title: A sensitive approach to map genome-wide 5-hydroxymethylcytosine and 5-formylcytosine at single-base resolution.
abstract: Mapping genome-wide 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC) at single-base resolution is important to understand their biological functions. We present a cost-efficient mapping method that combines 5hmC-specific restriction enzyme PvuRts1I with a 5hmC chemical labeling enrichment method. The sensitive method enables detection of low-abundance 5hmC sites, providing a more complete 5hmC landscape than available bisulfite-based methods. This method generated a genome-wide 5fC map at single-base resolution. Parallel analyses revealed that 5hmC and 5fC in non-CpG context exhibit lower abundance, more dynamically, than those in CpG context. In the genic region, distribution of 5hmCpG and 5fCpG differed from 5hmCH and 5fCH (H = A, T, C). 5hmC and 5fC were distributed distinctly at regulatory protein-DNA binding sites, depleted in permissive transcription factor binding sites, and enriched at active and poised enhancers. This sensitive bisulfite conversion-free method can be applied to biological samples with limited starting material or low-abundance cytosine modifications.
authors: New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA.
authors: Zhiyi
authors: Z
authors: Sun
authors: New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA.
authors: Nan
authors: N
authors: Dai
authors: New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA.
authors: Janine G
authors: JG
authors: Borgaro
authors: New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA.
authors: Aine
authors: A
authors: Quimby
authors: New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA.
authors: Dapeng
authors: D
authors: Sun
authors: New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA.
authors: Ivan R
authors: IR
authors: Corrêa
authors: New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA.
authors: Yu
authors: Y
authors: Zheng
authors: New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA. Electronic address: zhuz@neb.com.
authors: Zhenyu
authors: Z
authors: Zhu
authors: New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA. Electronic address: guans@neb.com.
authors: Shengxi
authors: S
authors: Guan
mesh_terms: D044503:5-Methylcytosine / Q000031:analogs & derivatives; D000818:Animals; D001483:Base Sequence; D003596:Cytosine / Q000031:analogs & derivatives* / Q000737:chemistry; D004262:DNA Restriction Enzymes / Q000737:chemistry; D053595:Embryonic Stem Cells; D044127:Epigenesis, Genetic; D015723:Gene Library; D006657:Histones / Q000378:metabolism; D051379:Mice; D015183:Restriction Mapping / Q000379:methods*
chemical_list: D006657:Histones; C011865:5-hydroxymethylcytosine; D044503:5-Methylcytosine; D003596:Cytosine; D004262:DNA Restriction Enzymes