Accurate and sensitive quantification of protein-DNA binding affinity.
作者： Chaitanya Rastogi , H. Tomas Rube , Judith F. Kribelbauer , Justin Crocker , Ryan E. Loker
关键词: Transcription factor 、 DNA footprinting 、 Binding site 、 Enhancer binding 、 Gene 、 Genetics 、 Electrophoretic mobility shift assay 、 Biology 、 Genomic library 、 DNA binding site
摘要: Transcription factors (TFs) control gene expression by binding to genomic DNA in a sequence-specific manner. Mutations TF sites are increasingly found be associated with human disease, yet we currently lack robust methods predict these sites. Here, developed versatile maximum likelihood framework named No Read Left Behind (NRLB) that infers biophysical model of protein-DNA recognition across the full affinity range from library vitro selected NRLB predicts Max homodimer near-perfect agreement existing low-throughput measurements. It can capture specificity p53 tetramer and distinguish multiple modes within single sample. Additionally, confirm newly identified low-affinity enhancer functional vivo, their contribution matches predicted affinity. Our results establish powerful paradigm for identifying protein interpreting regulatory sequences eukaryotic genomes.
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sci-hub.se 参考文章(49)
Richard S. Mann, Katherine M. Lelli, Rohit Joshi, Hox specificity unique roles for cofactors and collaborators. Current Topics in Developmental Biology. ,vol. 88, pp. 63- 101 ,(2009) , 10.1016/S0070-2153(09)88003-4
Babak Alipanahi, Andrew Delong, Matthew T Weirauch, Brendan J Frey, Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning Nature Biotechnology. ,vol. 33, pp. 831- 838 ,(2015) , 10.1038/NBT.3300
GTEx Consortium, Kristin G Ardlie, David S Deluca, Ayellet V Segrè, Timothy J Sullivan, Taylor R Young, Ellen T Gelfand, Casandra A Trowbridge, Julian B Maller, Taru Tukiainen, Monkol Lek, Lucas D Ward, Pouya Kheradpour, Benjamin Iriarte, Yan Meng, Cameron D Palmer, Tõnu Esko, Wendy Winckler, Joel N Hirschhorn, Manolis Kellis, Daniel G MacArthur, Gad Getz, Andrey A Shabalin, Gen Li, Yi-Hui Zhou, Andrew B Nobel, Ivan Rusyn, Fred A Wright, Tuuli Lappalainen, Pedro G Ferreira, Halit Ongen, Manuel A Rivas, Alexis Battle, Sara Mostafavi, Jean Monlong, Michael Sammeth, Marta Mele, Ferran Reverter, Jakob M Goldmann, Daphne Koller, Roderic Guigó, Mark I McCarthy, Emmanouil T Dermitzakis, Eric R Gamazon, Hae Kyung Im, Anuar Konkashbaev, Dan L Nicolae, Nancy J Cox, Timothée Flutre, Xiaoquan Wen, Matthew Stephens, Jonathan K Pritchard, Zhidong Tu, Bin Zhang, Tao Huang, Quan Long, Luan Lin, Jialiang Yang, Jun Zhu, Jun Liu, Amanda Brown, Bernadette Mestichelli, Denee Tidwell, Edmund Lo, Mike Salvatore, Saboor Shad, Jeffrey A Thomas, John T Lonsdale, Michael T Moser, Bryan M Gillard, Ellen Karasik, Kimberly Ramsey, Christopher Choi, Barbara A Foster, John Syron, Johnell Fleming, Harold Magazine, Rick Hasz, Gary D Walters, Jason P Bridge, Mark Miklos, Susan Sullivan, Laura K Barker, Heather M Traino, Maghboeba Mosavel, Laura A Siminoff, Dana R Valley, Daniel C Rohrer, Scott D Jewell, Philip A Branton, Leslie H Sobin, Mary Barcus, Liqun Qi, Jeffrey McLean, Pushpa Hariharan, Ki Sung Um, Shenpei Wu, David Tabor, Charles Shive, Anna M Smith, Stephen A Buia, Anita H Undale, Karna L Robinson, Nancy Roche, Kimberly M Valentino, Angela Britton, Robin Burges, Debra Bradbury, Kenneth W Hambright, John Seleski, Greg E Korzeniewski, Kenyon Erickson, Yvonne Marcus, Jorge Tejada, Mehran Taherian, Chunrong Lu, Margaret Basile, Deborah C Mash, Simona Volpi, Jeffery P Struewing, Gary F Temple, Joy Boyer, Deborah Colantuoni, Roger Little, Susan Koester, Latarsha J Carithers, Helen M Moore, Ping Guan, Carolyn Compton, Sherilyn J Sawyer, Joanne P Demchok, Jimmie B Vaught, Chana A Rabiner, Nicole C Lockhart, Kristin G Ardlie, Gad Getz, Fred A Wright, Manolis Kellis, Simona Volpi, Emmanouil T Dermitzakis, None, The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans Science. ,vol. 348, pp. 648- 660 ,(2015) , 10.1126/SCIENCE.1262110
R. J. A. Bell, H. T. Rube, A. Kreig, A. Mancini, S. D. Fouse, R. P. Nagarajan, S. Choi, C. Hong, D. He, M. Pekmezci, J. K. Wiencke, M. R. Wrensch, S. M. Chang, K. M. Walsh, S. Myong, J. S. Song, J. F. Costello, The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer Science. ,vol. 348, pp. 1036- 1039 ,(2015) , 10.1126/SCIENCE.AAB0015
Dawid Eckert, Sandra Buhl, Susanne Weber, Richard Jäger, Hubert Schorle, The AP-2 family of transcription factors. Genome Biology. ,vol. 6, pp. 246- 246 ,(2005) , 10.1186/GB-2005-6-13-246
Arttu Jolma, Yimeng Yin, Kazuhiro R. Nitta, Kashyap Dave, Alexander Popov, Minna Taipale, Martin Enge, Teemu Kivioja, Ekaterina Morgunova, Jussi Taipale, DNA-dependent formation of transcription factor pairs alters their binding specificity Nature. ,vol. 527, pp. 384- 388 ,(2015) , 10.1038/NATURE15518
Charles Vinson, Max Myakishev, Asha Acharya, Alain A. Mir, Jonathan R. Moll, Maria Bonovich, Classification of human B-ZIP proteins based on dimerization properties. Molecular and Cellular Biology. ,vol. 22, pp. 6321- 6335 ,(2002) , 10.1128/MCB.22.18.6321-6335.2002
Xiangdong Meng, Michael H Brodsky, Scot A Wolfe, A bacterial one-hybrid system for determining the DNA-binding specificity of transcription factors Nature Biotechnology. ,vol. 23, pp. 988- 994 ,(2005) , 10.1038/NBT1120
Tianyin Zhou, Ning Shen, Lin Yang, Namiko Abe, John Horton, Richard S. Mann, Harmen J. Bussemaker, Raluca Gordân, Remo Rohs, Quantitative modeling of transcription factor binding specificities using DNA shape Proceedings of the National Academy of Sciences of the United States of America. ,vol. 112, pp. 4654- 4659 ,(2015) , 10.1073/PNAS.1422023112
Michael F Berger, Anthony A Philippakis, Aaron M Qureshi, Fangxue S He, Preston W Estep, Martha L Bulyk, Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities Nature Biotechnology. ,vol. 24, pp. 1429- 1435 ,(2006) , 10.1038/NBT1246