ChIP-seq accurately predicts tissue-specific activity of enhancers Export

@article{citeulike:4036717, abstract = {A major yet unresolved quest in decoding the human genome is the identification of the regulatory sequences that control the spatial and temporal expression of genes. Distant-acting transcriptional enhancers are particularly challenging to uncover because they are scattered among the vast non-coding portion of the genome. Evolutionary sequence constraint can facilitate the discovery of enhancers, but fails to predict when and where they are active in vivo. Here we present the results of chromatin immunoprecipitation with the enhancer-associated protein p300 followed by massively parallel sequencing, and map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain and limb tissue. We tested 86 of these sequences in a transgenic mouse assay, which in nearly all cases demonstrated reproducible enhancer activity in the tissues that were predicted by p300 binding. Our results indicate that in vivo mapping of p300 binding is a highly accurate means for identifying enhancers and their associated activities, and suggest that such data sets will be useful to study the role of tissue-specific enhancers in human biology and disease on a genome-wide scale.}, author = {Visel, Axel and Blow, Matthew J. and Li, Zirong and Zhang, Tao and Akiyama, Jennifer A. and Holt, Amy and Plajzer-Frick, Ingrid and Shoukry, Malak and Wright, Crystal and Chen, Feng and Afzal, Veena and Ren, Bing and Rubin, Edward M. and Pennacchio, Len A.}, citeulike-article-id = {4036717}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature07730}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature07730}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19212405}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19212405}, day = {12}, doi = {10.1038/nature07730}, issn = {0028-0836}, journal = {Nature}, keywords = {chip\_seq, method}, month = {February}, number = {7231}, pages = {854--858}, posted-at = {2009-02-12 22:09:48}, priority = {3}, publisher = {Nature Publishing Group}, title = {ChIP-seq accurately predicts tissue-specific activity of enhancers}, url = {http://dx.doi.org/10.1038/nature07730}, volume = {457}, year = {2009} }

TY - JOUR ID - citeulike:4036717 L3 - citeulike-article-id:4036717 N2 - A major yet unresolved quest in decoding the human genome is the identification of the regulatory sequences that control the spatial and temporal expression of genes. Distant-acting transcriptional enhancers are particularly challenging to uncover because they are scattered among the vast non-coding portion of the genome. Evolutionary sequence constraint can facilitate the discovery of enhancers, but fails to predict when and where they are active in vivo. Here we present the results of chromatin immunoprecipitation with the enhancer-associated protein p300 followed by massively parallel sequencing, and map several thousand in vivo binding sites of p300 in mouse embryonic forebrain, midbrain and limb tissue. We tested 86 of these sequences in a transgenic mouse assay, which in nearly all cases demonstrated reproducible enhancer activity in the tissues that were predicted by p300 binding. Our results indicate that in vivo mapping of p300 binding is a highly accurate means for identifying enhancers and their associated activities, and suggest that such data sets will be useful to study the role of tissue-specific enhancers in human biology and disease on a genome-wide scale. IS - 7231 JF - Nature SN - 0028-0836 EP - 858 TI - ChIP-seq accurately predicts tissue-specific activity of enhancers PB - Nature Publishing Group VL - 457 SP - 854 KW - chip_seq KW - method AU - Visel, Axel AU - Blow, Matthew AU - Li, Zirong AU - Zhang, Tao AU - Akiyama, Jennifer AU - Holt, Amy AU - Plajzer-Frick, Ingrid AU - Shoukry, Malak AU - Wright, Crystal AU - Chen, Feng AU - Afzal, Veena AU - Ren, Bing AU - Rubin, Edward AU - Pennacchio, Len PY - 2009/02/12/ UR - http://dx.doi.org/10.1038/nature07730 ER -