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• W2013449615 startingPage "962" @default.
• W2013449615 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." @default.
• W2013449615 created "2016-06-24" @default.
• W2013449615 creator A5083312685 @default.
• W2013449615 date "2006-06-29" @default.
• W2013449615 modified "2023-10-10" @default.
• W2013449615 title "Extensive low-affinity transcriptional interactions in the yeast genome" @default.
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• W2013449615 doi "https://doi.org/10.1101/gr.5113606" @default.
• W2013449615 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/1524868" @default.
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• W2013449615 hasPublicationYear "2006" @default.
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