High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing Export

@article{citeulike:5098672, abstract = {10.1101/gr.095190.109 DNA methylation stabilizes developmentally programmed gene expression states. Aberrant methylation is associated with disease progression and is a common feature of cancer genomes. Presently, few methods enable quantitative, large-scale, single-base resolution mapping of DNA methylation states in desired regions of a complex mammalian genome. Here, we present an approach that combines array-based hybrid selection and massively parallel bisulfite sequencing to profile DNA methylation in genomic regions spanning hundreds of thousands of bases. This single molecule strategy enables methylation variable positions to be quantitatively examined with high sampling precision. Using bisulfite capture, we assessed methylation patterns across 324 randomly selected CpG islands (CGI) representing more than 25,000 CpG sites. A single lane of Illumina sequencing permitted methylation states to be definitively called for >90\% of target sties. The accuracy of the hybrid-selection approach was verified using conventional bisulfite capillary sequencing of cloned PCR products amplified from a subset of the selected regions. This confirmed that even partially methylated states could be successfully called. A comparison of human primary and cancer cells revealed multiple differentially methylated regions. More than 25\% of islands showed complex methylation patterns either with partial methylation states defining the entire CGI or with contrasting methylation states appearing in specific regional blocks within the island. We observed that transitions in methylation state often correlate with genomic landmarks, including transcriptional start sites and intron-exon junctions. Methylation, along with specific histone marks, was enriched in exonic regions, suggesting that chromatin states can foreshadow the content of mature mRNAs.}, author = {Hodges, Emily and Smith, Andrew D. and Kendall, Jude and Xuan, Zhenyu and Ravi, Kandasamy and Rooks, Michelle and Zhang, Michael Q. and Ye, Kenny and Bhattacharjee, Arindam and Brizuela, Leonardo and McCombie, W. Richard and Wigler, Michael and Hannon, Gregory J. and Hicks, James B.}, citeulike-article-id = {5098672}, citeulike-linkout-0 = {http://dx.doi.org/10.1101/gr.095190.109}, citeulike-linkout-1 = {http://genome.cshlp.org/content/gr.095190.109v1/.abstract}, citeulike-linkout-2 = {http://genome.cshlp.org/content/gr.095190.109v1/.full.pdf}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19581485}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19581485}, day = {6}, doi = {10.1101/gr.095190.109}, journal = {Genome Research}, keywords = {method, methylation}, month = {September}, number = {9}, pages = {1593--1605}, posted-at = {2009-09-11 19:20:52}, priority = {2}, title = {High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing}, url = {http://dx.doi.org/10.1101/gr.095190.109}, volume = {19}, year = {2009} }

TY - JOUR ID - citeulike:5098672 L3 - citeulike-article-id:5098672 N2 - 10.1101/gr.095190.109 DNA methylation stabilizes developmentally programmed gene expression states. Aberrant methylation is associated with disease progression and is a common feature of cancer genomes. Presently, few methods enable quantitative, large-scale, single-base resolution mapping of DNA methylation states in desired regions of a complex mammalian genome. Here, we present an approach that combines array-based hybrid selection and massively parallel bisulfite sequencing to profile DNA methylation in genomic regions spanning hundreds of thousands of bases. This single molecule strategy enables methylation variable positions to be quantitatively examined with high sampling precision. Using bisulfite capture, we assessed methylation patterns across 324 randomly selected CpG islands (CGI) representing more than 25,000 CpG sites. A single lane of Illumina sequencing permitted methylation states to be definitively called for >90% of target sties. The accuracy of the hybrid-selection approach was verified using conventional bisulfite capillary sequencing of cloned PCR products amplified from a subset of the selected regions. This confirmed that even partially methylated states could be successfully called. A comparison of human primary and cancer cells revealed multiple differentially methylated regions. More than 25% of islands showed complex methylation patterns either with partial methylation states defining the entire CGI or with contrasting methylation states appearing in specific regional blocks within the island. We observed that transitions in methylation state often correlate with genomic landmarks, including transcriptional start sites and intron-exon junctions. Methylation, along with specific histone marks, was enriched in exonic regions, suggesting that chromatin states can foreshadow the content of mature mRNAs. IS - 9 JF - Genome Research EP - 1605 TI - High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing VL - 19 SP - 1593 KW - method KW - methylation AU - Hodges, Emily AU - Smith, Andrew AU - Kendall, Jude AU - Xuan, Zhenyu AU - Ravi, Kandasamy AU - Rooks, Michelle AU - Zhang, Michael AU - Ye, Kenny AU - Bhattacharjee, Arindam AU - Brizuela, Leonardo AU - McCombie, Richard AU - Wigler, Michael AU - Hannon, Gregory AU - Hicks, James PY - 2009/09/06/ UR - http://dx.doi.org/10.1101/gr.095190.109 ER -