A pan-cancer analysis of CpG Island gene regulation reveals extensive plasticity within Polycomb target genes.
Yueyuan ZhengGuowei HuangTiago C SilvaQian YangYan-Yi JiangH Phillip KoefflerDe-Chen LinBenjamin P BermanPublished in: Nature communications (2021)
CpG Island promoter genes make up more than half of human genes, and a subset regulated by Polycomb-Repressive Complex 2 (PRC2+-CGI) become DNA hypermethylated and silenced in cancer. Here, we perform a systematic analysis of CGI genes across TCGA cancer types, finding that PRC2+-CGI genes are frequently prone to transcriptional upregulation as well. These upregulated PRC2+-CGI genes control important pathways such as Epithelial-Mesenchymal Transition (EMT) and TNFα-associated inflammatory response, and have greater cancer-type specificity than other CGI genes. Using publicly available chromatin datasets and genetic perturbations, we show that transcription factor binding sites (TFBSs) within distal enhancers underlie transcriptional activation of PRC2+-CGI genes, coinciding with loss of the PRC2-associated mark H3K27me3 at the linked promoter. In contrast, PRC2-free CGI genes are predominantly regulated by promoter TFBSs which are common to most cancer types. Surprisingly, a large subset of PRC2+-CGI genes that are upregulated in one cancer type are also hypermethylated/silenced in at least one other cancer type, underscoring the high degree of regulatory plasticity of these genes, likely derived from their complex regulatory control during normal development.
Keyphrases
- genome wide
- transcription factor
- papillary thyroid
- genome wide identification
- dna methylation
- bioinformatics analysis
- epithelial mesenchymal transition
- squamous cell
- genome wide analysis
- rheumatoid arthritis
- magnetic resonance imaging
- cell proliferation
- oxidative stress
- computed tomography
- long non coding rna
- single cell
- cell free
- single molecule