BACKGROUND: Regulated gene expression controls organismal development, and 
variation in regulatory patterns has been implicated in complex traits. Thus 
accurate prediction of enhancers is important for further understanding of these 
processes. Genome-wide measurement of epigenetic features, such as histone 
modifications and occupancy by transcription factors, is improving enhancer 
predictions, but the contribution of these features to prediction accuracy is 
not known. Given the importance of the hematopoietic transcription factor TAL1 
for erythroid gene activation, we predicted candidate enhancers based on genomic 
occupancy by TAL1 and measured their activity. Contributions of multiple 
features to enhancer prediction were evaluated based on the results of these and 
other studies.
RESULTS: TAL1-bound DNA segments were active enhancers at a high rate both in 
transient transfections of cultured cells (39 of 79, or 56%) and transgenic mice 
(43 of 66, or 65%). The level of binding signal for TAL1 or GATA1 did not help 
distinguish TAL1-bound DNA segments as active versus inactive enhancers, nor did 
the density of regulation-related histone modifications. A meta-analysis of 
results from this and other studies (273 tested predicted enhancers) showed that 
the presence of TAL1, GATA1, EP300, SMAD1, H3K4 methylation, H3K27ac, and CAGE 
tags at DNase hypersensitive sites gave the most accurate predictors of enhancer 
activity, with a success rate over 80% and a median threefold increase in 
activity. Chromatin accessibility assays and the histone modifications H3K4me1 
and H3K27ac were sensitive for finding enhancers, but they have high false 
positive rates unless transcription factor occupancy is also included.
CONCLUSIONS: Occupancy by key transcription factors such as TAL1, GATA1, SMAD1, 
and EP300, along with evidence of transcription, improves the accuracy of 
enhancer predictions based on epigenetic features.