5-Formylcytosine could be a semi-permanent base in specific genome sites

Su, Meng ; Kirchner, Angie ; Stazzoni, Samuele; Müller, Markus ; Wagner, Mirko; Schröder, Arne and Carell, Thomas (25. August 2016): 5-Formylcytosine could be a semi-permanent base in specific genome sites. In: Angewandte Chemie International Edition, Vol. 55, No. 39: pp. 11797-11800

Abstract

5-Formyl-2’-deoxycytosine (fdC) is a recently discovered epigenetic base in the genome of stem cells, with yet unknown functions. Sequencing data show that the base is enriched in CpG islands of promoters and hence likely involved in the regulation of transcription during cellular differentiation. fdC is known to be recognized and excised by the enzyme thymine-DNA-glycosylase (Tdg). As such, fdC is believed to function as an intermediate during active demethylation. In order to understand the function of the new epigenetic base fdC, it is important to analyze its formation and removal at defined genomic sites. Here, we report a new method that combines sequence-specific chemical derivatization of fdC with droplet digital PCR that enables such analysis. We show initial data, indicating that the repair protein Tdg removes only 50% of the fdCs at a given genomic site, arguing that fdC is a semi-permanent base.

• Item Type: Journal article
• EU Funded Grant Agreement Number: 642023
• EU Projects: Horizon 2020 > Marie Skłodowska Curie Actions > Marie Skłodowska-Curie Innovative Training Networks > 642023: ClickGene - Click Chemistry for Future Gene Therapies to Benefit Citizens, Researchers and Industry
• Form of publication: Submitted Version
• Keywords: epigenetic bases; click chemistry; 5-formylcytosine; genomic DNA; droplet digital PCR
• Faculties: Chemistry and Pharmacy > Department of Chemistry
• Subjects: 500 Science > 540 Chemistry; 500 Science > 570 Life sciences; biology
• ISSN: 1521-3773
• Language: English