生在8-16细胞阶段的胚胎发生过程中。我们确定了一个保守的主题,命名为消除序列(SFE),对于保留和消除的DNA的连接处的六个染色体上的所有12个断裂位点。SFE突变体仅在修饰位点表现出“无法消除”表型。END-seq揭示了在SFE内的多个位置可能发生断裂,广泛的末端切除,然后在保留和消除的末端添加端粒。我们在野生型胚胎中通过END-seq在染色体末端鉴定了许多功能性SFEs,SFE突变体的基因组测序,和23个野生分离株的比较基因组学。我们建议这些替代SFE在消除的序列中提供灵活性,并为PDE提供故障保护机制。这些研究将O.tipulae确立为新的,研究后生动物PDE的机制和后果的有吸引力的模型。
Programmed DNA elimination (PDE) is a notable exception to the paradigm of genome integrity. In metazoa, PDE often occurs coincident with germline to somatic cell differentiation. During PDE, portions of genomic DNA are lost, resulting in reduced somatic genomes. Prior studies have described the sequences lost, as well as chromosome behavior, during metazoan PDE. However, a system for studying the mechanisms and consequences of PDE in metazoa is lacking. Here, we present a functional and genetic model for PDE in the free-living Rhabditidae nematode Oscheius tipulae, a family that also includes Caenorhabditis elegans. O. tipulae was recently suggested to eliminate DNA. Using staged embryos and DNA FISH, we showed that O. tipulae PDE occurs during embryogenesis at the 8-16 cell stages. We identified a conserved motif, named Sequence For Elimination (SFE), for all 12 break sites on the six chromosomes at the junctions of retained and eliminated DNA. SFE mutants exhibited a \"fail-to-eliminate\" phenotype only at the modified sites. END-seq revealed that breaks can occur at multiple positions within the SFE, with extensive end resection followed by telomere addition to both retained and eliminated ends. We identified many functional SFEs at the chromosome ends through END-seq in the wild-type embryos, genome sequencing of SFE mutants, and comparative genomics of 23 wild isolates. We suggest that these alternative SFEs provide flexibility in the sequences eliminated and a fail-safe mechanism for PDE. These studies establish O. tipulae as a new, attractive model for studying the mechanisms and consequences of PDE in a metazoan.