Curated collection of yeast transcription factor DNA binding specificity data reveals novel structural and gene regulatory insights

Raluca Gordân,Kevin F Murphy,Rachel P Mccord,Anastasia Vedenko,Cong Zhu,Martha L Bulyk

doi:10.1186/gb-2011-12-12-r125

Abstract

BackgroundTranscription factors (TFs) play a central role in regulating gene expression by interacting with cis-regulatory DNA elements associated with their target genes. Recent surveys have examined the DNA binding specificities of most Saccharomyces cerevisiae TFs, but a comprehensive evaluation of their data has been lacking.ResultsWe analyzed in vitro and in vivo TF-DNA binding data reported in previous large-scale studies to generate a comprehensive, curated resource of DNA binding specificity data for all characterized S. cerevisiae TFs. Our collection comprises DNA binding site motifs and comprehensive in vitro DNA binding specificity data for all possible 8-bp sequences. Investigation of the DNA binding specificities within the basic leucine zipper (bZIP) and VHT1 regulator (VHR) TF families revealed unexpected plasticity in TF-DNA recognition: intriguingly, the VHR TFs, newly characterized by protein binding microarrays in this study, recognize bZIP-like DNA motifs, while the bZIP TF Hac1 recognizes a motif highly similar to the canonical E-box motif of basic helix-loop-helix (bHLH) TFs. We identified several TFs with distinct primary and secondary motifs, which might be associated with different regulatory functions. Finally, integrated analysis of in vivo TF binding data with protein binding microarray data lends further support for indirect DNA binding in vivo by sequence-specific TFs.ConclusionsThe comprehensive data in this curated collection allow for more accurate analyses of regulatory TF-DNA interactions, in-depth structural studies of TF-DNA specificity determinants, and future experimental investigations of the TFs' predicted target genes and regulatory roles.

Highlights

Transcription factors (TFs) play a central role in regulating gene expression by interacting with cisregulatory DNA elements associated with their target genes
Secondary motifs derived from protein binding microarray (PBM) data are unlikely to be attributable to a motif-finding artifact, and TF binding to secondary motifs has been confirmed by electrophoretic mobility shift assay for six mouse TFs [16]
We analyzed in detail one of these 39 TFs, Sko1, and found that both the primary and secondary motifs are utilized in vivo and that they are potentially associated with different regulatory functions of Sko1

Summary

Introduction

Transcription factors (TFs) play a central role in regulating gene expression by interacting with cisregulatory DNA elements associated with their target genes. Transcription factors (TFs) control and mediate cellular responses to environmental stimuli through sequencespecific interactions with cis regulatory DNA elements within the promoters and enhancers of their target genes, directing the expression of those genes in a coordinated manner. In addition to the comprehensive nature of the in vitro data reported in these studies (that is, covering all possible 8-mers), these data reflect the direct DNA binding preferences of the tested TFs; in contrast, ChIP data sometimes reflect indirect DNA binding of the immunoprecipitated TF by recruiting TFs [13]. The in vitro data reported in these studies are complementary to ChIP data, in that the in vitro data provide higher-resolution measurements of DNA binding preferences compared to ChIP (8 bp versus hundreds of base pairs, respectively) and they test the intrinsic DNA binding specificity of a TF in the absence of any protein co-factors or competitors (such as other TFs or nucleosomes)

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