title: 5-Formylcytosine Could Be a Semipermanent Base in Specific Genome Sites.
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 semipermanent base.
authors: Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377, München, Germany.
authors: Meng
authors: M
authors: Su
authors: Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377, München, Germany.
authors: Angie
authors: A
authors: Kirchner
authors: Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377, München, Germany.
authors: Samuele
authors: S
authors: Stazzoni
authors: Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377, München, Germany.
authors: Markus
authors: 0000-0002-3579-3317
authors: M
authors: Müller
authors: Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377, München, Germany.
authors: Mirko
authors: M
authors: Wagner
authors: Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377, München, Germany.
authors: Arne
authors: A
authors: Schröder
authors: Center for Integrated Protein Science at the Department of Chemistry, Ludwig-Maximilians-Universität München, Butenandtstrasse 5-13, 81377, München, Germany. thomas.carell@lmu.de.
authors: Thomas
authors: 0000-0001-7898-2831
authors: T
authors: Carell
mesh_terms: D000818:Animals; D001483:Base Sequence; D002478:Cells, Cultured; D057930:Click Chemistry; D018899:CpG Islands; D003596:Cytosine / Q000031:analogs & derivatives* / Q000032:analysis / Q000378:metabolism; D051379:Mice; D018345:Mice, Knockout; D000066450:Mouse Embryonic Stem Cells / Q000378:metabolism; D044502:Thymine DNA Glycosylase / Q000235:genetics / Q000378:metabolism*
chemical_list: C560973:5-formylcytosine; D003596:Cytosine; D044502:Thymine DNA Glycosylase
keywords: 5-formylcytosine; click chemistry; droplet digital PCR; epigenetic bases; genomic DNA