High resolution analyses of the DNA binding specificities of transcription factors

18 May 2007

Anthony Philippakis
Bulyk Lab, Division of Genetics
Brigham and Women's Hospital
Harvard Medical School


The Bulyk lab has developed the protein binding microarray (PBM) technology for high-throughput determination of TF binding site motifs. Recently, we have developed a universal PBM platform that can be applied to determine the binding preferences of any transcription factor, regardless of its structural class or genome of origin (citation below). Importantly, this design represents all possible sequence variants of a given length k on a single array, allowing a complete characterization of the DNA binding specificities of transcription factors.

Because this technology allows binding preferences of TFs to be examined with unprecedented resolution, it is possible to represent and interpret these preferences in novel ways. In this seminar, I will discuss how the binding preferences of transcription factors can be viewed as connected components of a network. These connected components are reminiscent of constructs known as "error correcting codes" developed in information theory, where they are used to make messages robust to errors during transmission. I will attempt to provide a biological interpretation of this parallel, as it pertains to the function and evolution of transcription factor binding sites.


MF Berger, AA Philippakis, A Qureshi, FS He, PW Estep 3rd, ML Bulyk, "Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities", Nature Biotechnology 24:1429-1435 1006. PubMed

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