High-throughput mapping of protein occupancy identifies functional elements without the restriction of a candidate factor approach.
High-throughput mapping of protein occupancy identifies functional elements without the restriction of a candidate factor approach.
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DOI：
10.1093/nar/gkq1213
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发表时间：
2011-03
影响因子：
14.9
通讯作者：
Fairbrother WG
中科院分区：
文献类型：
--
作者：
Ferraris L;Stewart AP;Gemberling MP;Reid DC;Lapadula MJ;Thompson WA;Fairbrother WG
There are a variety of in vivo and in vitro methods to determine the genome-wide specificity of a particular trans-acting factor. However there is an inherent limitation to these candidate approaches. Most biological studies focus on the regulation of particular genes, which are bound by numerous unknown trans-acting factors. Therefore, most biological inquiries would be better addressed by a method that maps all trans-acting factors that bind particular regions rather than identifying all regions bound by a particular trans-acting factor. Here, we present a high-throughput binding assay that returns thousands of unbiased measurements of complex formation on nucleic acid. We applied this method to identify transcriptional complexes that form on DNA regions upstream of genes involved in pluripotency in embryonic stem cells (ES cells) before and after differentiation. The raw binding scores, motif analysis and expression data are used to computationally reconstruct remodeling events returning the identity of the transcription factor(s) most likely to comprise the complex. The most significant remodeling event during ES cell differentiation occurred upstream of the REST gene, a transcriptional repressor that blocks neurogenesis. We also demonstrate how this method can be used to discover RNA elements and discuss applications of screening polymorphisms for allelic differences in binding.
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DOI：
10.1126/science.1162327
发表时间：
2009-06-26
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Badis G;Berger MF;Philippakis AA;Talukder S;Gehrke AR;Jaeger SA;Chan ET;Metzler G;Vedenko A;Chen X;Kuznetsov H;Wang CF;Coburn D;Newburger DE;Morris Q;Hughes TR;Bulyk ML
通讯作者：
Bulyk ML
结合速率常数与大肠杆菌FIS结合位点的个体信息之间的相关性。
影响因子：
14.9
作者：
Shultzaberger, Ryan K.;Roberts, Lindsey R.;Lyakhov, Ilya G.;Sidorov, Igor A.;Stephen, Andrew G.;Fisher, Robert J.;Schneider, Thomas D.
通讯作者：
Schneider, Thomas D.
影响因子：
4.8
作者：
Ule, J;Jensen, K;Darnell, RB
通讯作者：
Darnell, RB
影响因子：
64.5
作者：
Bond, GL;Hu, WW;Levine, AJ
通讯作者：
Levine, AJ
DOI：
10.2174/138620710790980522
发表时间：
2010-03-01
影响因子：
1.8
作者：
Chang, Brian;Levin, J.;Fairbrother, William G.
通讯作者：
Fairbrother, William G.