Alu insertion variants alter gene transcript levels
- Lindsay M. Payer1,
- Jared P. Steranka1,
- Maria S. Kryatova1,
- Giacomo Grillo2,
- Mathieu Lupien2,3,4,
- Pedro P. Rocha5,6 and
- Kathleen H. Burns1,7,8
- 1Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA;
- 2Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario M5G 1L7, Canada;
- 3Department of Medical Biophysics, University of Toronto, Toronto, Ontario M5G 1L7, Canada;
- 4Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada;
- 5Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, Maryland 20892-4340, USA;
- 6National Cancer Institute, NIH, Bethesda, Maryland 20892, USA;
- 7McKusick-Nathans Institute of Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA
Abstract
Alu are high copy number interspersed repeats that have accumulated near genes during primate and human evolution. They are a pervasive source of structural variation in modern humans. Impacts that Alu insertions may have on gene expression are not well understood, although some have been associated with expression quantitative trait loci (eQTLs). Here, we directly test regulatory effects of polymorphic Alu insertions in isolation of other variants on the same haplotype. To screen insertion variants for those with such effects, we used ectopic luciferase reporter assays and evaluated 110 Alu insertion variants, including more than 40 with a potential role in disease risk. We observed a continuum of effects with significant outliers that up- or down-regulate luciferase activity. Using a series of reporter constructs, which included genomic context surrounding the Alu, we can distinguish between instances in which the Alu disrupts another regulator and those in which the Alu introduces new regulatory sequence. We next focused on three polymorphic Alu loci associated with breast cancer that display significant effects in the reporter assay. We used CRISPR to modify the endogenous sequences, establishing cell lines varying in the Alu genotype. Our findings indicate that Alu genotype can alter expression of genes implicated in cancer risk, including PTHLH, RANBP9, and MYC. These data show that commonly occurring polymorphic Alu elements can alter transcript levels and potentially contribute to disease risk.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.261305.120.
- Received January 17, 2020.
- Accepted September 23, 2021.
This article is distributed exclusively by Cold Spring Harbor Laboratory Press for the first six months after the full-issue publication date (see https://genome.cshlp.org/site/misc/terms.xhtml). After six months, it is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
