Complex impact of DNA methylation on transcriptional dysregulation across 22 human cancer types.

Abstract

Accumulating evidence has demonstrated that transcriptional regulation is affected by DNA methylation. Understanding the perturbation of DNA methylation-mediated regulation between transcriptional factors (TFs) and targets is crucial for human diseases. However, the global landscape of DNA methylation-mediated transcriptional dysregulation (DMTD) across cancers has not been portrayed. Here, we systematically identified DMTD by integrative analysis of transcriptome, methylome and regulatome across 22 human cancer types. Our results revealed that transcriptional regulation was affected by DNA methylation, involving hundreds of methylation-sensitive TFs (MethTFs). In addition, pan-cancer MethTFs, the regulatory activity of which is generally affected by DNA methylation across cancers, exhibit dominant functional characteristics and regulate several cancer hallmarks. Moreover, pan-cancer MethTFs were found to be affected by DNA methylation in a complex pattern. Finally, we investigated the cooperation among MethTFs and identified a network module that consisted of 43 MethTFs with prognostic potential. In summary, we systematically dissected the transcriptional dysregulation mediated by DNA methylation across cancer types, and our results provide a valuable resource for both epigenetic and transcriptional regulation communities.

• Authors: Zishan Wang, Jiaqi Yin, Weiwei Zhou, Jing Bai, Yunjin Xie, Kang Xu, Xiangyi Zheng, Jun Xiao, Li Zhou, Xiaolin Qi, Yongsheng Li, Xia Li, Juan Xu
• Journal: Nucleic acids research (Nucleic Acids Res) Vol. 48 Issue 5 Pg. 2287-2302 (03 18 2020) ISSN: 1362-4962 [Electronic] England
• PMID: 32002550 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.

Chemical References

• Biomarkers, Tumor
• DNA, Neoplasm
• Transcription Factors

Topics

• Biomarkers, Tumor (genetics, metabolism)
• CpG Islands
• DNA Methylation
• DNA, Neoplasm (genetics, metabolism)
• Epigenesis, Genetic
• Female
• Gene Expression Regulation, Neoplastic
• Gene Regulatory Networks
• Genome, Human
• Humans
• Male
• Molecular Sequence Annotation
• Neoplasms (genetics, metabolism, mortality, pathology)
• Survival Analysis
• Transcription Factors (classification, genetics, metabolism)
• Transcriptome