Mapping Multiple Factors Mediated Chromatin Interactions to Assess Regulatory Network and Dysregulation of Lung Cancer-Related Genes

Studies on the lung cancer genome are indispensable for developing a cure for lung cancer. 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. The generated high-resolution data revealed chromatin interactions associated with RNA polymerase II (RNAPII), CCCTC-binding factor (CTCF), enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2), and histone 3 lysine 27 trimethylation (H3K27me3) using specific antibodies and long-read chromatin interaction analysis by paired-end tag sequencing (ChIA-PET). The EZH2/H3K27me3-mediated interactions further silenced target genes, either through loops or domains, and showed distributions along the genome distinct from and complementary to those associated with RNAPII. We found that cancer-related genes were highly enriched in chromatin interactions. We identified abnormal interactions associated with oncogenes and tumor suppressors, such as additional repressive interactions on FOXO4 and promoter - promoter interactions between NF1 and RNF135. Knockout of abnormal 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.