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Progress in Chemistry 2020, Vol. 32 Issue (11): 1634-1650 DOI: 10.7536/PC200606 Previous Articles   Next Articles

Detection of 5-Formylpyrimidines in DNA Based on Chemoselective Labeling

Qian Zhou1,2, Na Li2, Kun Li2, Xiaoqi Yu1,2,**()   

  1. 1. Department of Chemistry, Xihua University, Chengdu 610039, China
    2. Laboratory of Green Chemistry and Technology(Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, China
  • Received: Revised: Online: Published:
  • Contact: Xiaoqi Yu
  • Supported by:
    the National Natural Science Foundation of China(21877082)
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In addition to the four canonical nucleobases of A, G, T and C, hundreds of chemical modifications have been identified in genome DNA. Among them, 5-formylpyrimidines, including 5-formylcytosine(5fC) and 5-formyluracil(5fU), are naturally occurring pyrimidine-covalent-modifications and are widely distributed in mammalian cells. Emerging evidence indicates that 5fC not only serves as a key intermediate in active DNA demethylation but also carry independent epigenetic significance; while 5fU was always considered to be an oxidative DNA lesion with high genotoxicity. In order to further understand their regulatory functions, it is necessary to develop accurate, sensitive and facile methods for qualitative, quantitative, and localized detection of 5-formylpyrimidines in the whole genome. In this review, we summarized the recent progress in detecting 5-formylpyrimidines from the perspective of selective chemical labeling.

Contents

1 Introduction

1.1 DNA methylation and demethylation

1.2 5-Formylcytosine and 5-formyluracil

1.3 Detection methods of 5-formylpyrimidines

2 Detection of 5-formyluracil based on chemoselective modification

2.1 Fluorescent labelling of 5-formyluracil

2.2 Enrichment and sequencing of 5-formyluracil

3 Detection of 5-formylcytosine based on chemoselective modification

3.1 Fluorescent labelling of 5-formylcytosine

3.2 Enrichment and sequencing of 5-formylcytosine

4 Conclusion and outlook

Key words: 5-formylcytosine(5fC), 5-formyluracil(5fU), fluorescent sensor, DNA sequencing
Fig.1 DNA methylation and demethylation[4]
Fig.2 Fluorescent labeling of 5fU in DNA with 2-aminothiophenol derivative 1[69]
Fig.3 Fluorescent derivatization of 5fU with o-phenylenediamine derivatives[70]
Fig.4 Fluorescent labelling and enrichment of 5fU with Biotin-lys(3)[71]
Fig.5 Detection of 5fU in DNA with NBDH(4) by colorimetry and fluorescence[72]
Fig.6 Detection of 5fU in DNA with hydrazine derivative 5 by PAGE and fluorescence[73]. Copyright 2018, Royal Society of Chemistry.
Fig.7 Simultaneously labelling 5fU, 5fC and AP sites in DNA with hydroxylamine derivative 6(Conditions: NaOAc buffer, pH=5.0, 37 ℃, 5 h)[74]
Fig.8 Fluorescent labelling 5fU in DNA/RNA with Indole derivatives 7, 8 and 9[75]
Fig.9 Fluorescent labelling 5fU in DNA with Wittig reagent 10[76]. Copyright 2018, Royal Society of Chemistry.
Fig.10 Selective enrichment of 5fU with amino derivatives 11, 12 and 13[77]. Copyright 2015, American Chemical Society.
Fig.11 Selective 5fU labeling and genome-wide mapping with azi-BIAN(14)[48]
Fig.12 5fU:G mispairing and its application in single-base resolution sequencing[78]
Fig.13 Fluorescent labelling 5fC in DNA with primary amines 15 and 16[80]
Fig.14 Fluorescent labelling 5fC in DNA with hydroxylamine derivatives[74, 81~83]
Fig.15 Principle of the CCP-FRET-based assay to detect 5fC with hydroxylamine derivatives 17[84]. Copyright 2019, American Chemical Society.
Fig.16 Acridine-modified hydrazine derivative(HMA, 20) label 5fC in DNA and its functional regulation[85]. Copyright 2013, Royal Society of Chemistry.
Fig.17 Pyrene-modified hydrazine derivatives distinguish symmetric from asymmetric 5fCpG sites in dsDNA[86]. Copyright 2014, John Wiley and Sons.
Fig.18 Chemoselective fluorescent labelling 5fC in DNA with hydrazine derivative 5[73]
Fig.19 Fluorescent labelling 5fC in DNA/RNA with indole derivatives 7[75]
Fig.20 Selective fluorescent labelling of 5fC with Wittig reagent YC-CN(24)[87]. Copyright 2019, American Chemical Society.
Fig.21 Enrichment and single-base resolution sequencing of 5fC with 1,3-indanedione derivative[88]
Fig.22 Single-cell 5fC landscapes of mammalian early embryos and ESCs at single-base resolution[90]
Fig.23 Fluorescent labelling and single-base resolution sequencing of 5fC with CBAN(27)[91]
Fig.24 Gene specific-loci quantitative and single-base resolution analysis of 5fC by qPCR with azi-BP(28)[92]
Fig.25 Enrichment of 5fC with aldehyde reactive probe 11 and its cleavable version 29[33, 93]
Fig.26 Enrichment and sequencing of 5fC based on NaBH4 reduction[94]
Fig.27 Bisulfite sequencing of 5fC at single-base resolution[95]
[1]
Chen K, Zhao B S, He C. . Cell Chem. Biol., 2016,23:74.
[2]
Liu M Y , DeNizio J E, Schutsky E K, Kohli R M. Curr. Opin. Chem. Biol., 2016,33:67.
[3]
Carell T, Kurz M Q, Muller M, Rossa M , Spada F. Angew. Chem. Int. Ed., 2018,57:4296.
[4]
Hardwick J S, Lane A N, Brown T . Bioessays, 2018,40:1700199.
[5]
Liu T, Ma C J, Yuan B F , Feng Y Q. Sci. China Chem., 2018,61:381.
[6]
Zhu Q, Stoger R , Alberio R. Front. Cell. Dev. Biol., 2018,6.
[7]
Traube F R, Carell T. . RNA Biol 2017,14:1099.
[8]
Greenberg M V C, Bourc'his D . Nat. Rev. Mol. Cell Biol., 2019,20:590.
[9]
Nuovo G J, Plaia T W, Belinsky S A, Baylin S B , Herman J G. Proc. Natl. Acad. Sci. U. S. A., 1999,96:12754.
[10]
Jones P A , Baylin S B. Nat. Rev. Genet., 2002,3:415.
[11]
Issa J P. Nat. Rev. Cancer, 2004,4:988.
[12]
Dick K J, Nelson C P, Tsaprouni L, Sandling J K, Aissi D, Wahl S, Meduri E, Morange P E, Gagnon F, Grallert H, Waldenberger M, Peters A, Erdmann J, Hengstenberg C, Cambien F, Goodall A H, Ouwehand W H, Schunkert H, Thompson J R, Spector T D, Gieger C, Tregout D A, Deloukas P, Samani N J . Lancet, 2014,383:1990.
[13]
Kobayashi N, Shinagawa S, Nagata T, Shimada K, Shibata N, Ohnuma T, Kasanuki K, Arai H, Yamada H, Nakayama K, Kondo K . Plos One, 2016,11:e0146449.
[14]
Wei Y, Yang N, Xu Q, Sun Q, Guo J, Li K, Liu Z, Yan X, Zhu X, Tang B . Neurol. Sci., 2016,367:11.
[15]
Yokoyama A S, Rutledge J C, Medici V. . Environ. Epigenet. 2017, 3: dvx008.
[16]
Iwan K, Rahimoff R, Kirchner A, Spada F, Schroeder A S, Kosmatchev O, Ferizaj S, Steinbacher J, Parsa E, Mueller M , Carell T. Nat. Chem. Biol., 2018,14:72.
[17]
Schiesser S, Pfaffeneder T, Sadeghian K, Hackner B, Steigenberger B, Schroeder A S, Steinbacher J, Kashiwazaki G, Hoefner G, Wanner K T, Ochsenfeld C, Carell T .. Am. Chem. Soc., 2013,135:14593.
[18]
Globisch D, Muenzel M, Mueller M, Michalakis S, Wagner M, Koch S, Brueckl T, Biel M, Carell T . PloS ONE, 2010,5:e15367.
[19]
Liu P F, Burdzy A, Sowers L C . DNA Repair, 2003,2:199.
[20]
Anensen H, Provan F, Lian A T, Reinertsen S, Ueno Y, Matsuda A, Seeberg E, Bjelland S. .Mutat. Res., 2001,476:99.
[21]
Masaoka A, Matsubara M, Hasegawa R, Tanaka T, Kurisu S, Terato H, Ohyama Y, Karino N, Matsuda A, Ide H . Biochemistry, 2003,42:5003.
[22]
Wang Y, Zhang X, Zou G, Peng S, Liu C , Zhou X. Acc. Chem. Res., 2019,52:1016.
[23]
Bachman M, Uribe-Lewis S, Yang X, Burgess H E, Iurlaro M, Reik W, Murrell A , Balasubramanian S. Nat. Chem. Biol., 2015,11:555.
[24]
Su M, Kirchner A, Stazzoni S, Mueller M, Wagner M, Schroeder A , Carell T. Angew. Chem. Int. Ed., 2016,55:11797.
[25]
Kellinger M W, Song C X, Chong J, Lu X Y, He C , Wang D. Nat. Struct. Mol. Biol., 2012,19:831.
[26]
Song C X, Szulwach K E, Dai Q, Fu Y, Mao S Q, Lin L, Street C, Li Y, Poidevin M, Wu H, Gao J, Liu P, Li L, Xu G L, Jin P, He C . Cell, 2013,153:678.
[27]
Wang S R, Long Y L, Wang J Q, Ge Y S, Guo P, Liu Y, Tian T, Zhou X .. Am. Chem. Soc., 2014,136:56.
[28]
Raiber E A, Murat P, Chirgadze D Y, Beraldi D, Luisi B F , Balasubramanian S. Nat. Struct. Mol. Biol., 2015,22:44.
[29]
Dai Q, Sanstead P J, Peng C S, Han D, He C, Tokmakoff A. . ACS Chem. Biol., 2016,11:470.
[30]
Iurlaro M , McInroy G R, Burgess H E, Dean W, Raiber E A, Bachman M, Beraldi D, Balasubramanian S, Reik W. Genome Biol., 2016,17:141.
[31]
Ngo T T, Yoo J, Dai Q, Zhang Q, He C, Aksimentiev A, Ha T. . Nat. Commun., 2016,7:10813.
[32]
Hardwick J S, Ptchelkine D , El-Sagheer A H, Tear I, Singleton D, Phillips S E V, Lane A N, Brown T. Nat. Struct. Mol. Biol., 2017,24:544.
[33]
Raiber E A, Beraldi D, Ficz G, Burgess H E, Branco M R, Murat P, Oxley D, Booth M J, Reik W, Balasubramanian S. . Genome Biol, 2012,13:69.
[34]
Iurlaro M, Ficz G, Oxley D, Raiber E A, Bachman M, Booth M J, Andrews S, Balasubramanian S, Reik W. . Genome Biol, 2013,14:R119.
[35]
Ji S, Shao H, Han Q, Seiler C L , Tretyakova N Y. Angew. Chem. Int. Ed., 2017,56:14130.
[36]
Li F, Zhang Y, Bai J, Greenberg M M, Xi Z, Zhou C . Am. Chem. Soc., 2017,139:10617.
[37]
Ji S, Fu I, Naldiga S, Shao H, Basu A K, Broyde S , Tretyakova N Y. Nucleic Acids Res., 2018,46:6455.
[38]
Raiber E A, Portella G, Cuesta S M, Hardisty R, Murat P, Li Z, Iurlaro M, Dean W, Spindel J, Beraldi D, Liu Z, Dawson M A, Reik W, Balasubramanian S. . Nat. Chem., 2018,10:1258.
[39]
Bjelland S, Anensen H, Knevelsrud I, Seeberg E . Mutat. Res., 2001,486:147.
[40]
Cadetw J , Wagner J R. Cold Spring Harb. Perspect. Biol., 2013,5:a012559.
[41]
Rogstad D K, Heo J, Vaidehi N, Goddard W A, Burdzy A, Sowers L C . Biochemistry, 2004,43:5688.
[42]
Privat E J , Sowers L C. Mutat. Res., 1996,354:151.
[43]
Yoshida M, Makino K, Morita H, Terato H, Ohyama Y , Ide H. Nucleic Acids Res., 1997,25:1570.
[44]
Bullard W , Lopes da Rosa-Spiegler J, Liu S, Wang Y, Sabatini R. Biol. Chem., 2014,289:20273.
[45]
Li W, Zhang T , Ding J. Nucleic Acids Res., 2015,43:10026.
[46]
Pais J E, Dai N, Tamanaha E, Vaisvila R, Fomenkov A I, Bitinaite J, Sun Z, Guan S, Correa I R , Jr., Noren C J, Cheng X, Roberts R J, Zheng Y, Saleh L. Proc. Natl. Acad. Sci. U.S.A., 2015,112:4316.
[47]
Smiley J A, Kundracik M, Landfried D A, Barnes V R , Sr., Axhemi A A. Biochim. Biophys Acta, 2005,1723:256.
[48]
Wang Y, Liu C, Wu F, Zhang X, Liu S, Chen Z, Zeng W, Yang W, Zhang X, Zhou Y, Weng X, Wu Z, Zhou X . Iscience, 2018,9:423.
[49]
Kittaka A, Takayama H, Kurihara M, Horii C, Tanaka H, Miyasaka T, Inoue J . Nucleosides Nucleotides & Nucleic Acids, 2001,20:669.
[50]
Terato H, Morita H, Ohyama Y, Ide H . Nucleosides & Nucleotides, 1998,17:131.
[51]
Dohno C, Okamoto A, Saito I . Am. Chem. Soc., 2005,127:16681.
[52]
Chen Y, Hong T, Wang S, Mo J, Tian T , Zhou X. Chem. Soc. Rev., 2017,46:2844.
[53]
Olinski R, Gackowski D , Cooke M S. Biochim. Biophys. Acta, 2018,1869:29.
[54]
Cao L L, Liu H, Yue Z, Pei L, Wang H, Jia M . Hematology, 2019,24:567.
[55]
Stratton M S, Farina F M, Elia L . Mol. Cell. Cardiol., 2019,133:148.
[56]
Booth M J, Raiber E A, Balasubramanian S . Chem. Rev., 2015,115:2240.
[57]
Peng J, Xia B, Yi C . Sci China Life Sci., 2016,59:219.
[58]
Berney M , McGouran J F. Nat. Rev. Chem., 2018,2:332.
[59]
Dietzsch J, Feineis D, Hobartner C. . FEBS Lett., 2018,592:2032.
[60]
Ren R, Horton J R, Zhang X, Blumenthal R M , Cheng X. Curr. Opin. Struct. Biol., 2018,53:88.
[61]
Asenso J, Wang L, Du Y, Liu Q H, Xu B J, Guo M Z, Tang D Q . Sep. Sci., 2019,42:1105.
[62]
Hofer A, Liu Z J, Balasubramanian S . Am. Chem. Soc., 2019,141:6420.
[63]
Ivancova I, Leone D L , Hocek M. Curr. Opin. Chem. Biol., 2019,52:136.
[64]
Qi C, Ding J, Yuan B , Feng Y. Chin. Chem. Lett., 2019,30:1618.
[65]
Zeng H, He B, Yi C . ChemBioChem, 2019,20:1898.
[66]
Traube F R, Schiffers S, Iwan K, Kellner S, Spada F, Mueller M, Carell T. . Nat. Protoc., 2019,14:283.
[67]
Li Q Y, Yuan B F , Feng Y Q. Chem. Lett., 2018,47:1453.
[68]
Lan M D, Yuan B F , Feng Y Q. Chin. Chem. Lett., 2019,30:1.
[69]
Hirose W, Sato K , Matsuda A. Angew. Chem. Int. Ed., 2010,49:8392.
[70]
Guo P, Xu X, Qiu X, Zhou Y, Yan S, Wang C, Lu C, Ma W, Weng X, Zhang X , Zhou X. Org. Biomol. Chem., 2013,11:1610.
[71]
Liu C, Wang Y, Zhang X, Wu F, Yang W, Zou G, Yao Q, Wang J, Chen Y, Wang S, Zhou X . Chem. Sci., 2017,8:4505.
[72]
Liu C, Chen Y, Wang Y, Wu F, Zhang X, Yang W, Wang J, Chen Y, He Z, Zou G, Wang S, Zhou X. . Nano Res., 2017,10:2449.
[73]
Wang Y, Liu C, Yang W, Zou G, Zhang X, Wu F, Yu S, Luo X, Zhou X. . Chem. Commun., 2018,54:1497.
[74]
Liu C, Luo X, Chen Y, Wu F, Yang W, Wang Y, Zhang X, Zou G, Zhou X . Anal. Chem., 2018,90:14616.
[75]
Samanta B, Seikowski J , Hoebartner C. Angew. Chem. Int. Ed., 2016,55:1912.
[76]
Zhou Q, Li K, Liu Y H, Li L L, Yu K K, Zhang H , Yu X Q. Chem. Commun., 2018,54:13722.
[77]
Hardisty R E, Kawasaki F, Sahakyan A B, Balasubramanian S . Am. Chem. Soc., 2015,137:9270.
[78]
Kawasaki F, Cuesta S M, Beraldi D, Mahtey A, Hardisty R E, Carrington M , Balasubramanian S. Angew. Chem. Int. Ed., 2018,57:9694.
[79]
Munzel M, Lischke U, Stathis D, Pfaffeneder T, Gnerlich F A, Deiml C A, Koch S C, Karaghiosoff K, Carell T . Chem. -Eur. J., 2011,17:13782.
[80]
Hu J, Xing X, Xu X, Wu F, Guo P, Yan S, Xu Z, Xu J, Weng X, Zhou X . Chem. -Eur. J., 2013,19:5836.
[81]
Guo P, Yan S, Hu J, Xing X, Wang C, Xu X, Qiu X, Ma W, Lu C, Weng X, Zhou X . Org. Lett., 2013,15:3266.
[82]
Wang S R, Song Y Y, Wei L, Liu C X, Fu B S, Wang J Q, Yang X R, Liu Y N, Liu S M, Tian T, Zhou X . Am. Chem. Soc., 2017,139:16903.
[83]
Wang S R, Wang J Q, Fu B S, Chen K, Xiong W, Wei L, Qing G, Tian T, Zhou X . Am. Chem. Soc., 2018,140:15842.
[84]
Hong T, Wang T, Guo P, Xing X, Ding F, Chen Y, Wu J, Ma J, Wu F, Zhou X . Anal. Chem., 2013,85:10797.
[85]
Xu L, Chen Y C, Nakajima S, Chong J, Wang L, Lan L, Zhang C, Wang D . Chem. Sci., 2014,5:567.
[86]
Xu L, Chen Y C, Chong J, Fin A , McCoy L S, Xu J, Zhang C, Wang D. Angew. Chem. Int. Ed., 2014,53:11223.
[87]
Zhou Q, Li K, Li L L, Yu K K, Zhang H, Shi L, Chen H , Yu X Q. Anal. Chem., 2019,91:9366.
[88]
Xia B, Han D, Lu X, Sun Z, Zhou A, Yin Q, Zeng H, Liu M, Jiang X, Xie W, He C, Yi C . Nat. Methods, 2015,12:1047.
[89]
Zeng H, Mondal M, Song R, Zhang J, Xia B, Liu M, Zhu C, He B, Gao Y Q , Yi C. Angew. Chem. Int. Ed., 2019,58:130.
[90]
Zhu C, Gao Y, Guo H, Xia B, Song J, Wu X, Zeng H, Kee K, Tang F, Yi C . Cell Stem Cell, 2017,20:720.
[91]
Liu C, Wang Y, Yang W, Wu F, Zeng W, Chen Z, Huang J, Zou G, Zhang X, Wang S, Weng X, Wu Z, Zhou Y, Zhou X . Chem. Sci., 2017,8:7443.
[92]
Wang Y, Liu C, Zhang X, Yang W, Wu F, Zou G, Weng X, Zhou X . Chem. Sci., 2018,9:3723.
[93]
McInroy G R, Raiber E A, Balasubramanian S . Chem. Commun., 2014,50:12047.
[94]
Booth M J, Marsico G, Bachman M, Beraldi D, Balasubramanian S . Nat. Chem., 2014,6:435.
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