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):