Disclosing bias in bisulfite assay: MethPrimers underestimate high DNA methylation

PLoS ONE

Volumn 10, Issue 2, 2015, Pages

  Fuso, Andrea ^a,b   Ferraguti, Giampiero ^c   Scarpa, Sigfrido ^c   Ferrer, Isidre ^d   Lucarelli, Marco ^c  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b IRCCS FONDAZIONE SANTA LUCIA   (Italy)

^c SAPIENZA UNIVERSITY OF ROME   (Italy)

^d HOSPITAL UNIVERSITARI DE BELLVITGE   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BISULFITE; MYOGENIN; PRIMER DNA; HYDROGEN SULFITE; PRESENILIN 1; SULFITE;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CONTROLLED STUDY; CPG ISLAND; DNA DETERMINATION; DNA METHYLATION; DNA SEQUENCE; EMBRYO; EPIGENETICS; EXPERIMENTAL MODEL; GENE; GENE CONVERSION; HUMAN; HUMAN CELL; HUMAN TISSUE; MOUSE; MYOGENIN GENE; NONHUMAN; PROMOTER REGION; PSEN1 GENE; REAL TIME POLYMERASE CHAIN REACTION; SENSITIVITY ANALYSIS; ALZHEIMER DISEASE; ANIMAL; CELL LINE; COMPUTER PROGRAM; GENETICS; PATHOLOGY; PROCEDURES;

ALZHEIMER DISEASE; ANIMALS; CELL LINE; CPG ISLANDS; DNA METHYLATION; DNA PRIMERS; HUMANS; MICE; MYOGENIN; PRESENILIN-1; SEQUENCE ANALYSIS, DNA; SOFTWARE; SULFITES;

EID: 84923283339     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0118318     Document Type: Article

References (31)

1. Ramsahoye BH, Biniszkiewicz D, Lyko F, Clark V, Bird AP, Jaenisch R. Non-CpG methylation is prevalent in embryonic stem cells and may be mediated by DNA methyltransferase 3a. Proc Natl Acad Sci USA. 2000;97:5237-5342. PMID: 10805783
2. Fouse SD, Nagarajan RO, Costello JF. Genome-scale DNA methylation analysis. Epigenomics. 2010;2:105-117. doi: 10.2217/epi.09.35 PMID: 20657796
3. Gupta R, Nagarajan A, Wajapeyee N. Advances in genome-wide DNA methylation analysis. Biotechniques. 2010;49:iii-xi. doi: 10.2144/000113493 PMID: 20964631
4. Tomizawa S, Kobayashi H, Watanabe T, Andrews S, Hata K, Kelsey G, et al. Dynamic stage-specific changes in imprinted differentially methylated regions during early mammalian development and prevalence of non-CpG methylation in oocytes. Development. 2011;138:811-820. doi: 10.1242/dev. 061416 PMID: 21247965
5. Fuso A, Ferraguti G, Grandoni F, Ruggeri R, Scarpa S, et al. Early demethylation of non-CpG, CpCrich, elements in the myogenin 5'-flanking region: a priming effect on the spreading of active demethylation. Cell Cycle. 2010;9:3965-3976. PMID: 20935518
6. Li LC, Dahiya R. MethPrimer: designing primers for methylation PCRs. Bioinformatics. 2002;18:1427-1431. PMID: 12424112
7. Frommer M, McDonald LE, Millar DS, Collis CM, Watt F, Grigg GW, et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci USA. 1992;89:1827-1831. PMID: 1542678
8. Clark SJ, Harrison J, Paul CL, Frommer M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res. 1994;22:2990-2997. PMID: 8065911
9. Clark SJ, Harrison J, Frommer M. CpNpG methylation in mammalian cells. Nat. Genet. 1995;10:20-27. PMID: 7647784
10. Fuso A, Nicolia V, Pasqualato A, Fiorenza MT, Cavallaro RA, Scarpa S. Changes in Presenilin 1 gene methylation pattern in diet-induced B vitamin deficiency. Neurobiol Aging. 2011;32:187-199. doi: 10. 1016/j.neurobiolaging.2009.02.013 PMID: 19329227
11. Fuso A, Nicolia V, Ricceri L, Cavallaro RA, Isopi E, Mangia F, et al. S-adenosylmethionine reduces the progress of the Alzheimer-like features induced by B-vitamin deficiency in mice. Neurobiol Aging. 2012;33:1482.e1-1482.e16.
12. Yan J, Zierath JR, Barrès R. Evidence for non-CpG methylation in mammals. Exp Cell Res. 2011;317:2555-2561. doi: 10.1016/j.yexcr.2011.08.019 PMID: 21925168
13. Patil V, Ward RL, Hesson LB. The evidence for functional non-CpG methylation in mammalian cells. Epigenetics. 2014;9:823-828. doi: 10.4161/epi.28741 PMID: 24717538
14. Arand J, Spieler D, Karius T, Branco MR, Meilinger D, Meissner A, et al. In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases. PLoS Genet. 2012;8:e1002750. doi: 10.1371/journal.pgen. 1002750 PMID: 22761581
15. Ziller MJ, Müller F, Liao J, Zhang Y, Gu H, Bock C, et al. Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. PLoS Genet. 2011;7:e1002389. doi: 10.1371/journal.pgen. 1002389 PMID: 22174693
16. Nishino K, Hattori N, Sato S, Arai Y, Tanaka S, Nagy A, et al. Non-CpG methylation occurs in the regulatory region of the Sry gene. J Reprod Dev. 2011;57:586-593. PMID: 21636956
17. Teng C, Gladwell W, Raphiou I, Liu E. Methylation and expression of the lactoferrin gene in human tissues and cancer cells. Biometals. 2004;17:317-323. PMID: 15222484
18. Barrès R, Osler ME, Yan J, Rune A, Fritz T, Caidahl K, et al. Non-CpG methylation of the PGC-1alpha promoter through DNMT3B controls mitochondrial density. Cell Metab. 2009;10:189-198. doi: 10. 1016/j.cmet.2009.07.011 PMID: 19723495
19. Guo JU, Su Y, Shin JH, Shin J, Li H, Xie B, et al. Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain. Nat Neurosci. 2014;17:215-222. doi: 10.1038/nn. 3607 PMID: 24362762
20. Kozlenkov A, Roussos P, Timashpolsky A, Barbu M, Rudchenko S, Bibikova M, et al. Differences in DNA methylation between human neuronal and glial cells are concentrated in enhancers and non-CpG sites. Nucleic Acids Res. 2014;42:109-127. doi: 10.1093/nar/gkt838 PMID: 24057217
21. Lister R, Pelizzola M, Dowen RH, Hawkins RD, Hon G, Tonti-Filippini J, et al. Human DNA methylomes at base resolution show widespread epigenomic differences. Nature. 2009;462:315-322. doi: 10. 1038/nature08514 PMID: 19829295
22. Laurent L, Wong E, Li G, Huynh T, Tsirigos A, Ong CT, et al. Dynamic changes in the human methylome during differentiation. Genome Res. 2010;20:320-331. doi: 10.1101/gr.101907.109 PMID: 20133333
23. Xie W, Barr CL, Kim A, Yue F, Lee AY, Eubanks J, et al. Base-resolution analyses of sequence and parentof-origin dependent DNA methylation in the mouse genome. Cell. 2012;148:816-831. doi: 10. 1016/j.cell.2011.12.035 PMID: 22341451
24. Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, et al. Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell. 2013;153:1134-1148. doi: 10.1016/j.cell.2013.04. 022 PMID: 23664764
25. Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, Johnson ND, et al. Global epigenomic reconfiguration during mammalian brain development. Science. 2013;341:1237905. doi: 10.1126/science. 1237905 PMID: 23828890
26. Guo W, Chung WY, Qian M, Pellegrini M, Zhang MQ. Characterizing the strand-specific distribution of non-CpG methylation in human pluripotent cells. Nucleic Acids Res. 2014;42:3009-3016. doi: 10. 1093/nar/gkt1306 PMID: 24343027
27. Varley KE, Gertz J, Bowling KM, Parker SL, Reddy TE, Pauli-Behn F, et al. Dynamic DNA methylation across diverse human cell lines and tissues. Genome Res. 2013;23:555-567. doi: 10.1101/gr. 147942.112 PMID: 23325432
28. Lister R, Ecker JR. Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res. 2009;19:959-966. doi: 10.1101/gr.083451.108 PMID: 19273618
29. Fuso A, Scarpa S, Grandoni F, Strom R, Lucarelli M. A reassessment of semiquantitative analytical procedures for DNA methylation: Comparison of bisulfite- and HpaII polymerase-chain-reaction-based methods. Anal Biochem. 2006;350:24-31. PMID: 16445884
30. Genereux DP, Johnson WC, Burden AF, Stöger R, Laird CD. Errors in the bisulfite conversion of DNA: modulating inappropriate- and failed-conversion frequencies. Nucleic Acids Res. 2008;36:e150. doi: 10.1093/nar/gkn691 PMID: 18984622
31. Lucarelli M, Fuso A, Strom R, Scarpa S. The dynamics of myogenin site-specific demethylation is strongly correlated with its expression and with muscle differentiation. J Biol Chem. 2001;276:7500-7506. PMID: 11096088