Combinatorial binding predicts spatio-temporal cis-regulatory activity Export

@article{citeulike:6071240, abstract = {Development requires the establishment of precise patterns of gene expression, which are primarily controlled by transcription factors binding to cis-regulatory modules. Although transcription factor occupancy can now be identified at genome-wide scales, decoding this regulatory landscape remains a daunting challenge. Here we used a novel approach to predict spatio-temporal cis-regulatory activity based only on in vivo transcription factor binding and enhancer activity data. We generated a high-resolution atlas of cis-regulatory modules describing their temporal and combinatorial occupancy during Drosophila mesoderm development. The binding profiles of cis-regulatory modules with characterized expression were used to train support vector machines to predict five spatio-temporal expression patterns. In vivo transgenic reporter assays demonstrate the high accuracy of these predictions and reveal an unanticipated plasticity in transcription factor binding leading to similar expression. This data-driven approach does not require previous knowledge of transcription factor sequence affinity, function or expression, making it widely applicable.}, author = {Zinzen, Robert P. and Girardot, Charles and Gagneur, Julien and Braun, Martina and Furlong, Eileen E. M.}, booktitle = {Nature}, citeulike-article-id = {6071240}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature08531}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature08531}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19890324}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19890324}, day = {05}, doi = {10.1038/nature08531}, issn = {0028-0836}, journal = {Nature}, keywords = {combinatorial\_control, fly, tfnets}, month = {November}, number = {7269}, pages = {65--70}, posted-at = {2009-11-08 19:15:53}, priority = {2}, publisher = {Nature Publishing Group}, title = {Combinatorial binding predicts spatio-temporal cis-regulatory activity }, url = {http://dx.doi.org/10.1038/nature08531}, volume = {462}, year = {2009} }

TY - JOUR ID - citeulike:6071240 L3 - citeulike-article-id:6071240 N2 - Development requires the establishment of precise patterns of gene expression, which are primarily controlled by transcription factors binding to cis-regulatory modules. Although transcription factor occupancy can now be identified at genome-wide scales, decoding this regulatory landscape remains a daunting challenge. Here we used a novel approach to predict spatio-temporal cis-regulatory activity based only on in vivo transcription factor binding and enhancer activity data. We generated a high-resolution atlas of cis-regulatory modules describing their temporal and combinatorial occupancy during Drosophila mesoderm development. The binding profiles of cis-regulatory modules with characterized expression were used to train support vector machines to predict five spatio-temporal expression patterns. In vivo transgenic reporter assays demonstrate the high accuracy of these predictions and reveal an unanticipated plasticity in transcription factor binding leading to similar expression. This data-driven approach does not require previous knowledge of transcription factor sequence affinity, function or expression, making it widely applicable. IS - 7269 JF - Nature SN - 0028-0836 EP - 70 TI - Combinatorial binding predicts spatio-temporal cis-regulatory activity PB - Nature Publishing Group VL - 462 T2 - Nature SP - 65 KW - combinatorial_control KW - fly KW - tfnets AU - Zinzen, Robert AU - Girardot, Charles AU - Gagneur, Julien AU - Braun, Martina AU - Furlong, Eileen PY - 2009/11/05/ UR - http://dx.doi.org/10.1038/nature08531 ER -