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Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array

BACKGROUND: Recent progress in high-throughput technologies has greatly contributed to the development of DNA methylation profiling. Although there are several reports that describe methylome detection of whole genome bisulfite sequencing, the high cost and heavy demand on bioinformatics analysis pr...

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Autores principales: Yang, Liu, Zhang, Kunlin, Dai, Wei, He, Ximiao, Zhao, Qian, Wang, Jing, Sun, Zhong Sheng
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2011
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3023747/
https://www.ncbi.nlm.nih.gov/pubmed/21211017
http://dx.doi.org/10.1186/1471-2164-12-10
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author Yang, Liu
Zhang, Kunlin
Dai, Wei
He, Ximiao
Zhao, Qian
Wang, Jing
Sun, Zhong Sheng
author_facet Yang, Liu
Zhang, Kunlin
Dai, Wei
He, Ximiao
Zhao, Qian
Wang, Jing
Sun, Zhong Sheng
author_sort Yang, Liu
collection PubMed
description BACKGROUND: Recent progress in high-throughput technologies has greatly contributed to the development of DNA methylation profiling. Although there are several reports that describe methylome detection of whole genome bisulfite sequencing, the high cost and heavy demand on bioinformatics analysis prevents its extensive application. Thus, current strategies for the study of mammalian DNA methylomes is still based primarily on genome-wide methylated DNA enrichment combined with DNA microarray detection or sequencing. Methylated DNA enrichment is a key step in a microarray based genome-wide methylation profiling study, and even for future high-throughput sequencing based methylome analysis. RESULTS: In order to evaluate the sensitivity and accuracy of methylated DNA enrichment, we investigated and optimized a number of important parameters to improve the performance of several enrichment assays, including differential methylation hybridization (DMH), microarray-based methylation assessment of single samples (MMASS), and methylated DNA immunoprecipitation (MeDIP). With advantages and disadvantages unique to each approach, we found that assays based on methylation-sensitive enzyme digestion and those based on immunoprecipitation detected different methylated DNA fragments, indicating that they are complementary in their relative ability to detect methylation differences. CONCLUSIONS: Our study provides the first comprehensive evaluation for widely used methodologies for methylated DNA enrichment, and could be helpful for developing a cost effective approach for DNA methylation profiling.
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spelling pubmed-30237472011-01-20 Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array Yang, Liu Zhang, Kunlin Dai, Wei He, Ximiao Zhao, Qian Wang, Jing Sun, Zhong Sheng BMC Genomics Research Article BACKGROUND: Recent progress in high-throughput technologies has greatly contributed to the development of DNA methylation profiling. Although there are several reports that describe methylome detection of whole genome bisulfite sequencing, the high cost and heavy demand on bioinformatics analysis prevents its extensive application. Thus, current strategies for the study of mammalian DNA methylomes is still based primarily on genome-wide methylated DNA enrichment combined with DNA microarray detection or sequencing. Methylated DNA enrichment is a key step in a microarray based genome-wide methylation profiling study, and even for future high-throughput sequencing based methylome analysis. RESULTS: In order to evaluate the sensitivity and accuracy of methylated DNA enrichment, we investigated and optimized a number of important parameters to improve the performance of several enrichment assays, including differential methylation hybridization (DMH), microarray-based methylation assessment of single samples (MMASS), and methylated DNA immunoprecipitation (MeDIP). With advantages and disadvantages unique to each approach, we found that assays based on methylation-sensitive enzyme digestion and those based on immunoprecipitation detected different methylated DNA fragments, indicating that they are complementary in their relative ability to detect methylation differences. CONCLUSIONS: Our study provides the first comprehensive evaluation for widely used methodologies for methylated DNA enrichment, and could be helpful for developing a cost effective approach for DNA methylation profiling. BioMed Central 2011-01-06 /pmc/articles/PMC3023747/ /pubmed/21211017 http://dx.doi.org/10.1186/1471-2164-12-10 Text en Copyright ©2011 Yang et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<url>http://creativecommons.org/licenses/by/2.0</url>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Yang, Liu
Zhang, Kunlin
Dai, Wei
He, Ximiao
Zhao, Qian
Wang, Jing
Sun, Zhong Sheng
Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array
title Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array
title_full Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array
title_fullStr Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array
title_full_unstemmed Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array
title_short Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array
title_sort systematic evaluation of genome-wide methylated dna enrichment using a cpg island array
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3023747/
https://www.ncbi.nlm.nih.gov/pubmed/21211017
http://dx.doi.org/10.1186/1471-2164-12-10
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