Affinity for Enhancer Prediction

RESEARCH HIGHLIGHTS

FUNCTIONAL GENOMICS enhancer element locator (EEL) for The expression of reporter genes in genome-wide enhancer analysis. EEL tissues where the studied transcrip- aligns the order of transcription- tion factors are potentially not active Affinity for factor binding sites on orthologous could in turn be explained by the DNA sequences by taking into presence of other transcription-fac- account clustering, affinity and site tor binding-site modules within the enhancer conservation. Moreover, a system of enhancers tested. correction factors is used to account The experimental and compu- prediction for cooperativity between transcrip- tational approached described by tion factors at a given enhancer. Hallikas, Palin and colleagues are Differences in the DNA-binding Having tested EEL on well- genome-wide and can be easily affinities of transcription factors and defined Drosophila enhancers and generalized to any transcription fac- in the tissue-specific combinations on mammalian MyoD, the authors tor for which binding specificity is in which transcription factors bind carried out pairwise genome-wide known. Together with other recently regulatory elements underlie the alignments of human genes with developed methods to study DNA temporal and spatial patterns of gene their orthologues from the mouse, binding on a global scale, they will expression that characterize develop- rat, chicken and pufferfish. Several help us to dissect the spatio-temporal ment. Although transcription-factor potential enhancers were chosen complexity of gene regulation. binding sites within promoter and for further study — for example, to Magdalena Skipper 3′ UTR sequences have received test their ability to drive expression much attention, similar studies of of reporter genes. The confirmation

distal enhancer elements have been rate was impressive for the highest ORIGINAL RESEARCH PAPER Hallikas, O. & hindered by both experimental and scoring enhancers, although there Palin, K. et al. Genome-wide prediction of computational difficulties. In their were also a few surprises. Some mammalian enhancers based on analysis of transcription-factor binding affinity. Cell 124, recent study, Hallikas, Palin and enhancer–reporter gene constructs 47–59 (2006) their colleagues have tackled both recapitulated only a part of the FURTHER READING Wasserman, W. W. & Sandelin, A. Applied bioinformatics for the problems. They have developed expression pattern of the correspond- identification of regulatory elements. Nature Rev. a high-throughput method for ing gene, indicating the regulation of Genet. 5, 276–287 (2004) determining the DNA-binding spe- these genes by multiple enhancers. cificities of representative members of three transcription-factor families and a computational tool to predict the location of novel mammalian enhancers. To address the issue of varying affinities of transcription factors for different DNA sequences, the authors developed a microwell-plate-based, high-throughput method in which the DNA-binding domains of a transcription factor of interest were fused to a luciferase reporter. The fusion proteins were incubated with biotinylated oligonucleotides that had the highest affinity to the transcription factor of interest. Binding was detected by measuring luciferase activity that could be captured by immobilized streptavidin. By adding competing unlabelled oligonucleotides that carried single base substi- tutions to the reaction, the authors could determine the relative affinity of the given transcription factor. The utility of the assay was demonstrated for members of the GLI family, and for TCF4 and ETS1 transcription factors. Parallel to the experimental approach, the authors developed a computational tool — called