Genome-wide analysis of mammalian promoter architecture and evolution Export

@article{citeulike:678440, abstract = {Mammalian promoters can be separated into two classes, conserved TATA box–enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We have sequenced tags corresponding to several hundred thousand transcription start sites (TSSs) in the mouse and human genomes, allowing precise analysis of the sequence architecture and evolution of distinct promoter classes. Different tissues and families of genes differentially use distinct types of promoters. Our tagging methods allow quantitative analysis of promoter usage in different tissues and show that differentially regulated alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N termini. Among the TSSs, we identified new start sites associated with the majority of exons and with 3' UTRs. These data permit genome-scale identification of tissue-specific promoters and analysis of the cis-acting elements associated with them. NOTE: In the version of this article initially published online, the x-axis of Figure 4b was mislabeled. Specifically, the five groups on the x-axis should be labeled: No mutation PyPu to PuPu PyPu to PuPy PyPu to PyPu PyPu to PyPy The error has been corrected for all versions of the article. NOTE: In the version of this article initially published, two of the smaller bar plots in Figure 1e were mistakenly duplicated. Specifically, the Zfp385 plot is an erroneous copy of the 137774 plot, and the Txndc7 plot is an erroneous copy of the Pik3r5 plot. See below for the corrected version of the figure. This error does not change the conclusions of the study in any way, as the bar plots are just a few visual examples of more than 5,000 tag clusters, and the correct plots follow the same distribution patterns as the erroneous ones. This error has been corrected in the HTML and PDF versions of the article.}, author = {Carninci, Piero and Sandelin, Albin and Lenhard, Boris and Katayama, Shintaro and Shimokawa, Kazuro and Ponjavic, Jasmina and Semple, Colin A. M. and Taylor, Martin S. and Engstrom, Par G. and Frith, Martin C. and Forrest, Alistair R. R. and Alkema, Wynand B. and Tan, Sin L. and Plessy, Charles and Kodzius, Rimantas and Ravasi, Timothy and Kasukawa, Takeya and Fukuda, Shiro and Kanamori-Katayama, Mutsumi and Kitazume, Yayoi and Kawaji, Hideya and Kai, Chikatoshi and Nakamura, Mari and Konno, Hideaki and Nakano, Kenji and Mottagui-Tabar, Salim and Arner, Peter and Chesi, Alessandra and Gustincich, Stefano and Persichetti, Francesca and Suzuki, Harukazu and Grimmond, Sean M. and Wells, Christine A. and Orlando, Valerio and Wahlestedt, Claes and Liu, Edison T. and Harbers, Matthias and Kawai, Jun and Bajic, Vladimir B. and Hume, David A. and Hayashizaki, Yoshihide}, booktitle = {Nat Genet}, citeulike-article-id = {678440}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/ng1789}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/ng1789}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/16645617}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=16645617}, day = {28}, doi = {10.1038/ng1789}, issn = {1061-4036}, journal = {Nature Genetics}, keywords = {analysis, genome, wide}, month = {April}, number = {6}, pages = {626--635}, posted-at = {2008-12-02 06:30:11}, priority = {2}, publisher = {Nature Publishing Group}, title = {Genome-wide analysis of mammalian promoter architecture and evolution}, url = {http://dx.doi.org/10.1038/ng1789}, volume = {38}, year = {2006} }

TY - JOUR ID - citeulike:678440 L3 - citeulike-article-id:678440 N2 - Mammalian promoters can be separated into two classes, conserved TATA box–enriched promoters, which initiate at a well-defined site, and more plastic, broad and evolvable CpG-rich promoters. We have sequenced tags corresponding to several hundred thousand transcription start sites (TSSs) in the mouse and human genomes, allowing precise analysis of the sequence architecture and evolution of distinct promoter classes. Different tissues and families of genes differentially use distinct types of promoters. Our tagging methods allow quantitative analysis of promoter usage in different tissues and show that differentially regulated alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N termini. Among the TSSs, we identified new start sites associated with the majority of exons and with 3' UTRs. These data permit genome-scale identification of tissue-specific promoters and analysis of the cis-acting elements associated with them. NOTE: In the version of this article initially published online, the x-axis of Figure 4b was mislabeled. Specifically, the five groups on the x-axis should be labeled: No mutation PyPu to PuPu PyPu to PuPy PyPu to PyPu PyPu to PyPy The error has been corrected for all versions of the article. NOTE: In the version of this article initially published, two of the smaller bar plots in Figure 1e were mistakenly duplicated. Specifically, the Zfp385 plot is an erroneous copy of the 137774 plot, and the Txndc7 plot is an erroneous copy of the Pik3r5 plot. See below for the corrected version of the figure. This error does not change the conclusions of the study in any way, as the bar plots are just a few visual examples of more than 5,000 tag clusters, and the correct plots follow the same distribution patterns as the erroneous ones. This error has been corrected in the HTML and PDF versions of the article. IS - 6 JF - Nature Genetics SN - 1061-4036 EP - 635 TI - Genome-wide analysis of mammalian promoter architecture and evolution PB - Nature Publishing Group VL - 38 T2 - Nat Genet SP - 626 KW - analysis KW - genome KW - wide AU - Carninci, Piero AU - Sandelin, Albin AU - Lenhard, Boris AU - Katayama, Shintaro AU - Shimokawa, Kazuro AU - Ponjavic, Jasmina AU - Semple, Colin AU - Taylor, Martin AU - Engstrom, Par AU - Frith, Martin AU - Forrest, Alistair AU - Alkema, Wynand AU - Tan, Sin AU - Plessy, Charles AU - Kodzius, Rimantas AU - Ravasi, Timothy AU - Kasukawa, Takeya AU - Fukuda, Shiro AU - Kanamori-Katayama, Mutsumi AU - Kitazume, Yayoi AU - Kawaji, Hideya AU - Kai, Chikatoshi AU - Nakamura, Mari AU - Konno, Hideaki AU - Nakano, Kenji AU - Mottagui-Tabar, Salim AU - Arner, Peter AU - Chesi, Alessandra AU - Gustincich, Stefano AU - Persichetti, Francesca AU - Suzuki, Harukazu AU - Grimmond, Sean AU - Wells, Christine AU - Orlando, Valerio AU - Wahlestedt, Claes AU - Liu, Edison AU - Harbers, Matthias AU - Kawai, Jun AU - Bajic, Vladimir AU - Hume, David AU - Hayashizaki, Yoshihide PY - 2006/04/28/ UR - http://dx.doi.org/10.1038/ng1789 ER -