BACKGROUND: Ultraconserved elements (UCEs) are highly constrained elements of 
mammalian genomes, whose functional role has not been completely elucidated yet. 
Previous studies have shown that some of them act as enhancers in mouse, while 
some others are expressed in both normal and cancer-derived human tissues. Only 
one UCE element so far was shown to present these two functions concomitantly, 
as had been observed in other isolated instances of single, non ultraconserved 
enhancer elements.
RESULTS: We used a custom microarray to assess the levels of UCE transcription 
during mouse development and integrated these data with published microarray and 
next-generation sequencing datasets as well as with newly produced PCR 
validation experiments. We show that a large fraction of non-exonic UCEs is 
transcribed across all developmental stages examined from only one DNA strand. 
Although the nature of these transcripts remains a mistery, our meta-analysis of 
RNA-Seq datasets indicates that they are unlikely to be short RNAs and that some 
of them might encode nuclear transcripts. In the majority of cases this function 
overlaps with the already established enhancer function of these elements during 
mouse development. Utilizing several next-generation sequencing datasets, we 
were further able to show that the level of expression observed in non-exonic 
UCEs is significantly higher than in random regions of the genome and that this 
is also seen in other regions which act as enhancers.
CONCLUSION: Our data shows that the concurrent presence of enhancer and 
transcript function in non-exonic UCE elements is more widespread than 
previously shown. Moreover through our own experiments as well as the use of 
next-generation sequencing datasets, we were able to show that the RNAs encoded 
by non-exonic UCEs are likely to be long RNAs transcribed from only one DNA 
strand.