The impact of changes in chromatin architecture on cancer phenotypes and tumor progression

摘要-总体 新出现的数据表明，基因组被组织成边界划定的领土和子领土， 其中存在表观遗传标记和转录状态的高度协调。越大 结构域已被定义为分别由活性和非活性组分组成的区室A和B 染色质这些可以被分解成保守的TAD（拓扑相关结构域）。后者 由高度自相互作用的区域组成，由绝缘边界隔离。在更高的分辨率 在水平上，基因表达是通过细胞环境特异性基因增强子与启动子之间的环连接来实现的， 而不经常超越边界。最保守的结构接触是介导的， 至少部分通过CTCF的作用调节，CTCF是一种DNA结合TF和边界因子，沿着 虽然细胞类型特异性增强子-启动子相互作用是由粘附素促进的， 介体复合物和细胞转录因子。值得注意的是，CTCF和粘附素复合物通常是突变的， 癌症，并在正常发育和分化途径中发挥关键作用。他们也可以直接 与恶性肿瘤相关的转录因子和组蛋白修饰复合物相互作用或间接控制 转型基于这些概念，我们的P01提出了以下总体假设： CTCF或粘着蛋白调节剂的作用破坏了染色质的结构组织（影响染色质的结构和亚结构）。 边界和增强子相互作用），并通过该机制建立致癌表观遗传和 转录程序。相反，我们提出，招募的建筑蛋白质复合物也是 被体细胞突变或特定转录因子、组蛋白修饰酶和 控制DNA甲基化的酶，将这些变化置于染色体改变的上游， 建筑作为肿瘤发生的原因。为了测试我们的模型，我们的目标是比较基因突变的影响， CTCF、粘附素卸载因子PDS 5 B和控制增强子功能的蛋白质（NOTCH 1 致癌转录因子，组蛋白修饰酶如Polycomb和CREBBP/EP 300，以及 改变DNA甲基化状态的酶DNMT 3A）。关注血液恶性肿瘤，我们将：（i） 确定Ctcf和粘附素调节蛋白Pds 5 b的突变是否以及如何破坏正常的 发展和诱导恶性转化;（ii）确定如何改变3D染色体 由Ctcf或粘着蛋白调节因子突变引起的结构，Pds 5 b诱导肿瘤发生表观遗传， （iii）确定转录因子和表观遗传修饰因子的突变是否 通过对3D染色体结构的影响驱动恶性转化;以及（iv）确定是否 靶向转录因子活性和表观遗传修饰剂的药物可以“纠正”; 致癌染色体结构

SUMMARY - OVERALL Emerging data indicate that sets of genes are organized into boundary delimited territories and sub-territories, within which there is a high level of coordination of epigenetic marks and transcriptional states. The larger domains have been defined as compartments A and B that are respectively comprised of active and inactive chromatin. These can be broken down into conserved TADs (topologically associated domains). The latter are composed of highly self-interacting regions, segregated by insulated boundaries. At an even higher resolution level, gene expression is conferred through looping of cell context specific gene enhancers to promoters within, and less frequently beyond TAD boundaries. The most conserved TAD structural contacts are mediated and regulated at least in part through the action of CTCF, a DNA binding TF and boundary factor, along with the cohesin complex, while cell-type specific enhancer-promoter interactions are facilitated by cohesin, the mediator complex and cell transcription factors. Notably, CTCF and the cohesin complex are often mutated in cancer and play critical roles in normal development and differentiation pathways. They may also directly interact with, or indirectly control transcription factors and histone modifying complexes linked to malignant transformation. Based on these notions, our P01 proposes the following overall hypothesis: Somatic mutations of CTCF or cohesin regulators disrupt the architectural organization of chromatin (affecting TAD, and sub-TAD boundaries and enhancer interactions) and through this mechanism establish oncogenic epigenetic and transcriptional programs. Conversely, we propose that recruitment of architectural protein complexes are also disrupted by somatic mutation or deregulation of specific transcription factors, histone modifying enzymes and enzymes controlling DNA methylation, which place these changes upstream of alterations in chromosome architecture as a cause of tumorigenesis. To test our model we aim to compare the impact of mutations in CTCF, the cohesin unloading factor PDS5B, and proteins that control enhancer function (the NOTCH1 oncogenic transcription factor, histone modifying enzymes such as Polycomb and CREBBP/EP300, as well as enzymes that alter DNA methylation status DNMT3A). Focusing on hematologic malignancies we will: (i) determine whether and how mutations of Ctcf and the cohesin regulatory protein, Pds5b disrupt normal development and induce malignant transformation; (ii) determine how alterations in 3D chromosomal architecture caused by mutation of Ctcf or the cohesin regulator, Pds5b induce tumorigenic epigenetic and transcriptional programming; (iii) Determine whether transcription factors and mutations of epigenetic modifiers drive malignant transformation through effects on 3D chromosomal architecture; and (iv) determine whether drugs targeting transcription factor activity and epigenetic modifiers can `correct; the deleterious effects of oncogenic chromosomal architecture.