Background. Transcriptional enhancers are generally known to regulate gene transcription from afar. Their activation involves a series of changes in chromatin marks and recruitment of protein factors. These enhancers may also occur inside genes, but how many may be active in human cells and their effects on the regulation of the host gene remains unclear./nResults. We describe a novel semi-supervised method based on the relative enrichment of chromatin signals between 2 conditions to predict active enhancers. We applied this method to the tumoral K562 and the normal GM12878 cell lines to predict enhancers that are differentially active in one cell type. These predictions show enhancer-like properties according to positional distribution, correlation with gene expression and production of enhancer RNAs. Using this model, we predict 10,365 and 9777 intragenic active enhancers in K562 and GM12878, respectively, and relate the differential activation of these enhancers to expression and splicing differences of the host genes./nConclusions. We propose that the activation or silencing of intragenic transcriptional enhancers modulate the regulation of the host gene by means of a local change of the chromatin and the recruitment of enhancer-related factors that may interact with the RNA directly or through the interaction with RNA binding proteins. Predicted enhancers are available at http://regulatorygenomics.upf.edu/Projects/enhancers.html.

The authors would like to thank E. Furlong, Y. Barash, B. Blencowe and U. Braunschweig for useful discussions. This work was supported by grants from Plan Nacional I + D (BIO2011-23920) and Consolider (CSD2009-00080) from MINECO (Spanish Government), and by the Sandra Ibarra Foundation for Cancer (FSI 2013). JGV and BS were supported FPI grants from the MINECO (Spanish Government) BES-2009-018064 and BES-2012-052683, respectively.