Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription. Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription

Extrachromosomal, circular DNA (ecDNA) is emerging as a prevalent yet less characterized oncogenic alteration in cancer genomes. We leverage ChIA-PET and ChIA-Drop chromatin interaction assays to characterize genome-wide ecDNA-mediated chromatin contacts that impact transcriptional programs in cancers. ecDNAs in glioblastoma patient-derived neurosphere and prostate cancer cell cultures are marked by widespread intra-ecDNA and genome-wide chromosomal interactions. ecDNA-chromatin contact foci are characterized by broad and high-level H3K27ac signals converging predominantly on chromosomal genes of increased expression levels. Prostate cancer cells harboring synthetic ecDNA circles composed of characterized enhancers result in the genome-wide activation of chromosomal gene transcription. Deciphering the chromosomal targets of ecDNAs at single-molecule resolution reveals an association with actively expressed oncogenes spatially clustered within ecDNA-directed interaction networks. Our results suggest that ecDNA can function as mobile transcriptional enhancers to promote tumor progression and manifest a potential synthetic aneuploidy mechanism of transcription control in cancer. Overall design: Perform the chromatin interaction assay ChIA-PET, ChIA-Drop, H3K27ac ChIPseq and RNAseq to define genome-wide ecDNA-mediated chromatin interactomes and to characterize their functional impact on transcription programs in cancers.

染色体外环状DNA（extrachromosomal circular DNA, ecDNA）正逐渐成为癌症基因组中一类高发但研究尚不充分的致癌性基因组变异。本研究利用ChIA-PET与ChIA-Drop染色质互作分析技术，对癌症中影响转录程序的全基因组范围ecDNA介导的染色质相互作用进行表征。胶质母细胞瘤患者来源神经球及前列腺癌细胞培养物中的ecDNA，存在广泛的ecDNA内部互作及全基因组染色体间互作特征。ecDNA-染色质互作焦点呈现出宽峰且高水平的组蛋白H3赖氨酸27乙酰化（H3K27ac）信号，且这些信号主要富集于表达上调的染色体基因区域。将经功能验证的增强子构建为人工合成ecDNA环状结构并转入前列腺癌细胞后，可引发全基因组范围内染色体基因的转录激活。在单分子分辨率下解析ecDNA的染色体靶标发现，其与ecDNA介导互作网络中空间聚集的活跃表达致癌基因存在关联。本研究结果表明，ecDNA可作为可移动的转录增强子促进肿瘤进展，并揭示了癌症中一种潜在的合成非整倍体转录调控机制。实验整体设计：通过染色质互作分析技术ChIA-PET、ChIA-Drop，以及H3K27ac 染色质免疫沉淀测序（H3K27ac ChIP-seq）与RNA测序（RNA-seq），解析全基因组范围ecDNA介导的染色质互作组，并表征其对癌症转录程序的功能影响。