Diversity and Complexity in DNA Recognition by Transcription Factors Export

@article{citeulike:4521968, abstract = {Sequence preferences of DNA binding proteins are a primary mechanism by which cells interpret the genome. Despite the central importance of these proteins in physiology, development, and evolution, comprehensive DNA binding specificities have been determined experimentally for only a few proteins. Here, we used microarrays containing all 10-base pair sequences to examine the binding specificities of 104 distinct mouse DNA binding proteins representing 22 structural classes. Our results reveal a complex landscape of binding, with virtually every protein analyzed possessing unique preferences. Roughly half of the proteins each recognized multiple distinctly different sequence motifs, challenging our molecular understanding of how proteins interact with their DNA binding sites. This complexity in DNA recognition may be important in gene regulation and in the evolution of transcriptional regulatory networks. 10.1126/science.1162327}, author = {Badis, Gwenael and Berger, Michael F. and Philippakis, Anthony A. and Talukder, Shaheynoor and Gehrke, Andrew R. and Jaeger, Savina A. and Chan, Esther T. and Metzler, Genita and Vedenko, Anastasia and Chen, Xiaoyu and Kuznetsov, Hanna and Wang, Chi-Fong and Coburn, David and Newburger, Daniel E. and Morris, Quaid and Hughes, Timothy R. and Bulyk, Martha L.}, citeulike-article-id = {4521968}, citeulike-linkout-0 = {http://dx.doi.org/10.1126/science.1162327}, citeulike-linkout-1 = {http://www.sciencemag.org/content/1162327/.abstract}, citeulike-linkout-2 = {http://www.sciencemag.org/content/1162327/.full.pdf}, citeulike-linkout-3 = {http://www.sciencemag.org/cgi/content/abstract/1162327//}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19443739}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19443739}, day = {26}, doi = {10.1126/science.1162327}, issn = {1095-9203}, journal = {Science}, keywords = {transcription\_factors}, month = {June}, number = {5935}, pages = {1720--1723}, posted-at = {2009-05-18 10:04:47}, priority = {2}, title = {Diversity and Complexity in DNA Recognition by Transcription Factors}, url = {http://dx.doi.org/10.1126/science.1162327}, volume = {324}, year = {2009} }

TY - JOUR ID - citeulike:4521968 L3 - citeulike-article-id:4521968 N2 - Sequence preferences of DNA binding proteins are a primary mechanism by which cells interpret the genome. Despite the central importance of these proteins in physiology, development, and evolution, comprehensive DNA binding specificities have been determined experimentally for only a few proteins. Here, we used microarrays containing all 10-base pair sequences to examine the binding specificities of 104 distinct mouse DNA binding proteins representing 22 structural classes. Our results reveal a complex landscape of binding, with virtually every protein analyzed possessing unique preferences. Roughly half of the proteins each recognized multiple distinctly different sequence motifs, challenging our molecular understanding of how proteins interact with their DNA binding sites. This complexity in DNA recognition may be important in gene regulation and in the evolution of transcriptional regulatory networks. 10.1126/science.1162327 IS - 5935 JF - Science SN - 1095-9203 EP - 1723 TI - Diversity and Complexity in DNA Recognition by Transcription Factors VL - 324 SP - 1720 KW - transcription_factors AU - Badis, Gwenael AU - Berger, Michael AU - Philippakis, Anthony AU - Talukder, Shaheynoor AU - Gehrke, Andrew AU - Jaeger, Savina AU - Chan, Esther AU - Metzler, Genita AU - Vedenko, Anastasia AU - Chen, Xiaoyu AU - Kuznetsov, Hanna AU - Wang, Chi-Fong AU - Coburn, David AU - Newburger, Daniel AU - Morris, Quaid AU - Hughes, Timothy AU - Bulyk, Martha PY - 2009/06/26/ UR - http://dx.doi.org/10.1126/science.1162327 ER -