Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Export

@article{citeulike:1427755, abstract = {We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations.}, author = {Mikkelsen, Tarjei S. and Ku, Manching and Jaffe, David B. and Issac, Biju and Lieberman, Erez and Giannoukos, Georgia and Alvarez, Pablo and Brockman, William and Kim, Tae-Kyung K. and Koche, Richard P. and Lee, William and Mendenhall, Eric and O'Donovan, Aisling and Presser, Aviva and Russ, Carsten and Xie, Xiaohui and Meissner, Alexander and Wernig, Marius and Jaenisch, Rudolf and Nusbaum, Chad and Lander, Eric S. and Bernstein, Bradley E.}, citeulike-article-id = {1427755}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature06008}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature06008}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/17603471}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=17603471}, day = {2}, doi = {10.1038/nature06008}, issn = {1476-4687}, journal = {Nature}, keywords = {nsf}, month = {August}, number = {7153}, pages = {553--560}, posted-at = {2009-11-06 02:34:25}, priority = {2}, publisher = {Nature Publishing Group}, title = {Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.}, url = {http://dx.doi.org/10.1038/nature06008}, volume = {448}, year = {2007} }

TY - JOUR ID - citeulike:1427755 L3 - citeulike-article-id:1427755 N2 - We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. By obtaining over four billion bases of sequence from chromatin immunoprecipitated DNA, we generated genome-wide chromatin-state maps of mouse embryonic stem cells, neural progenitor cells and embryonic fibroblasts. We find that lysine 4 and lysine 27 trimethylation effectively discriminates genes that are expressed, poised for expression, or stably repressed, and therefore reflect cell state and lineage potential. Lysine 36 trimethylation marks primary coding and non-coding transcripts, facilitating gene annotation. Trimethylation of lysine 9 and lysine 20 is detected at satellite, telomeric and active long-terminal repeats, and can spread into proximal unique sequences. Lysine 4 and lysine 9 trimethylation marks imprinting control regions. Finally, we show that chromatin state can be read in an allele-specific manner by using single nucleotide polymorphisms. This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations. IS - 7153 JF - Nature SN - 1476-4687 EP - 560 TI - Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. PB - Nature Publishing Group VL - 448 SP - 553 KW - nsf AU - Mikkelsen, Tarjei AU - Ku, Manching AU - Jaffe, David AU - Issac, Biju AU - Lieberman, Erez AU - Giannoukos, Georgia AU - Alvarez, Pablo AU - Brockman, William AU - Kim, Tae-Kyung AU - Koche, Richard AU - Lee, William AU - Mendenhall, Eric AU - O'Donovan, Aisling AU - Presser, Aviva AU - Russ, Carsten AU - Xie, Xiaohui AU - Meissner, Alexander AU - Wernig, Marius AU - Jaenisch, Rudolf AU - Nusbaum, Chad AU - Lander, Eric AU - Bernstein, Bradley PY - 2007/08/02/ UR - http://dx.doi.org/10.1038/nature06008 ER -