Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado School of Medicine, Aurora, CO 80045, USA; Department of Biochemistry and 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.
Curr Biol. 2020 Sep 7;30(17):3397-3413.e4. doi: 10.1016/j.cub.2020.06.058. Epub 2020 Jul 16.
Germline and somatic genomes are in general the same in a multicellular organism. However, programmed DNA elimination leads to a reduced somatic genome compared to germline cells. Previous work on the parasitic nematode Ascaris demonstrated that programmed DNA elimination encompasses high-fidelity chromosomal breaks and loss of specific genome sequences including a major tandem repeat of 120 bp and ~1,000 germline-expressed genes. However, the precise chromosomal locations of these repeats, breaks regions, and eliminated genes remained unknown. We used PacBio long-read sequencing and chromosome conformation capture (Hi-C) to obtain fully assembled chromosomes of Ascaris germline and somatic genomes, enabling a complete chromosomal view of DNA elimination. We found that all 24 germline chromosomes undergo comprehensive chromosome end remodeling with DNA breaks in their subtelomeric regions and loss of distal sequences including the telomeres at both chromosome ends. All new Ascaris somatic chromosome ends are recapped by de novo telomere healing. We provide an ultrastructural analysis of Ascaris DNA elimination and show that eliminated DNA is incorporated into double membrane-bound structures, similar to micronuclei, during telophase of a DNA elimination mitosis. These micronuclei undergo dynamic changes including loss of active histone marks and localize to the cytoplasm following daughter nuclei formation and cytokinesis where they form autophagosomes. Comparative analysis of nematode chromosomes suggests that chromosome fusions occurred, forming Ascaris sex chromosomes that become independent chromosomes following DNA elimination breaks in somatic cells. These studies provide the first chromosomal view and define novel features and functions of metazoan programmed DNA elimination.
多细胞生物的种系和体细胞基因组通常是相同的。然而，程序化的 DNA 消除导致体细胞基因组相对于生殖细胞减少。以前对寄生线虫蛔虫的研究表明，程序化的 DNA 消除包括高保真染色体断裂和特定基因组序列的丢失，包括 120bp 的主要串联重复序列和约 1000 个生殖细胞表达的基因。然而，这些重复、断裂区域和消除基因的确切染色体位置仍然未知。我们使用 PacBio 长读测序和染色体构象捕获 (Hi-C) 获得了蛔虫生殖系和体细胞基因组的完全组装染色体，从而能够全面了解 DNA 消除的染色体情况。我们发现，所有 24 条生殖系染色体都经历了全面的染色体末端重塑，在其端粒区发生 DNA 断裂，并丢失了包括染色体末端的端粒在内的远端序列。所有新的蛔虫体细胞染色体末端都通过从头端粒愈合重新覆盖。我们提供了对蛔虫 DNA 消除的超微结构分析，并表明消除的 DNA 被掺入到双膜结合结构中，类似于有丝分裂末期的微核，在 DNA 消除有丝分裂末期。这些微核经历动态变化，包括失去活性组蛋白标记，并在子核形成和胞质分裂后定位于细胞质中，在那里它们形成自噬体。对线虫染色体的比较分析表明，染色体融合发生，形成蛔虫性染色体，在体细胞中的 DNA 消除断裂后成为独立染色体。这些研究提供了第一个染色体视图，并定义了后生动物程序化 DNA 消除的新特征和功能。
