CRISPR deletion of a SINE-VNTR-<i>Alu</i> (SVA_67) retrotransposon demonstrates its ability to differentially modulate gene expression at the <i>MAPT</i> locus.

Fröhlich, Alexander, Hughes, Lauren S, Middlehurst, Ben ORCID: 0000-0002-2603-2719, Pfaff, Abigail L, Bubb, Vivien J ORCID: 0000-0003-2763-7004, Koks, Sulev ORCID: 0000-0001-6087-6643 and Quinn, John P ORCID: 0000-0003-3551-7803 (2023) CRISPR deletion of a SINE-VNTR-<i>Alu</i> (SVA_67) retrotransposon demonstrates its ability to differentially modulate gene expression at the <i>MAPT</i> locus. Frontiers in neurology, 14. 1273036-.

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Official URL: http://dx.doi.org/10.3389/fneur.2023.1273036

Abstract

<h4>Background</h4>SINE-VNTR-<i>Alu</i> (SVA) retrotransposons are hominid-specific elements which have been shown to play important roles in processes such as chromatin structure remodelling and regulation of gene expression demonstrating that these repetitive elements exert regulatory functions. We have previously shown that the presence or absence of a specific SVA element, termed SVA_67, was associated with differential expression of several genes at the <i>MAPT</i> locus, a locus associated with Parkinson's Disease (PD) and frontotemporal dementia. However, we were not able to demonstrate that causation of differential gene expression was directed by the SVA due to lack of functional validation.<h4>Methods</h4>We performed CRISPR to delete SVA_67 in the HEK293 cell line. Quantification of target gene expression was performed using qPCR to assess the effects on expression in response to the deletion of SVA_67. Differences between CRISPR edit and control cell lines were analysed using two-tailed t-test with a minimum 95% confidence interval to determine statistical significance.<h4>Results</h4>In this study, we provide data highlighting the SVA-specific effect on differential gene expression. We demonstrate that the hemizygous deletion of the endogenous SVA_67 in CRISPR edited cell lines was associated with differential expression of several genes at the <i>MAPT</i> locus associated with neurodegenerative diseases including <i>KANSL1</i>, <i>MAPT</i> and <i>LRRC37A</i>.<h4>Discussion</h4>This data is consistent with our previous bioinformatic work of differential gene expression analysis using transcriptomic data from the Parkinson's Progression Markers Initiative (PPMI) cohort. As SVAs have regulatory influences on gene expression, and insertion polymorphisms contribute to interpersonal differences in expression patterns, these results highlight the potential contribution of these elements to complex diseases with potentially many genetic components, such as PD.

Item Type:	Article
Uncontrolled Keywords:	CRISPR, MAPT locus, Parkinson’s disease, SINE-VNTR-Alu, gene expression, gene regulation, retrotransposon
Divisions:	Faculty of Health and Life Sciences Faculty of Health and Life Sciences > Institute of Systems, Molecular and Integrative Biology
Depositing User:	Symplectic Admin
Date Deposited:	16 Oct 2023 14:52
Last Modified:	27 Oct 2023 12:52
DOI:	10.3389/fneur.2023.1273036
Open Access URL:	https://doi.org/10.3389/fneur.2023.1273036
Related URLs:	Author Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3173772