MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome - PubMed (original) (raw)
MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome
David Serre et al. Nucleic Acids Res. 2010 Jan.
Abstract
DNA methylation is an epigenetic modification involved in both normal developmental processes and disease states through the modulation of gene expression and the maintenance of genomic organization. Conventional methods of DNA methylation analysis, such as bisulfite sequencing, methylation sensitive restriction enzyme digestion and array-based detection techniques, have major limitations that impede high-throughput genome-wide analysis. We describe a novel technique, MBD-isolated Genome Sequencing (MiGS), which combines precipitation of methylated DNA by recombinant methyl-CpG binding domain of MBD2 protein and sequencing of the isolated DNA by a massively parallel sequencer. We utilized MiGS to study three isogenic cancer cell lines with varying degrees of DNA methylation. We successfully detected previously known methylated regions in these cells and identified hundreds of novel methylated regions. This technique is highly specific and sensitive and can be applied to any biological settings to identify differentially methylated regions at the genomic scale.
Figures
Figure 1.
Bisulfite sequencing of newly identified methylated regions. Bisulfite sequencing was performed on (A) peri-centromeric CpG island on chromosome 16, (B) promoter CpG island of PTCHD1 and (C) ZEB1 intronic CpG island in HCT116, DICERex5 and DKO cells. Genomic coordinates (NCBI Build 36.1) for the bisulfite sequencing amplicon of chromosome 16 peri-centromeric CpG island are shown. Positions relative to the transcription start site are indicated for the amplicons of PTCHD1 and ZEB1. Each circle represents a CpG dinucleotide with black circles representing methylated cytosines and white ones representing unmethylated cytosines. Each row represents one individual allele sequenced. Rectangles above each cell line represent the non-overlapping 100-bp windows covered by each amplicon. Methylated windows identified by MiGS are shaded in gray while unmethylated windows are in white.
Figure 2.
Sampling curves for HCT116 and DICERex5. The curves show the number of 100-bp windows identified as being methylated (_y_-axis) for a given number of sequences randomly drawn from the entire dataset (_x_-axis). Blue lines represent sampling curves for HCT116, and red lines correspond to data for DICERex5. The solid lines show the results obtained when considering all significantly methylated windows (≥4 reads), while the dash lines represent the results for highly methylated loci (≥10 reads) only. The vertical black line shows the number of reads used in this study.
Similar articles
- 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.
Nair SS, Coolen MW, Stirzaker C, Song JZ, Statham AL, Strbenac D, Robinson MD, Clark SJ. Nair SS, et al. Epigenetics. 2011 Jan;6(1):34-44. doi: 10.4161/epi.6.1.13313. Epub 2011 Jan 1. Epigenetics. 2011. PMID: 20818161 - Identification of methylated regions with peak search based on Poisson model from massively parallel methylated DNA immunoprecipitation-sequencing data.
Yang Y, Wang W, Li Y, Tu J, Bai Y, Xiao P, Zhang D, Lu Z. Yang Y, et al. Electrophoresis. 2010 Oct;31(21):3537-44. doi: 10.1002/elps.201000326. Electrophoresis. 2010. PMID: 20925052 - High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing.
Hodges E, Smith AD, Kendall J, Xuan Z, Ravi K, Rooks M, Zhang MQ, Ye K, Bhattacharjee A, Brizuela L, McCombie WR, Wigler M, Hannon GJ, Hicks JB. Hodges E, et al. Genome Res. 2009 Sep;19(9):1593-605. doi: 10.1101/gr.095190.109. Epub 2009 Jul 6. Genome Res. 2009. PMID: 19581485 Free PMC article. - Methyl-CpG-binding proteins. Targeting specific gene repression.
Ballestar E, Wolffe AP. Ballestar E, et al. Eur J Biochem. 2001 Jan;268(1):1-6. doi: 10.1046/j.1432-1327.2001.01869.x. Eur J Biochem. 2001. PMID: 11121095 Review. - Detection of DNA methylation by MeDIP and MBDCap assays: an overview of techniques.
Hsu HK, Weng YI, Hsu PY, Huang TH, Huang YW. Hsu HK, et al. Methods Mol Biol. 2014;1105:61-70. doi: 10.1007/978-1-62703-739-6_5. Methods Mol Biol. 2014. PMID: 24623219 Review.
Cited by
- Translation of Epigenetics in Cell-Free DNA Liquid Biopsy Technology and Precision Oncology.
Tan WY, Nagabhyrava S, Ang-Olson O, Das P, Ladel L, Sailo B, He L, Sharma A, Ahuja N. Tan WY, et al. Curr Issues Mol Biol. 2024 Jun 27;46(7):6533-6565. doi: 10.3390/cimb46070390. Curr Issues Mol Biol. 2024. PMID: 39057032 Free PMC article. Review. - DNA methyltransferase 1 (DNMT1) promotes cyst growth and epigenetic age acceleration in autosomal dominant polycystic kidney disease.
Zhou JX, Li LX, Zhang H, Agborbesong E, Harris PC, Calvet JP, Li X. Zhou JX, et al. Kidney Int. 2024 Aug;106(2):258-272. doi: 10.1016/j.kint.2024.04.017. Epub 2024 May 21. Kidney Int. 2024. PMID: 38782200 - Induction of double-strand breaks with the non-steroidal androgen receptor ligand flutamide in patients on androgen suppression: a study protocol for a randomized, double-blind prospective trial.
Lee E, Coulter J, Mishra A, Caramella-Pereira F, Demarzo A, Rudek M, Hu C, Han M, DeWeese TL, Yegnasubramanian S, Song DY. Lee E, et al. Trials. 2023 Dec 16;24(1):809. doi: 10.1186/s13063-023-07838-4. Trials. 2023. PMID: 38104131 Free PMC article. - The Principles and Applications of High-Throughput Sequencing Technologies.
Lee JY. Lee JY. Dev Reprod. 2023 Apr;27(1):9-24. doi: 10.12717/DR.2023.27.1.9. Epub 2023 Mar 31. Dev Reprod. 2023. PMID: 38075439 Free PMC article. - The Development of Plant Genome Sequencing Technology and Its Conservation and Application in Endangered Gymnosperms.
Hong K, Radian Y, Manda T, Xu H, Luo Y. Hong K, et al. Plants (Basel). 2023 Nov 28;12(23):4006. doi: 10.3390/plants12234006. Plants (Basel). 2023. PMID: 38068641 Free PMC article. Review.
References
- Gruenbaum Y, Cedar H, Razin A. Substrate and sequence specificity of a eukaryotic DNA methylase. Nature. 1982;295:620–622. - PubMed
- Bird A. Perceptions of epigenetics. Nature. 2007;447:396–398. - PubMed
- Holliday R, Pugh JE. DNA modification mechanisms and gene activity during development. Science. 1975;187:226–232. - PubMed
- Cedar H, Stein R, Gruenbaum Y, Naveh-Many T, Sciaky-Gallili N, Razin A. Effect of DNA methylation on gene expression. Cold Spring Harb. Symp. Quant. Biol. 1983;47 (Pt 2):605–609. - PubMed
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Miscellaneous