Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array
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| Title: | Systematic evaluation of genome-wide methylated DNA enrichment using a CpG island array |
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| Authors: | Yang, Liu, Zhang, Kunlin, Dai, Wei, He, Ximiao, Zhao, Qian, Wang, Jing, Sun, Zhong Sheng, Wang, J (reprint author), Chinese Acad Sci, Inst Psychol, Key Lab Mental Hlth, Beijing 100101, Peoples R China. |
| Source: | BMC Genomics BMC Genomics, Vol 12, Iss 1, p 10 (2011) |
| Publisher Information: | Springer Science and Business Media LLC, 2011. |
| Publication Year: | 2011 |
| Subject Terms: | 0301 basic medicine, QH426-470, DNA Methylation, Physiological Psychology/biological Psychology, Sensitivity and Specificity, 03 medical and health sciences, Genetics, Animals, Humans, CpG Islands, TP248.13-248.65, Biotechnology, Research Article, Oligonucleotide Array Sequence Analysis |
| 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. |
| Document Type: | Article Other literature type Report |
| Language: | English |
| ISSN: | 1471-2164 |
| DOI: | 10.1186/1471-2164-12-10 |
| Access URL: | https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-12-10 https://pubmed.ncbi.nlm.nih.gov/21211017 https://doaj.org/article/286ff7301a9548219ce79a823c153e82 https://doaj.org/article/286ff7301a9548219ce79a823c153e82 http://ir.psych.ac.cn/handle/311026/13275 http://www.irgrid.ac.cn/handle/1471x/972413 https://paperity.org/p/57034762/systematic-evaluation-of-genome-wide-methylated-dna-enrichment-using-a-cpg-island-array https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-10 https://link.springer.com/article/10.1186/1471-2164-12-10 |
| Rights: | Springer TDM CC BY |
| Accession Number: | edsair.doi.dedup.....cd6344a701e546fad5390a9b99161cdf |
| Database: | OpenAIRE |
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Nájsť tento článok vo Web of Science | Abstract: | 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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| ISSN: | 14712164 |
| DOI: | 10.1186/1471-2164-12-10 |