Methylomic and genomic impacts of organic pollutants in Dup15q syndrome

描述（由申请人提供）：本研究旨在测试人类基因组与环境动态相互作用以及表观遗传机制处于基因组-环境相互作用界面的新范式。人类基因组以结构变异为特征，包括大量拷贝数变异和重复序列差异。环境毒素如多氯联苯（PCBs）可以诱导DNA低甲基化。DNA低甲基化是灵长类谱系中富含cpg的Alu重复序列基因组不稳定的已知因素。染色体15q11-13重复综合征（Dup15q）是在神经发育障碍中观察到的最常见的拷贝数变异，导致1-3%的自闭症病例。这一建议是基于一个偶然的发现，即患有Dup15q综合征的人脑样本中持久性有机污染物多氯联苯-95的含量明显高于对照组或特发性自闭症病例。此外，与对照组相比，围产期暴露于相关阻燃剂BDE-47的遗传易感小鼠表现出大脑低甲基化和社交能力下降。本研究旨在实验确定PCB-95和/或BDE-47是否在15q的结构重排中发挥因果或复合作用，使用基因组学和表观基因组学相结合的方法。此外，本研究将直接研究基因组和环境联合损伤对人脑样本中甲基组和转录组完整性的影响。第一个目标是通过实验模拟新的人类细胞系系统中的15号染色体复制，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（MethylC-seq）的影响。在第二个目标中，遗传和表观遗传变化对15q11-q13内远端染色质环结构的影响将通过染色质构象捕获测序（4C-seq）进行检查，并与特定的转录改变相关。第三个目标是直接研究具有或不具有15号染色体重复和高多氯联苯-95水平的人脑样本中特定的15q基因靶点的表观遗传和转录变化。这些研究的结果有望正式验证特定环境污染物降低DNA甲基化水平可能导致基因组重排和远端染色质改变，从而导致转录变化的假设。此外，自闭症候选基因参与突触发生的人类大脑样本的表观遗传改变有望通过这种方法发现。最后，这些研究的结果有望对理解基因组、环境暴露和人类健康和疾病中的表观基因组之间的关系具有广泛的意义。

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.