Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.
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. We present 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. We constructed such all k-mer microarrays covering all 10-base pair (bp) binding sites by converting high-density single-stranded oligonucleotide arrays to double-stranded (ds) DNA arrays. Using these microarrays we comprehensively determined the binding specificities over a full range of affinities for five TFs of different structural classes from yeast, worm, mouse and human. The unbiased coverage of all k-mers permits high-throughput interrogation of binding site preferences, including nucleotide interdependencies, at unprecedented resolution.
Berger
Michael F
MF
Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts 02115, USA.
Philippakis
Anthony A
AA
Qureshi
Aaron M
AM
He
Fangxue S
FS
Estep
Preston W
PW
Bulyk
Martha L
ML
D000818:Animals; D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors / Q000737:chemistry; D001665:Binding Sites / Q000502:physiology; D017173:Caenorhabditis elegans; D029742:Caenorhabditis elegans Proteins / Q000737:chemistry; D051766:Early Growth Response Protein 1 / Q000737:chemistry; D018398:Homeodomain Proteins / Q000737:chemistry; D006801:Humans; D051379:Mice; D050811:Octamer Transcription Factor-1 / Q000737:chemistry; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D011485:Protein Binding; D012441:Saccharomyces cerevisiae; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry; D000089804:Shelterin Complex; D034501:Telomere-Binding Proteins / Q000737:chemistry; D014157:Transcription Factors / Q000737:chemistry / Q000378:metabolism*
D051778:Basic Helix-Loop-Helix Leucine Zipper Transcription Factors; C064042:CBF1 protein, S cerevisiae; C109217:CEH-22 protein, C elegans; D029742:Caenorhabditis elegans Proteins; D051766:Early Growth Response Protein 1; C486109:Egr1 protein, mouse; D018398:Homeodomain Proteins; D050811:Octamer Transcription Factor-1; C440829:RAP1 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; D000089804:Shelterin Complex; D034501:Telomere-Binding Proteins; D014157:Transcription Factors