Sequencing the cancer methylome

Austin Y. Shull, Satish K. Noonepalle, Eun Joon Lee, Jeong Hyeon Choi, Huidong Shi

Research output: Contribution to journalArticlepeer-review

12 Scopus citations


DNA methylation is the most studied epigenetic event in cancer, with focus being placed on studying the entire DNA methylation landscape in specifi c cancers. Due to the recent advances of next-generation sequencing technology, several effective methods have been developed for high-throughput analysis of DNA methylation, enabling DNA methylation markers to be innovative diagnostic and therapeutic strategies in cancer. In this review, we discuss various current and emerging technologies in DNA methylation analysis that integrate next-generation sequencing with the basic principles of methylation detections including methylation sensitive restriction enzyme digestion, affinity purification with antibody or binding proteins, and bisulfite treatment. Variations to these described methods have also allowed for detection of 5-hydroxymethylcytosine marks on a genome-wide scale. We also describe several of the bioinformatic tools used to properly analyze methylome-sequencing data. Finally, recently developed artificial transcription-factor (ATF) targeting tools may provide fl exible manipulation of DNA methylation events in specific gene regions, revealing the functional consequences of particular DNA methylation events.

Original languageEnglish (US)
Pages (from-to)627-651
Number of pages25
JournalMethods in Molecular Biology
StatePublished - 2015


  • 5-Hydroxymethylation
  • Cancer
  • Epigenetics
  • Marker
  • Methylation
  • Methylome
  • Nextgeneration sequencing

ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)


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