. Author manuscript; available in PMC: 2013 May 1.

Published in final edited form as: Nat Biotechnol. 2012 Nov;30(11):1107–1116. doi: 10.1038/nbt.2398

Table 1.

Proteins that deposit, bind to, modify or remove nucleotide variants, and the known genomic locations of some of these nucleotide variants.

Modification	Proteins that deposit the modification	Proteins that modify, remove or bind the modification	Genomic or transcriptomic location
5hmC	TET1-3^4,8	TET1-3^6,7	With affinity-based profiling, it is shown to be enriched at TSSs, promoters, exons, CTCF-binding sites and enhancers^{18-20,22,61,62,65,66}. With single-base resolution sequencing, it shows highest enrichment at distal regulatory regions, near but not on transcription factor-binding sites⁶⁹.
5fC	TET1-3⁶	TET1-3⁶, TDG^23,24	Unknown
5caC	TET1-3^6,7	TDG^7,23,24	Unknown
m⁶A in mRNA	MT-A70 (A 70 kD subunit protein in a 200 kD protein complex)¹²⁰	FTO³⁷, YTHDF2-3 and ELAVL1 (binding proteins)¹⁰¹	Enriched around stop codons, in 3′ UTRs and within long internal exons^101,102
5mC in RNA	NSUN2⁹²	Unknown	Enriched in untranslated regions (both 5′ and 3′ UTRs) and near Argonaute-binding regions within mRNA⁹²