7. Chedin F, Lieber MR, Hsieh CL (2002) The DNA methyltransferase-like protein DNMT3L
stimulates de novo methylation by Dnmt3a. Proc Natl Acad Sci U S A 99(26):16916–16921.
https://doi.org/10.1073/pnas.262443999
8. Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu
DR, Aravind L, Rao A (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in
mammalian DNA by MLL partner TET1. Science 324(5929):930–935
9. Pfaffeneder T, Hackner B, Truss M, Munzel M, Muller M, Deiml CA, Hagemeier C, Carell T
(2011) The discovery of 5-formylcytosine in embryonic stem cell DNA. Angew Chem Int Ed
Engl 50(31):7008–7012
10. Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA, He C, Zhang Y (2011) Tet proteins
can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333
(6047):1300–1303
11. He YF, Li BZ, Li Z, Liu P, Wang Y, Tang Q, Ding J, Jia Y, Chen Z, Li L, Sun Y, Li X, Dai Q,
Song CX, Zhang K, He C, Xu GL (2011) Tet-mediated formation of 5-carboxylcytosine and
its excision by TDG in mammalian DNA. Science 333(6047):1303–1307
12. Valinluck V, Sowers LC (2007) Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1. Cancer Res 67(3):946–950
13. Kotandeniya D, Seiler CL, Fernandez J, Pujari SS, Curwick L, Murphy K, Wickramaratne S,
Yan S, Murphy D, Sham YY, Tretyakova NY (2018) Can 5-methylcytosine analogues with
extended alkyl side chains guide DNA methylation? Chem Commun (Camb) 54
(9):1061–1064. https://doi.org/10.1039/c7cc06867k
14. Seiler CL, Fernandez J, Koerperich Z, Andersen MP, Kotandeniya D, Nguyen ME, Sham YY,
Tretyakova NY (2018) Maintenance DNA methyltransferase activity in the presence of
oxidized forms of 5-methylcytosine: structural basis for ten eleven translocation-mediated
DNA demethylation. Biochemistry 57(42):6061–6069. https://doi.org/10.1021/acs.biochem.
8b00683
15. Kweon SM, Zhu B, Chen Y, Aravind L, Xu SY, Feldman DE (2017) Erasure of Tet-oxidized
5-methylcytosine by a SRAP nuclease. Cell Rep 21(2):482–494. https://doi.org/10.1016/j.
celrep.2017.09.055
16. Song CX, He C (2013) Potential functional roles of DNA demethylation intermediates. Trends
Biochem Sci 38(10):480–484
17. Bachman M, Uribe-Lewis S, Yang X, Burgess HE, Iurlaro M, Reik W, Murrell A,
Balasubramanian S (2015) 5-Formylcytosine can be a stable DNA modification in mammals.
Nat Chem Biol 11:555
18. Kriukiene E, Liutkeviciute Z, Klimasauskas S (2012) 5-Hydroxymethylcytosine--the elusive
epigenetic mark in mammalian DNA. Chem Soc Rev 41(21):6916–6930
19. Fu Y, He C (2012) Nucleic acid modifications with epigenetic significance. Curr Opin Chem
Biol 16(5–6):516–524
20. Spruijt CG, Gnerlich F, Smits AH, Pfaffeneder T, Jansen PW, Bauer C, Munzel M, Wagner M,
Muller M, Khan F, Eberl HC, Mensinga A, Brinkman AB, Lephikov K, Muller U, Walter J,
Boelens R, van Ingen H, Leonhardt H, Carell T, Vermeulen M (2013) Dynamic readers for
5-(hydroxy)methylcytosine and its oxidized derivatives. Cell 152(5):1146–1159
21. Iurlaro M, Ficz G, Oxley D, Raiber EA, Bachman M, Booth MJ, Andrews S,
Balasubramanian S, Reik W (2013) A screen for hydroxymethylcytosine and formylcytosine
binding proteins suggests functions in transcription and chromatin regulation. Genome Biol 14
(10):R119. https://doi.org/10.1186/gb-2013-14-10-r119
22. Ngo TT, Yoo J, Dai Q, Zhang Q, He C, Aksimentiev A, Ha T (2016) Effects of cytosine
modifications on DNA flexibility and nucleosome mechanical stability. Nat Commun
7:10813. https://doi.org/10.1038/ncomms10813
23. Globisch D, Munzel M, Muller M, Michalakis S, Wagner M, Koch S, Bruckl T, Biel M, Carell
T (2010) Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation
intermediates. PLoS One 5(12):e15367
514
C. L. Seiler et al.
stimulates de novo methylation by Dnmt3a. Proc Natl Acad Sci U S A 99(26):16916–16921.
https://doi.org/10.1073/pnas.262443999
8. Tahiliani M, Koh KP, Shen Y, Pastor WA, Bandukwala H, Brudno Y, Agarwal S, Iyer LM, Liu
DR, Aravind L, Rao A (2009) Conversion of 5-methylcytosine to 5-hydroxymethylcytosine in
mammalian DNA by MLL partner TET1. Science 324(5929):930–935
9. Pfaffeneder T, Hackner B, Truss M, Munzel M, Muller M, Deiml CA, Hagemeier C, Carell T
(2011) The discovery of 5-formylcytosine in embryonic stem cell DNA. Angew Chem Int Ed
Engl 50(31):7008–7012
10. Ito S, Shen L, Dai Q, Wu SC, Collins LB, Swenberg JA, He C, Zhang Y (2011) Tet proteins
can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333
(6047):1300–1303
11. He YF, Li BZ, Li Z, Liu P, Wang Y, Tang Q, Ding J, Jia Y, Chen Z, Li L, Sun Y, Li X, Dai Q,
Song CX, Zhang K, He C, Xu GL (2011) Tet-mediated formation of 5-carboxylcytosine and
its excision by TDG in mammalian DNA. Science 333(6047):1303–1307
12. Valinluck V, Sowers LC (2007) Endogenous cytosine damage products alter the site selectivity of human DNA maintenance methyltransferase DNMT1. Cancer Res 67(3):946–950
13. Kotandeniya D, Seiler CL, Fernandez J, Pujari SS, Curwick L, Murphy K, Wickramaratne S,
Yan S, Murphy D, Sham YY, Tretyakova NY (2018) Can 5-methylcytosine analogues with
extended alkyl side chains guide DNA methylation? Chem Commun (Camb) 54
(9):1061–1064. https://doi.org/10.1039/c7cc06867k
14. Seiler CL, Fernandez J, Koerperich Z, Andersen MP, Kotandeniya D, Nguyen ME, Sham YY,
Tretyakova NY (2018) Maintenance DNA methyltransferase activity in the presence of
oxidized forms of 5-methylcytosine: structural basis for ten eleven translocation-mediated
DNA demethylation. Biochemistry 57(42):6061–6069. https://doi.org/10.1021/acs.biochem.
8b00683
15. Kweon SM, Zhu B, Chen Y, Aravind L, Xu SY, Feldman DE (2017) Erasure of Tet-oxidized
5-methylcytosine by a SRAP nuclease. Cell Rep 21(2):482–494. https://doi.org/10.1016/j.
celrep.2017.09.055
16. Song CX, He C (2013) Potential functional roles of DNA demethylation intermediates. Trends
Biochem Sci 38(10):480–484
17. Bachman M, Uribe-Lewis S, Yang X, Burgess HE, Iurlaro M, Reik W, Murrell A,
Balasubramanian S (2015) 5-Formylcytosine can be a stable DNA modification in mammals.
Nat Chem Biol 11:555
18. Kriukiene E, Liutkeviciute Z, Klimasauskas S (2012) 5-Hydroxymethylcytosine--the elusive
epigenetic mark in mammalian DNA. Chem Soc Rev 41(21):6916–6930
19. Fu Y, He C (2012) Nucleic acid modifications with epigenetic significance. Curr Opin Chem
Biol 16(5–6):516–524
20. Spruijt CG, Gnerlich F, Smits AH, Pfaffeneder T, Jansen PW, Bauer C, Munzel M, Wagner M,
Muller M, Khan F, Eberl HC, Mensinga A, Brinkman AB, Lephikov K, Muller U, Walter J,
Boelens R, van Ingen H, Leonhardt H, Carell T, Vermeulen M (2013) Dynamic readers for
5-(hydroxy)methylcytosine and its oxidized derivatives. Cell 152(5):1146–1159
21. Iurlaro M, Ficz G, Oxley D, Raiber EA, Bachman M, Booth MJ, Andrews S,
Balasubramanian S, Reik W (2013) A screen for hydroxymethylcytosine and formylcytosine
binding proteins suggests functions in transcription and chromatin regulation. Genome Biol 14
(10):R119. https://doi.org/10.1186/gb-2013-14-10-r119
22. Ngo TT, Yoo J, Dai Q, Zhang Q, He C, Aksimentiev A, Ha T (2016) Effects of cytosine
modifications on DNA flexibility and nucleosome mechanical stability. Nat Commun
7:10813. https://doi.org/10.1038/ncomms10813
23. Globisch D, Munzel M, Muller M, Michalakis S, Wagner M, Koch S, Bruckl T, Biel M, Carell
T (2010) Tissue distribution of 5-hydroxymethylcytosine and search for active demethylation
intermediates. PLoS One 5(12):e15367
514
C. L. Seiler et al.