首页|Mapping Multi-factor-mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-related Genes
Mapping Multi-factor-mediated Chromatin Interactions to Assess Dysregulation of Lung Cancer-related Genes
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Studies on the lung cancer genome are indispensable for developing a cure for lung can-cer.Whole-genome resequencing,genome-wide association studies,and transcriptome sequencing have greatly improved our understanding of the cancer genome.However,dysregulation of long-range chromatin interactions in lung cancer remains poorly described.To better understand the three-dimensional(3D)genomic interaction features of the lung cancer genome,we used the A549 cell line as a model system and generated high-resolution chromatin interactions associated with RNA polymerase Ⅱ(RNAPⅡ),CCCTC-binding factor(CTCF),enhancer of zeste homolog 2(EZH2),and histone 3 lysine 27 trimethylation(H3K27me3)using long-read chromatin interac-tion analysis by paired-end tag sequencing(ChIA-PET).Analysis showed that EZH2/H3K27me3-mediated interactions further repressed target genes,either through loops or domains,and their dis-tributions along the genome were distinct from and complementary to those associated with RNAPⅡ.Cancer-related genes were highly enriched with chromatin interactions,and chromatin interactions specific to the A549 cell line were associated with oncogenes and tumor suppressor genes,such as additional repressive interactions on FOXO4 and promoter-promoter interactions between NF1 and RNF135.Knockout of an anchor associated with chromatin interactions reversed the dysregulation of cancer-related genes,suggesting that chromatin interactions are essential for proper expression of lung cancer-related genes.These findings demonstrate the 3D landscape and gene regulatory relationships of the lung cancer genome.
Yan Zhang、Jingwen Zhang、Wei Zhang、Mohan Wang、Shuangqi Wang、Yao Xu、Lun Zhao、Xingwang Li、Guoliang Li
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National Key Laboratory of Crop Genetic Improvement,Huazhong Agricultural University,Wuhan 430070,China
Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data,3D Genomics Research Center,Huazhong Agricultural University,Wuhan 430070,China
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