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Dev Cell. 2011 Oct 18;21(4):611-26. doi: 10.1016/j.devcel.2011.09.008.

Animal transcription networks as highly connected, quantitative continua.

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Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road MS 84-171, Berkeley, CA 94720, USA.


To understand how transcription factors function, it is essential to determine the range of genes that they each bind and regulate in vivo. Here I review evidence that most animal transcription factors each bind to a majority of genes over a quantitative series of DNA occupancy levels. These continua span functional, quasifunctional, and nonfunctional DNA binding events. Factor regulatory specificities are distinguished by quantitative differences in DNA occupancy patterns. I contrast these results with models for transcription networks that define discrete sets of direct target and nontarget genes and consequently do not fully capture the complexity observed in vivo.

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