Extensive low-affinity transcriptional interactions in the yeast genome.

@article{citeulike:767781, abstract = {Major experimental and computational efforts are targeted at the characterization of transcriptional networks on a genomic scale. The ultimate goal of many of these studies is to construct networks associating transcription factors with genes via well-defined binding sites. Weaker regulatory interactions other than those occurring at high-affinity binding sites are largely ignored and are not well understood. Here I show that low-affinity interactions are abundant in vivo and quantifiable from current high-throughput ChIP experiments. I develop algorithms that predict DNA-binding energies from sequences and ChIP data across a wide dynamic range of affinities and use them to reveal widespread functionality of low-affinity transcription factor binding. Evolutionary analysis suggests that binding energies of many transcription factors are conserved even in promoters lacking classical binding sites. Gene expression analysis shows that such promoters can generate significant expression. I estimate that while only a small percentage of the genome is strongly regulated by a typical transcription factor, up to an order of magnitude more may be involved in weaker interactions. Low-affinity transcription factor-DNA interaction may therefore be important both evolutionarily and functionally.}, address = {Center for Studies in Physics and Biology, Rockefeller University, New York, New York 10021, USA.}, author = {Tanay, Amos }, citeulike-article-id = {767781}, comment = {are genes regulated by an average of 3 TFs or an average of 30? either revolutinonary or methodologically flawed. }, doi = {10.1101/gr.5113606}, issn = {1088-9051}, journal = {Genome Res}, keywords = {gene, regulation}, month = {June}, posted-at = {2007-02-09 20:09:41}, priority = {0}, title = {Extensive low-affinity transcriptional interactions in the yeast genome.}, url = {http://dx.doi.org/10.1101/gr.5113606}, year = {2006} }

TY - JOUR ID - citeulike:767781 L3 - citeulike-article-id:767781 TI - Extensive low-affinity transcriptional interactions in the yeast genome. JF - Genome Res AD - Center for Studies in Physics and Biology, Rockefeller University, New York, New York 10021, USA. SN - 1088-9051 N2 - Major experimental and computational efforts are targeted at the characterization of transcriptional networks on a genomic scale. The ultimate goal of many of these studies is to construct networks associating transcription factors with genes via well-defined binding sites. Weaker regulatory interactions other than those occurring at high-affinity binding sites are largely ignored and are not well understood. Here I show that low-affinity interactions are abundant in vivo and quantifiable from current high-throughput ChIP experiments. I develop algorithms that predict DNA-binding energies from sequences and ChIP data across a wide dynamic range of affinities and use them to reveal widespread functionality of low-affinity transcription factor binding. Evolutionary analysis suggests that binding energies of many transcription factors are conserved even in promoters lacking classical binding sites. Gene expression analysis shows that such promoters can generate significant expression. I estimate that while only a small percentage of the genome is strongly regulated by a typical transcription factor, up to an order of magnitude more may be involved in weaker interactions. Low-affinity transcription factor-DNA interaction may therefore be important both evolutionarily and functionally. KW - gene KW - regulation N1 - are genes regulated by an average of 3 TFs or an average of 30? either revolutinonary or methodologically flawed. AU - Tanay, Amos PY - 2006/06/29/ UR - http://dx.doi.org/10.1101/gr.5113606 ER -