DNA immunoprecipitation semiconductor sequencing (DIP-SC-seq) as a rapid method to generate genome wide epigenetic signatures

John P Thomson, Angie Fawkes, Raffaele Ottaviano, Jennifer M Hunter, Ruchi Shukla, Heidi K Mjoseng, Richard Clark, Audrey Coutts, Lee Murphy, Richard R Meehan

Research output: Contribution to journalArticlepeer-review

Abstract

Modification of DNA resulting in 5-methylcytosine (5 mC) or 5-hydroxymethylcytosine (5hmC) has been shown to influence the local chromatin environment and affect transcription. Although recent advances in next generation sequencing technology allow researchers to map epigenetic modifications across the genome, such experiments are often time-consuming and cost prohibitive. Here we present a rapid and cost effective method of generating genome wide DNA modification maps utilising commercially available semiconductor based technology (DNA immunoprecipitation semiconductor sequencing; "DIP-SC-seq") on the Ion Proton sequencer. Focussing on the 5hmC mark we demonstrate, by directly comparing with alternative sequencing strategies, that this platform can successfully generate genome wide 5hmC patterns from as little as 500 ng of genomic DNA in less than 4 days. Such a method can therefore facilitate the rapid generation of multiple genome wide epigenetic datasets.

Original languageEnglish
Article number9778
JournalScientific Reports
Volume5
DOIs
Publication statusPublished - 18 May 2015

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