Publikation
Two are better than one: HPoxBS - hairpin oxidative bisulfite sequencing
Pascal Giehr; Charalampos Kyriakopoulos; Konstantin Lepikhov; Stefan Wallner; Verena Wolf; Jörn Walter
In: Nucleic Acids Research, Vol. 46, No. 15, Pages 1-10, Oxford University Press, 6/2018.
Zusammenfassung
The controlled and stepwise oxidation of 5mC to 5hmC, 5fC and 5caC by Tet enzymes is influencing the chemical and biological properties of cytosine. Besides direct effects on gene regulation, oxidised forms influence the dynamics of demethylation and re-methylation processes. So far, no combined methods exist which allow to precisely determine the strand specific localisation of cytosine modifications along with their CpG symmetric distribution. Here we describe a comprehensive protocol combining conventional hairpin bisulfite with oxidative bisulfite sequencing (HPoxBS) to determine the strand specific distribution of 5mC and 5hmC at base resolution. We apply this method to analyse the contribution of local oxidative effects on DNA demethylation in mouse ES cells. Our method includes the HPoxBS workflow and subsequent data analysis using our developed software tools. Besides a precise …
