Project 3 Zha

项目摘要/摘要(&lt；31行) 基因组不稳定是人类癌症的一个标志。ATM和BRCA1(项目1)无处不在 表达的肿瘤抑制基因与DNA双链断裂(DSB)修复有关。然而，他们的损失导致 不同类型的癌症--主要是ATM缺乏症中的淋巴瘤，以及 BRCA1--缺乏(项目1)。这种组织特异性恶性肿瘤风险的原因尚不完全清楚。 人类癌症的序列分析发现了一种独特的替换和重排特征，其中一些 它们(例如替换签名3和短串联复制)已与BRCA1缺乏症相关联。ATM机- 丢失与任何签名没有关联，部分原因是在许多情况下自动柜员机失活的频率较低(2-8% 癌症类型。因此，ATM丢失签名被特定于组织的基因组签名和 人类基因组的异质性。在这里，我们使用近交系小鼠模型(相同的基因组)来揭示ATM-Lost 淋巴细胞(均一细胞类型)中的相关替代和重排特征并使用高 吞吐量基因组易位测序(HTGTS)检测淋巴瘤相关易位 抗原受体基因。使用ATAC-seq，它通过Tn5转座酶测量染色体的可及性 插入时，我们观察到DSB周围局部可及性的时间变化，令人惊讶的是，极化 远离目标中断区域的全球可访问性：增加可访问区域的可访问性 以依赖于53BP1的方式减少不可访问区域的可访问性。和高可访问性 通过末端序列和染色体易位测量的区域也有额外断裂的风险 由HTGTS提供。因为ATM使组蛋白H_2AX和53BP1磷酸化以促进它们向核小体募集 ，我们假设DNA损伤反应导致染色质的重新分布 基于核小体密度的结合因子(例如53BP1)，并对细胞类型特定的基因组有贡献 不稳定(断裂和移位)和恶性肿瘤。为了测试这一点，我们将1)解决分子 ATM介导的DNA损伤反应调节的模式和结果的机制 抗原受体基因产物组装和修饰过程中的染色体易位 淋巴肿大，2)表征细胞周期时相(G1、G2、增殖)对易位模式的影响， 3)阐明了不同类型的破损--干净破损、RAG或AID引发的转位结果 断裂和复制应激引起的损伤。与P01中的其他人合作，我们将整合 损伤引起的可及性变化与替换和重排签名(项目1和2)，细胞周期 (项目2和4)和3D组织(项目4)。通过比较ATM缺陷和BRCA1的签名- 缺乏细胞(项目1)，结果将揭示这两个主要抑癌基因的缺失是如何导致 不同的基因组不稳定特征，并最终导致组织/器官特有的恶性肿瘤。

PROJECT SUMMARY/ABSTRACT (<31 LINES) Genomic instability is a hallmark of human cancers. Both ATM and BRCA1 (Project 1) are ubiquitously expressed tumor suppressor genes implicated in DNA double strand break (DSB) repair. Yet, their losses cause very different types of cancers – predominantly lymphomas in ATM-deficiency, and breast or ovarian cancers in BRCA1-deficiency (Project 1). The causes for such tissue-specific malignancy risk are not fully understood. Sequence analyses of human cancers identified a unique substitution and rearrangement signatures, some of which (e.g. substitution signature 3 and short tandem duplications) have been linked to BRCA1 deficiency. ATM- loss has not been linked to any signature, in part due to the low frequency (2-8%) ATM-inactivation in many cancer types. As such, the ATM-loss signatures is concealed by tissue-specific genomic signatures and the heterogeneity of human genomes. Here we use inbred mouse models (identical genome) to uncover ATM-loss associated substitution and rearrangement signatures in lymphocytes (uniform cell type) and use the High Throughput Genomic Translocation Sequencing (HTGTS) to examine lymphoma relevant translocations from antigen receptor genes. Using ATAC-seq, which measures chromosomal accessibility via Tn5 transposase insertion, we observed temporal changes of local accessibility around DSBs and, surprisingly, polarization of global accessibility in regions distant from the targeted breaks: increases accessibility of accessible regions and decrease the accessibility of non-accessible regions in a 53BP1-dependent manner. And the high accessibility regions are also at risk for additional breaks measured by End-Seq and chromosomal translocations measured by HTGTS. Since ATM phosphorylates histone H2AX and 53BP1 to promotes their recruitment to nucleosome occupied regions, we hypothesize that DNA damage response leads to redistribution of the chromatin bounded factors (e.g. 53BP1) based on nucleosome density and contribute to cell type specific genomic instability (breaks and translocations) and malignancies. To test this, we will 1) address the molecular mechanisms by which ATM mediated DNA damage response regulates the pattern and outcome of chromosomal translocations during the assembly and modification of antigen receptor gene products and during lymphomagenesis, 2) characterize the impact of cell cycle phases (G1, G2, proliferating) on translocation pattern, and 3) elucidate the translocation outcome of different type of breaks – clean breaks, RAG or AID initiated breaks and replication stress induced lesions. In collaboration with others in the P01, we will integrate the damage induced accessibility changes with substitution and rearrangement signatures (Project 1 & 2), cell cycle (Project 2 & 4) and 3D organization (Project 4). By comparing the signatures from ATM-deficient vs BRCA1- deficient (Project 1) cells, the results will shed lights on how loss of these two major tumor suppressors cause different genomic instability signatures and eventually lead to tissue/organ specific malignancies.