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Open Access Highly Accessed Research article

Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements

Danilo Licastro1, Vincenzo A Gennarino2, Francesca Petrera1, Remo Sanges1, Sandro Banfi2* and Elia Stupka34*

Author affiliations

1 CBM scrl - Genomics, Area Science Park, Basovizza, Trieste, Italy

2 Telethon Institute of Genetics and Medicine (TIGEM), via Pietro Castellino 111, 80131, Napoli, Italy

3 UCL Cancer Institute, University College London, London, WC1E 6BT, UK

4 Centre for Gastroenterology, Institute of Cell and Molecular Science, Queen Mary University of London, London, E1 2AT, UK

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Citation and License

BMC Genomics 2010, 11:151  doi:10.1186/1471-2164-11-151

Published: 4 March 2010

Abstract

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.