Cellular and Molecular Features of Developmentally Programmed Genome Rearrangement in a Vertebrate (Sea Lamprey: Petromyzon marinus).
Cellular and Molecular Features of Developmentally Programmed Genome Rearrangement in a Vertebrate (Sea Lamprey: Petromyzon marinus).
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DOI：
10.1371/journal.pgen.1006103
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发表时间：
2016-06
期刊：
影响因子：
4.5
通讯作者：
Smith JJ
中科院分区：
文献类型：
--
作者：
Timoshevskiy VA;Herdy JR;Keinath MC;Smith JJ
海七鳃鳗（Petromyzon marinus）是已知在其正常发育过程中经历大规模基因组DNA程序性消除的少数脊椎动物物种之一。程序性基因组重排（PGR）导致在早期胚胎发生过程中体细胞谱系中约20%的基因组可再现地丢失。PGR的研究有可能提供与细胞周期期间基因组稳定性的维持以及负责染色体准确分布到子细胞中的机制之间的协调有关的新见解，但关于PGR在此或任何其他脊椎动物谱系中的机制基础或细胞背景知之甚少。在这里，我们确定了与DNA的程序化消除相关的表观遗传沉默事件，并描述了七鳃鳗胚胎发生过程中PGR的时空动态。原位分析表明，最早的DNA甲基化（和在一定程度上H3 K9三甲基化）事件仅限于特定的双核结构（微核）含有消除的DNA。在早期胚胎发生期间，大多数微核（约60%）显示出抑制性染色质修饰（H3 K9 me 3和5 meC）的强烈富集。这些分析还发现，消除的DNA被包装到染色质中，在后期不与体细胞保留的染色体一起迁移，这种情况与在一些癌症亚型中观察到的落后染色体表面上相似。对“滞后”染色质的仔细检查揭示了重复元件、细胞骨架接触和染色质接触的分布，这些分布为这些片段的程序性丢失的细胞机制提供了新的见解。我们的分析提供了关于PCR的细胞和分子背景的额外视角，确定了与DNA消除相关的新结构，并揭示了PCR在几个连续的细胞分裂过程中完成。七鳃鳗拥有迷人的基因组生物学，其中大部分基因组，包括大量的基因，在发育过程中被编程删除。因此，七鳃鳗代表了一个独特的信息系统方面的几个广泛的领域的生物学，包括基因组稳定性/重排，表观遗传沉默，建立和维护的多能性。然而，关于细胞背景或缺失机制知之甚少，部分原因是观察原位重排的挑战。在这里，我们提出的分析和新技术，显着推进我们的程序性重排和程序性缺失和典型的DNA沉默机制之间的相互作用的亚细胞背景的理解。这些分析表明，DNA消除发生在胚胎发生早于以前认识到，并揭示了几个新的细胞和分子方面的程序性DNA丢失。具体来说，我们表明，消除DNA在细胞分裂过程中表现出独特的迁移模式，在细胞周期后期被包装成离散的亚细胞结构，并通过DNA和组蛋白甲基化进行表观遗传沉默。这些观察结果为程序性DNA丢失的机制提供了新的见解，并表明程序性DNA丢失与其他更保守的基因沉默途径之间存在功能联系。
The sea lamprey (Petromyzon marinus) represents one of the few vertebrate species known to undergo large-scale programmatic elimination of genomic DNA over the course of its normal development. Programmed genome rearrangements (PGRs) result in the reproducible loss of ~20% of the genome from somatic cell lineages during early embryogenesis. Studies of PGR hold the potential to provide novel insights related to the maintenance of genome stability during the cell cycle and coordination between mechanisms responsible for the accurate distribution of chromosomes into daughter cells, yet little is known regarding the mechanistic basis or cellular context of PGR in this or any other vertebrate lineage. Here we identify epigenetic silencing events that are associated with the programmed elimination of DNA and describe the spatiotemporal dynamics of PGR during lamprey embryogenesis. In situ analyses reveal that the earliest DNA methylation (and to some extent H3K9 trimethylation) events are limited to specific extranuclear structures (micronuclei) containing eliminated DNA. During early embryogenesis a majority of micronuclei (~60%) show strong enrichment for repressive chromatin modifications (H3K9me3 and 5meC). These analyses also led to the discovery that eliminated DNA is packaged into chromatin that does not migrate with somatically retained chromosomes during anaphase, a condition that is superficially similar to lagging chromosomes observed in some cancer subtypes. Closer examination of “lagging” chromatin revealed distributions of repetitive elements, cytoskeletal contacts and chromatin contacts that provide new insights into the cellular mechanisms underlying the programmed loss of these segments. Our analyses provide additional perspective on the cellular and molecular context of PGR, identify new structures associated with elimination of DNA and reveal that PGR is completed over the course of several successive cell divisions. Lampreys possess a fascinating genome biology wherein large portions of the genome, including large numbers of genes, are programmatically deleted during development. The lamprey therefore represents a uniquely informative system with respect to several broad areas of biology, including genome stability/rearrangement, epigenetic silencing, and the establishment and maintenance of pluripotency. However, little is known regarding the cellular context or mechanism of deletion, partly due to the challenges of observing rearrangements in situ. Here we present analyses and new techniques that significantly advance our understanding of the subcellular context of programmed rearrangements and interactions between programmed deletion and canonical DNA silencing mechanisms. These analyses demonstrate that DNA elimination occurs earlier in embryogenesis than was previously recognized and reveal several new cellular and molecular aspects of programmed DNA loss. Specifically we show that eliminated DNA exhibits a unique migration pattern during cell division, is packaged into discreet subcellular structures later in the cell cycle, and undergoes epigenetic silencing through DNA and histone methylation. These observations provide new insight into the mechanisms underlying programmed DNA loss and suggest a functional link between programmed DNA loss and other, more conserved gene silencing pathways.