Nature:庄小威团队实现染色质组织的直接成像
2016/01/25
1月21日Nature上报导了庄小威及同事用超分辨率成像方法来直接观测果蝇染色质的组织,其观测尺度小至单一基因的大小、大至基因调控区域的大小。研究发现转录活性染色质状态、非转录活性染色质状态和被Polycomb抑制的染色质状态,都有截然不同的空间组织。


后生动物基因组在空间的多个尺度上,通过DNA围绕着核小体将整条染色体分为不同的区域隔离包装。染色质在细胞核中是怎样折叠的对从基因表达的调控到DNA复制的很多生物过程都有重要意义。从千碱基到兆碱基的规模,其中包括基因的大小,基因簇和调控域,三维DNA的组织方式在多基因调控机制被涉及到,但了解这个组织方式仍然是个挑战。在这个尺度上,基因组被划分成不同的表观遗传状态的域,这是调节基因表达是必不可少的。1月21日Nature上报导了庄小威及同事使用超分辨率成像,调查了染色质在不同的表观遗传状态的三维组织方式。

用不同的表观遗传状态下的空间组织直接成像,需要对基因组原位标记和染色质结构高分辨率成像。在这篇文章中,庄小威团队使用荧光原位杂交(FISH)标签,即荧光染料标记的互补寡核苷酸探针来标记基因组的特定区域。此研究采用和修改先前报道的Oligopaint方法产生的数以千计的寡核苷酸探针。使用大规模并行合成寡核苷酸,标记数千到数兆碱基长的基因组区域。实现了最近所描述的,如图所示的酶扩增法高收率探针合成。使用的渗透平衡固定条件,以尽量减少收缩效应观察染色质收缩(扩展)。然后,她们使用标记的染色质区域进行超分辨率成像。三维随机光学重建显微镜(3D-STORM)的方法产生20 nm xy和50 nm z的细胞分辨率的特定基因组区域图像。


她们将果蝇细胞基因组的分为转录活性的,非转录活性的和转录抑制因子Polycomb抑制状态,并观察不同每个状态的染色质组织。所有这三种类型的染色质域在它们的三维物理尺寸和它们的域长度上表现出指数比例变化,但每种类型有一个不同的缩放指数。

Polycomb抑制域显示密集的包装和最有趣的染色质折叠行为,其中染色质堆积密度随长度的增加而增加。和转录活跃和非活跃的染色质不同,Polycomb抑制域具有高程度的染色质的域内混合。此外,与非活跃的域相比,Polycomb抑制域在空间上更强地排斥相邻的活跃染色质。

非转录活性染色质与一个聚合物分子的 “fractal globule”状态相似,而 Polycomb抑制域则有独特的紧凑组织,并与其他区域在空间上是分离的,这可解释为什么基因表达在这种状态下受到如此强烈的抑制。

计算模型实验表明,由Polycomb蛋白介导的可逆的染色质的相互作用,在压缩染色质包装的独特属性中,发挥重要的作用。此研究的超分辨率图像显示了,在千碱基到兆碱基的长度规模,不同的表观遗传状态下,染色质包装是不同的。其长度的规模是直接相关的基因组调控。

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  • Super-resolution imaging reveals distinct chromatin folding for different epigenetic states

    Metazoan genomes are spatially organized at multiple scales, from packaging of DNA around individual nucleosomes to segregation of whole chromosomes into distinct territories1, 2, 3, 4, 5. At the intermediate scale of kilobases to megabases, which encompasses the sizes of genes, gene clusters and regulatory domains, the three-dimensional (3D) organization of DNA is implicated in multiple gene regulatory mechanisms2, 3, 4, 6, 7, 8, but understanding this organization remains a challenge. At this scale, the genome is partitioned into domains of different epigenetic states that are essential for regulating gene expression9, 10, 11. Here we investigate the 3D organization of chromatin in different epigenetic states using super-resolution imaging. We classified genomic domains in Drosophila cells into transcriptionally active, inactive or Polycomb-repressed states, and observed distinct chromatin organizations for each state. All three types of chromatin domains exhibit power-law scaling between their physical sizes in 3D and their domain lengths, but each type has a distinct scaling exponent. Polycomb-repressed domains show the densest packing and most intriguing chromatin folding behaviour, in which chromatin packing density increases with domain length. Distinct from the self-similar organization displayed by transcriptionally active and inactive chromatin, the Polycomb-repressed domains are characterized by a high degree of chromatin intermixing within the domain. Moreover, compared to inactive domains, Polycomb-repressed domains spatially exclude neighbouring active chromatin to a much stronger degree. Computational modelling and knockdown experiments suggest that reversible chromatin interactions mediated by Polycomb-group proteins play an important role in these unique packaging properties of the repressed chromatin. Taken together, our super-resolution images reveal distinct chromatin packaging for different epigenetic states at the kilobase-to-megabase scale, a length scale that is directly relevant to genome regulation.

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