Structural biology of chromosome folding and dysregulation in disease

1953年DNA结构的阐明开启了生命科学研究的革命，标志着现代分子生物学的开始。虽然我们确实知道DNA在原子级分辨率下的结构，但DNA是如何包装在细胞中的仍然是个谜。人类基因组DNA，如果拉伸，总长度将超过两米。在细胞中，所有这些DNA都需要被压缩成一个微米大小的细胞核。DNA卷曲的一个基本单位是核小体，几十年来，它一直被视为DNA凝结的第一步。然而，现在很清楚的是，核小体的主要功能不是实现大规模的基因组打包。相反，高阶基因组折叠是由染色体结构维护(SMC)蛋白介导的，SMC蛋白是一类古老的ATPase，存在于生命的所有领域。SMC蛋白是一种大的环状蛋白，通过DNA环挤出发挥作用。虽然细节目前尚不清楚，但后果是SMC蛋白质将DNA组织成大型、动态的环路。越来越明显的是，这种染色体折叠反应对基因组生物学的许多最基本的方面都很重要：由遥远的调控元件控制基因调控，基因组复制和修复，以及有丝分裂和减数分裂过程中的染色体分离。有迹象表明，粘附素亚基的突变在许多癌症和‘粘附素病’中起着重要的作用。我们在这里提出了在这种SMC蛋白复合体上由粘附素催化的基因组折叠反应的两个关键方面。我们的目标是了解：1.粘附素如何催化3D基因组折叠的结构机制；2.允许粘附素在许多不同的基因组交易中部署的机制.为了实现这些目标，我们需要更好地了解粘附素全复合体的结构以及它们如何与DNA相互作用并催化折叠.我们还需要解决粘附素如何与调节器相互作用，以便在不同的基因组交易中进行特定的部署。粘附素复合体的不同蛋白质亚基在从癌症到发育障碍的许多“粘附素疾病”中都会发生突变。更具体地说，卵母细胞减数分裂过程中的粘附素失调可导致染色体的错误分离，导致染色体数目错误，这是唐氏综合症(21三体)的标志，也是与年龄相关的非整倍体和不孕不育的主要原因。粘附素复合体的突变与遗传性疾病有关，如导致严重发育缺陷的科妮莉亚·德朗格和罗伯茨综合征。粘附素突变还可以由于染色体环的错误处理、染色体复制、修复或分离的失调而导致基因组不稳定。环路的错误处理可能是染色体外DNA环过度表达癌基因的根源，并且在一半的实体肿瘤中被发现频率很高。因此，我们需要更好地了解不同染色质交易中粘附素的功能、调节和部署的分子机制。这将使我们更好地了解突变是如何导致疾病的。这反过来将使我们能够更好地了解不同疾病背后的分子机制，并有可能开发治疗与粘附素相关的癌症和粘附素疾病的新方法。长期存在的挑战将是理解基因组折叠的分子机制如何导致基因组分层组织，这种组织如何导致基因组功能的新特性(如远程基因调控)，以及调控失调如何导致疾病。

The elucidation of the structure of DNA in 1953 kick-started the revolution in life science research and marked the beginning of modern molecular biology. While we do know the structure of DNA at atomic level resolution, it is still mysterious how DNA is packaged in the cell. Human genomic DNA that, if it were stretched out, would reach over two meters in total. In a cell, all this DNA needs to be compacted into a micron-sized nucleus. One basic unit of coiling DNA is the nucleosome, which has for decades been viewed as the first step in condensation of the DNA. However, it is now clear that the main function of nucleosomes is not to enable large-scale genome packaging. Instead, higher-order genome folding is mediated by Structural maintenance of chromosomes (SMC) proteins, an ancient class of ATPases that is found in all domains of life. SMC proteins are large, ring-shaped proteins that act by DNA loop extrusion. While the details are currently unknown, the consequences are that SMC proteins organise DNA into large, dynamic loops. It is becoming increasingly apparent that this chromosome folding reaction is important for many of the most fundamental aspects of genome biology: control of gene regulation by distant regulatory elements, genome replication and repair as well as chromosome segregation during mitosis and meiosis. There are indications that mutation of cohesin subunits plays an important role in a number of cancers and 'cohesinopathies'.We here propose to address two key aspects of this genome folding reaction catalysed by cohesin, on such SMC protein complex. We aim to understand: 1. The structural mechanism of how cohesin catalyses 3D genome folding, and 2. The mechanism that allows cohesin to be deployed during a number of different genome transactions.To achieve these goals, we need to understand better the structure of cohesin holocomplexes and how they interact with DNA and catalyse folding. We also need to address how cohesin interacts with regulators that allow specific deployment during different genome transactions. The different protein subunits of the cohesin complex are mutated in many 'Cohesinopathies' that range from cancer to developmental disorders. More specifically, cohesin dysregulation during meiosis in oocytes can lead to mis-segregation of chromosomes resulting in cells with the wrong number of chromosomes, a hallmark of Down's syndrome (Trisomy 21) and a leading cause of age-related aneuploidy and infertility. Mutations in the cohesin complex are associated with genetic diseases such as Cornelia de Lange and Roberts syndrome which result in severe development defects. Cohesin mutations also can result in genomic instability due to mis-processing of chromosome loops, dysregulation of chromosome replication, repair or segregation. Mis-processing of loops may be at the origin of extrachromosomal DNA loops that overexpress oncogenes and have been identified with high frequency in half of all solid tumor cancers.We therefore need a much better understanding of the molecular mechanisms of cohesin function, regulation and deployment in different chromatin transactions. This will allow us to better understand how mutations contribute to disease. This in turn will allow us to better understand the molecular mechanisms underlying different diseases and to potentially develop new approaches in treatment against cohesin-related cancer and Cohesinopathies. The long-standing challenge will be to understand how the molecular mechanism of genome folding leads to hierarchical genome organisation, and how such organisation leads to emergent properties of genome function (such as long-range gene regulation) and how dysregulation contributes to disease.