Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells Export

@article{citeulike:4285348, abstract = { Studies of epigenetic modifications would benefit from improved methods for high-throughput methylation profiling. We introduce two complementary approaches that use next-generation sequencing technology to detect cytosine methylation. In the first method, we designed |[sim]|10,000 bisulfite padlock probes to profile |[sim]|7,000 CpG locations distributed over the ENCODE pilot project regions and applied them to human B-lymphocytes, fibroblasts and induced pluripotent stem cells. This unbiased choice of targets takes advantage of existing expression and chromatin immunoprecipitation data and enabled us to observe a pattern of low promoter methylation and high gene-body methylation in highly expressed genes. The second method, methyl-sensitive cut counting, generated nontargeted genome-scale data for |[sim]|1.4 million HpaII sites in the DNA of B-lymphocytes and confirmed that gene-body methylation in highly expressed genes is a consistent phenomenon throughout the human genome. Our observations highlight the usefulness of techniques that are not inherently or intentionally biased towards particular subsets like CpG islands or promoter regions.}, author = {Ball, Madeleine P. and Li, Jin B. and Gao, Yuan and Lee, Je-Hyuk and LeProust, Emily M. and Park, In-Hyun and Xie, Bin and Daley, George Q. and Church, George M.}, citeulike-article-id = {4285348}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nbt.1533}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/nbt.1533}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19329998}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19329998}, day = {29}, doi = {10.1038/nbt.1533}, issn = {1087-0156}, journal = {Nature Biotechnology}, keywords = {methylation}, month = {March}, number = {4}, pages = {361--368}, posted-at = {2009-04-16 18:27:56}, priority = {2}, publisher = {Nature Publishing Group}, title = {Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells}, url = {http://dx.doi.org/10.1038/nbt.1533}, volume = {27}, year = {2009} }

TY - JOUR ID - citeulike:4285348 L3 - citeulike-article-id:4285348 N2 - Studies of epigenetic modifications would benefit from improved methods for high-throughput methylation profiling. We introduce two complementary approaches that use next-generation sequencing technology to detect cytosine methylation. In the first method, we designed |[sim]|10,000 bisulfite padlock probes to profile |[sim]|7,000 CpG locations distributed over the ENCODE pilot project regions and applied them to human B-lymphocytes, fibroblasts and induced pluripotent stem cells. This unbiased choice of targets takes advantage of existing expression and chromatin immunoprecipitation data and enabled us to observe a pattern of low promoter methylation and high gene-body methylation in highly expressed genes. The second method, methyl-sensitive cut counting, generated nontargeted genome-scale data for |[sim]|1.4 million HpaII sites in the DNA of B-lymphocytes and confirmed that gene-body methylation in highly expressed genes is a consistent phenomenon throughout the human genome. Our observations highlight the usefulness of techniques that are not inherently or intentionally biased towards particular subsets like CpG islands or promoter regions. IS - 4 JF - Nature Biotechnology SN - 1087-0156 EP - 368 TI - Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells PB - Nature Publishing Group VL - 27 SP - 361 KW - methylation AU - Ball, Madeleine AU - Li, Jin AU - Gao, Yuan AU - Lee, Je-Hyuk AU - LeProust, Emily AU - Park, In-Hyun AU - Xie, Bin AU - Daley, George AU - Church, George PY - 2009/03/29/ UR - http://dx.doi.org/10.1038/nbt.1533 ER -