RECOMB Conference report
Igor Ulitsky, TAU
Elucidating transcription factor preferences using Protein Binding Microarrays
Abstract:
Transcription factors (TFs) interact with specific DNA regulatory sequences
to control gene expression throughout myriad cellular processes. However,
the DNA binding specificities of only a small fraction of TFs are
sufficiently characterized to predict the sequences that they can and cannot
bind. Recently, Martha Bulyk's lab presented a maximally compact, synthetic
DNA sequence design for protein binding microarray (PBM) experiments that
represents all possible DNA sequence variants of a given length k (that is,
all 'k-mers') on a single, universal microarray. Using these microarrays the
binding specificities over a full range of affinities for five TFs of
different structural classes from yeast, worm, mouse and human were
analyzed. The unbiased coverage of all k-mers permits high-throughput
interrogation of binding site preferences, including nucleotide
interdependencies, at unprecedented resolution.
I will introduce the PBM technology and present related algorithmic work, as
described in the following three papers (presented in RECOMB Satellite on
Systems Biology and RECOMB07):
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Berger MF, Philippakis AA, Qureshi A, He FS, Estep PW 3rd, Bulyk ML.
"Compact, universal DNA microarrays to comprehensively determine
transcription-factor binding site specificities".
Nature Biotechnology 2006 Nov;24(11):1429-1435
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McCord RP, Berger MF, Philippakis AA, Bulyk ML.
"Inferring condition-specific transcription factor function from DNA binding and gene expression".
Molecular Systems Biology 2007; 3:100.
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Philippakis AA, Qureshi A, Berger MF, Bulyk ML.
"Design of compact, universal DNA microarrays for protein binding microarray experiments".
RECOMB 2007.