Small genomic insertions form enhancers that misregulate oncogenes


The non-coding regions of tumour cell genomes harbour a considerable fraction of total DNA sequence variation, but the functional contribution of these variants to tumorigenesis is ill-defined. Among these non-coding variants, somatic insertions are among the least well characterized due to challenges with interpreting short-read DNA sequences. Here, using a combination of Chip-seq to enrich enhancer DNA and a computational approach with multiple DNA alignment procedures, we identify enhancer-associated small insertion variants. Among the 102 tumour cell genomes we analyse, small insertions are frequently observed in enhancer DNA sequences near known oncogenes. Further study of one insertion, somatically acquired in primary leukaemia tumour genomes, reveals that it nucleates formation of an active enhancer that drives expression of the LMO2 oncogene. The approach described here to identify enhancer-associated small insertion variants provides a foundation for further study of these abnormalities across human cancers.

DOI: 10.1038/ncomms14385

Cite this paper

@inproceedings{Abraham2017SmallGI, title={Small genomic insertions form enhancers that misregulate oncogenes}, author={Brian J Abraham and Denes Hnisz and Abraham S Weintraub and Nicholas Kwiatkowski and Charles H Li and Zhaodong Li and Nina Weichert-Leahey and Sunniyat Rahman and Yu Liu and Julia Etchin and Benshang Li and Shuhong Shen and Tong Ihn Lee and Jinghui Zhang and A Thomas Look and Marc R Mansour and Richard A Young}, booktitle={Nature communications}, year={2017} }