Evaluation of methyl-binding domain based enrichment approaches revisited

PLoS ONE

Volumn 10, Issue 7, 2015, Pages

  Aberg, Karolina A ^a   Xie, Linying ^a   Chan, Robin F ^a   Zhao, Min ^a   Pandey, Ashutosh K ^b   Kumar, Gaurav ^a   Clark, Shaunna L ^a   Van Den Oord, Edwin J C G ^a  

^a VIRGINIA COMMONWEALTH UNIVERSITY   (United States)

^b UNIVERSITY OF TENNESSEE HEALTH SCIENCE CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BISULFITE; GENOMIC DNA; DNA;

ADULT; ANIMAL TISSUE; ARTICLE; CHEMICAL PROCEDURES; CPG ISLAND; DNA DETERMINATION; DNA METHYLATION; DNA SEQUENCE; GENE TARGETING; GENERAL MEDICAL DEVICE; GENOME; MALE; MATHEMATICAL MODEL; METHYL BINDING DOMAIN ENRICHMENT; METHYL BINDING DOMAIN ENRICHMENT KIT; METHYLOME; MOUSE; NONHUMAN; PYROSEQUENCING; VALIDATION PROCESS; ANIMAL; CHEMISTRY; CONFORMATION; DBA MOUSE; EVALUATION STUDY; ISOLATION AND PURIFICATION; METABOLISM;

ANIMALS; CPG ISLANDS; DNA; DNA METHYLATION; GENOME; MALE; MICE; MICE, INBRED DBA; NUCLEIC ACID CONFORMATION; SEQUENCE ANALYSIS, DNA;

EID: 84941331214     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0132205     Document Type: Article

References (24)

1. Hsieh CL. Dependence of transcriptional repression on CpG methylation density. Mol Cell Biol. 1994; 14(8):5487-94. Epub 1994/08/01. PMID: 7518564; PubMed Central PMCID: PMC359068.
2. Kulis M, Heath S, Bibikova M, Queiros AC, Navarro A, Clot G, et al. Epigenomic analysis detects widespread gene-body DNA hypomethylation in chronic lymphocytic leukemia. Nat Genet. 2012; 44 (11):1236-42. Epub 2012/10/16. doi: ng.2443 [pii] doi: 10.1038/ng.2443 PMID: 23064414.
3. 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 U S A. 1992; 89(5):1827-31. Epub 1992/03/01. PMID: 1542678; PubMed Central PMCID: PMC48546.
4. Rakyan VK, Down TA, Balding DJ, Beck S. Epigenome-wide association studies for common human diseases. Nat Rev Genet. 2011; 12(8):529-41. Epub 2011/07/13. doi: nrg3000 [pii] doi: 10.1038/nrg3000 PMID: 21747404.
5. Aberg KA, McClay JL, Nerella S, Xie LY, Clark SL, Hudson AD, et al. MBD-seq as a cost-effective approach for methylome-wide association studies: demonstration in 1500 case-control samples. Epigenomics. 2012; 4(6):605-21. Epub 2012/12/19. doi: 10.2217/epi.12.59 PMID: 23244307.
6. Serre D, Lee BH, Ting AH. MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome. Nucleic Acids Res. 2010; 38(2):391-9. Epub 2009/11/13. doi: gkp992 [pii] doi: 10.1093/nar/gkp992 PMID: 19906696; PubMed Central PMCID: PMC2811030.
7. Bock C, Tomazou EM, Brinkman AB, Muller F, Simmer F, Gu H, et al. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol. 2010; 28(10):1106-14. Epub 2010/09/21. doi: nbt.1681 [pii] doi: 10.1038/nbt.1681 PMID: 20852634; PubMed Central PMCID: PMC3066564.
8. Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, et al. Comparison of sequencingbased methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010; 28(10):1097-105. Epub 2010/09/21. doi: nbt.1682 [pii] doi: 10.1038/nbt.1682 PMID: 20852635; PubMed Central PMCID: PMC2955169.
9. Hogart A, Lichtenberg J, Ajay SS, Anderson S, Margulies EH, Bodine DM. Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites. Genome Res. 2012; 22(8):1407-18. Epub 2012/06/12. doi: gr.132878.111 [pii] doi: 10.1101/gr.132878.111 PMID: 22684279; PubMed Central PMCID: PMC3409254.
10. Lan X, Adams C, Landers M, Dudas M, Krissinger D, Marnellos G, et al. High resolution detection and analysis of CpG dinucleotides methylation using MBD-Seq technology. PLoS One. 2011; 6(7):e22226. Epub 2011/07/23. doi: 10.1371/journal.pone.0022226 PONE-D-11-02256 [pii]. PMID: 21779396; PubMed Central PMCID: PMC3136941.
11. Nair SS, Coolen MW, Stirzaker C, Song JZ, Statham AL, Strbenac D, et al. Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias. Epigenetics. 2011; 6(1):34-44. Epub 2010/09/08. doi: 13313 [pii] doi: 10.4161/epi.6.1.13313 PMID: 20818161.
12. McClay JL, Aberg KA, Clark SL, Nerella S, Kumar G, Xie LY, et al. A methylome-wide study of aging using massively parallel sequencing of the methyl-CpG-enriched genomic fraction from blood in over 700 subjects. Hum Mol Genet. 2014; 23(5):1175-85. Epub 2013/10/19. doi: ddt511 [pii] doi: 10.1093/hmg/ddt511 PMID: 24135035; PubMed Central PMCID: PMC3919012.
13. Aberg KA, McClay JL, Nerella S, Clark S, Kumar G, Chen W, et al. Methylome-wide association study of schizophrenia: identifying blood biomarker signatures of environmental insults. JAMA Psychiatry. 2014; 71(3):255-64. Epub 2014/01/10. doi: 1810320 [pii] doi: 10.1001/jamapsychiatry.2013.3730 PMID: 24402055.
14. De Meyer T, Mampaey E, Vlemmix M, Denil S, Trooskens G, Renard JP, et al. Quality evaluation of methyl binding domain based kits for enrichment DNA-methylation sequencing. PLoS One. 2013; 8(3): e59068. Epub 2013/04/05. doi: 10.1371/journal.pone.0059068 PONE-D-13-01161 [pii]. PMID: 23554971; PubMed Central PMCID: PMC3598902.
15. Wang X, Agarwala R, Capra JA, Chen Z, Church DM, Ciobanu DC, et al. High-throughtput sequenceing of the DBA/2J mouse genome. BMC Bioinformatics. 2010; 11(Suppl 04):O7.
16. van den Oord EJ, Bukszar J, Rudolf G, Nerella S, McClay JL, Xie LY, et al. Estimation of CpG coverage in whole methylome next-generation sequencing studies. BMC Bioinformatics. 2013; 14(1):50. Epub 2013/02/13. doi: 1471-2105-14-50 [pii] doi: 10.1186/1471-2105-14-50 PMID: 23398781.
17. Down TA, Rakyan VK, Turner DJ, Flicek P, Li H, Kulesha E, et al. A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol. 2008; 26(7):779-85. Epub 2008/07/10. doi: nbt1414 [pii] doi: 10.1038/nbt1414 PMID: 18612301; PubMed Central PMCID: PMC2644410.
18. Royo JL, Hidalgo M, Ruiz A. Pyrosequencing protocol using a universal biotinylated primer for mutation detection and SNP genotyping. Nat Protoc. 2007; 2(7):1734-9. doi: 10.1038/nprot.2007.244 PMID: 17641638.
19. Colella S, Shen L, Baggerly KA, Issa JP, Krahe R. Sensitive and quantitative universal Pyrosequencing methylation analysis of CpG sites. Biotechniques. 2003; 35(1):146-50. PMID: 12866414.
20. Invitrogen. Enrichment of differntially methylated regions with MethylMinerTM fraction and deep sequencing with teh Solid SystemTM. Application Note.
21. Fraga MF, Ballestar E, Montoya G, Taysavang P, Wade PA, Esteller M. The affinity of different MBD proteins for a specific methylated locus depends on their intrinsic binding properties. Nucleic Acids Res. 2003; 31(6):1765-74. PMID: 12626718; PubMed Central PMCID: PMC152853.
22. Khrapunov S, Warren C, Cheng H, Berko ER, Greally JM, Brenowitz M. Unusual characteristics of the DNA binding domain of epigenetic regulatory protein MeCP2 determine its binding specificity. Biochemistry. 2014; 53(21):3379-91. doi: 10.1021/bi500424z PMID: 24828757; PubMed Central PMCID: PMC4045320.
23. Lister R, Mukamel EA, Nery JR, Urich M, Puddifoot CA, Johnson ND, et al. Global epigenomic reconfiguration during mammalian brain development. Science. 2013; 341(6146):1237905. Epub 2013/07/06. doi: science.1237905 [pii] doi: 10.1126/science.1237905 PMID: 23828890; PubMed Central PMCID: PMC3785061.
24. Aberg KA, Xie LY, Nerella S, Copeland WE, Costello EJ, van den Oord EJ. High quality methylomewide investigations through next-generation sequencing of DNA from a single archived dry blood spot. Epigenetics. 2013; 8(5):542-7. Epub 2013/05/07. doi: 24508 [pii] doi: 10.4161/epi.24508 PMID: 23644822; PubMed Central PMCID: PMC3741224.