Transposable elements as tissue-specific enhancers in cancers of endodermal lineage

Konsta Karttunen, Divyesh Patel, Jihan Xia, Liangru Fei, Kimmo Palin, Lauri Aaltonen and Biswajyoti Sahu ()
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Konsta Karttunen: University of Helsinki
Divyesh Patel: University of Helsinki
Jihan Xia: University of Helsinki
Liangru Fei: University of Helsinki
Kimmo Palin: University of Helsinki
Lauri Aaltonen: University of Helsinki
Biswajyoti Sahu: University of Helsinki

Nature Communications, 2023, vol. 14, issue 1, 1-19

Abstract: Abstract Transposable elements (TE) are repetitive genomic elements that harbor binding sites for human transcription factors (TF). A regulatory role for TEs has been suggested in embryonal development and diseases such as cancer but systematic investigation of their functions has been limited by their widespread silencing in the genome. Here, we utilize unbiased massively parallel reporter assay data using a whole human genome library to identify TEs with functional enhancer activity in two human cancer types of endodermal lineage, colorectal and liver cancers. We show that the identified TE enhancers are characterized by genomic features associated with active enhancers, such as epigenetic marks and TF binding. Importantly, we identify distinct TE subfamilies that function as tissue-specific enhancers, namely MER11- and LTR12-elements in colon and liver cancers, respectively. These elements are bound by distinct TFs in each cell type, and they have predicted associations to differentially expressed genes. In conclusion, these data demonstrate how different cancer types can utilize distinct TEs as tissue-specific enhancers, paving the way for comprehensive understanding of the role of TEs as bona fide enhancers in the cancer genomes.

Date: 2023
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DOI: 10.1038/s41467-023-41081-4

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