Methylomic and genomic impacts of organic pollutants in Dup15q syndrome

描述(申请人提供)：这项研究旨在测试一种新的范式，即人类基因组与环境动态相互作用，表观遗传机制位于基因组与环境相互作用的界面上。人类基因组的特点是结构变异，包括大拷贝数变异和重复序列的差异。多氯联苯(PCBS)等环境毒素可引起DNA低甲基化。DNA低甲基化是灵长类物种中富含CpG的Alu重复序列基因组不稳定的一个已知因素。染色体15q11-13重复综合征(Dup15q)是神经发育障碍中最常见的拷贝数变异，与1-3%的自闭症病例有关。这一建议是基于一项偶然的发现，即患有Dup15q综合征的人脑样本显示出比对照组或特发性自闭症患者显著更高的持久性有机污染物PCB-95水平。此外，与对照组相比，出生时暴露于相关阻燃剂BDE-47的遗传易感小鼠的大脑表现出低甲基化和社交能力降低。本研究旨在利用基因组和表观基因组学相结合的方法，从实验上确定PCB-95和/或BDE-47在15q的结构重排中是否起到因果或复合作用。此外，这项研究将直接调查基因组和环境联合侮辱对人脑样本中甲基组和转录组完整性的影响。第一个目标是在一种新的人类细胞系系统中建立15号染色体复制的实验模型，以使用下一代测序技术检查PCB-95或BDE-47暴露对基因组稳定性(DNA-seq)和DNA甲基化(甲基C-seq)的影响。在第二个目标中，将通过染色质构象捕获测序(4C-SEQ)来检测遗传和表观遗传变化对15q11-q13内长距离染色质环结构的影响，并将其与特定的转录变化相关联。第三个目标旨在直接研究人类大脑样本中表观遗传和转录变化的特定15q基因靶点，这些样本具有和不具有15号染色体重复和高水平的PCB-95。预计这些研究的结果将正式检验这一假说，即特定环境污染物降低的DNA甲基化水平可能会导致基因组重排和远程染色质的变化，从而导致转录变化。此外，人类大脑样本中涉及突触发生的自闭症候选基因的表观遗传学变化有望通过这种方法被发现。最后，这些研究的结果有望广泛地与理解基因组、环境暴露和表观基因组在人类健康和疾病中的关系有关。

DESCRIPTION (provided by applicant): This study is designed to test a novel paradigm that the human genome dynamically interacts with the environment and that epigenetic mechanisms are at the interface of genome- environment interactions. The human genome is marked by structural variations including large copy number variations and differences in repetitive sequences. Environmental toxins such as polychlorinated biphenyls (PCBs) can induce DNA hypomethylation. DNA hypomethylation is a known contributor to genomic instability of CpG-rich Alu repeats in the primate lineage. Chromosome 15q11-13 duplication syndrome (Dup15q), is the most common copy number variation observed in neurodevelopmental disorders, and is responsible for 1-3% of autism cases. This proposal is based on the serendipitous finding that human brain samples with Dup15q syndrome showed significantly higher levels of the persistent organic pollutant PCB-95 than controls or idiopathic autism cases. Furthermore, a genetically susceptible mouse perinatally exposed to the related flame retardant BDE-47 exhibited hypomethylation in brain and reduced sociability compared to controls. This study is designed to experimentally determine if PCB-95 and/or BDE-47 play a causal or compounding role in structural rearrangements of 15q using combined genomic and epigenomic approaches. In addition, this study will directly investigate the effect of combined genomic and environmental insults on the integrity of the methylome and transcriptome in human brain samples. The first aim seeks to experimentally model chromosome 15 duplication in a novel human cell line system to examine effects of PCB-95 or BDE-47 exposures on genomic stability (DNA-seq) and DNA methylation (MethylC-seq) using next generation sequencing technology. In the second aim, the effect of genetic and epigenetic changes on long-range chromatin loop structure within 15q11-q13 will be examined by chromatin conformation capture sequencing (4C-seq) and correlated to specific transcriptional alterations. The third aim seeks to directly investigate specific 15q gene targets for epigenetic and transcriptional changes in human brain samples with and without chromosome 15 duplication and high PCB-95 levels. The results of these studies are expected to formally test the hypothesis that DNA methylation levels reduced by specific environmental pollutants may result in genomic rearrangements and alterations in long-range chromatin, leading to transcriptional changes. In addition, epigenetic alterations of autism candidate genes involved in synaptogenesis in human brain samples are expected to be uncovered by this approach. Finally, the results of these studies are expected to be broadly relevant to understanding the relationship between the genome, environmental exposures, and the epigenome in human health and disease.