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MICMIC: identification of DNA methylation of distal regulatory regions with causal effects on tumorigenesis.

ABSTRACT: Aberrant promoter methylation is a common mechanism for tumor suppressor inactivation in cancer. We develop a set of tools to identify genome-wide DNA methylation in distal regions with causal effect on tumorigenesis called MICMIC. Many predictions are directly validated by dCas9-based epigenetic editing to support the accuracy and efficiency of our tool. Oncogenic and lineage-specific transcription factors are shown to aberrantly shape the methylation landscape by modifying tumor-subtype core regulatory circuitry. Notably, the gene regulatory networks orchestrated by enhancer methylation across different cancer types are seen to converge on a common architecture. MICMIC is available on https://github.com/ZhangJlab/MICMIC .

SUBMITTER: Tong Y

PROVIDER: S-EPMC5989391 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

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MICMIC: identification of DNA methylation of distal regulatory regions with causal effects on tumorigenesis.

Tong Yin Y Sun Jianlong J Wong Chi Fat CF Kang Qingzheng Q Ru Beibei B Wong Ching Ngar CN Chan April Sheila AS Leung Suet Yi SY Zhang Jiangwen J

Genome biology 20180605 1

Aberrant promoter methylation is a common mechanism for tumor suppressor inactivation in cancer. We develop a set of tools to identify genome-wide DNA methylation in distal regions with causal effect on tumorigenesis called MICMIC. Many predictions are directly validated by dCas9-based epigenetic editing to support the accuracy and efficiency of our tool. Oncogenic and lineage-specific transcription factors are shown to aberrantly shape the methylation landscape by modifying tumor-subtype core r ...[more]

PMID: 29871649

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