A novel hypervariable variable number tandem repeat in the dopamine transporter gene (SLC6A3)

Apsley, Abner T.; Domico, Emma R.; Verbiest, Max A.; Brogan, Carly A.; Buck, Evan R.; Burich, Andrew J.; Cardone, Kathleen M.; Stone, Wesley J.; Anisimova, Maria; Vandenbergh, David J.

doi:10.26508/lsa.202201677

Please use this identifier to cite or link to this item: https://doi.org/10.21256/zhaw-27409

Publication type:	Article in scientific journal
Type of review:	Open peer review
Title:	A novel hypervariable variable number tandem repeat in the dopamine transporter gene (SLC6A3)
Authors:	Apsley, Abner T. Domico, Emma R. Verbiest, Max A. Brogan, Carly A. Buck, Evan R. Burich, Andrew J. Cardone, Kathleen M. Stone, Wesley J. Anisimova, Maria Vandenbergh, David J.
et. al:	No
DOI:	10.26508/lsa.202201677 10.21256/zhaw-27409
Published in:	Life Science Alliance
Volume(Issue):	6
Issue:	4
Page(s):	e202201677
Issue Date:	Apr-2023
Publisher / Ed. Institution:	Life Science Alliance
ISSN:	2575-1077
Language:	English
Subjects:	Allele; Haplotype; Intron; Human; Dopamine plasma membrane transport protein; Minisatellite repeat
Subject (DDC):	572: Biochemistry
Abstract:	The dopamine transporter gene, SLC6A3, has received substantial attention in genetic association studies of various phenotypes. Although some variable number tandem repeats (VNTRs) present in SLC6A3 have been tested in genetic association studies, results have not been consistent. VNTRs in SLC6A3 that have not been examined genetically were characterized. The Tandem Repeat Annotation Library was used to characterize the VNTRs of 64 unrelated long-read haplotype-phased SLC6A3 sequences. Sequence similarity of each repeat unit of the five VNTRs is reported, along with the correlations of SNP-SNP, SNP-VNTR, and VNTR-VNTR alleles across the gene. One of these VNTRs is a novel hyper-VNTR (hyVNTR) in intron 8 of SLC6A3, which contains a range of 3.4-133.4 repeat copies and has a consensus sequence length of 38 bp, with 82% G+C content. The 38-base repeat was predicted to form G-quadruplexes in silico and was confirmed by circular dichroism spectroscopy. In addition, this hyVNTR contains multiple putative binding sites for PRDM9, which, in combination with low levels of linkage disequilibrium around the hyVNTR, suggests it might be a recombination hotspot.
URI:	https://digitalcollection.zhaw.ch/handle/11475/27409
Fulltext version:	Published version
License (according to publishing contract):	CC BY 4.0: Attribution 4.0 International
Departement:	Life Sciences and Facility Management
Organisational Unit:	Institute of Computational Life Sciences (ICLS)
Published as part of the ZHAW project:	REFRACT – Repeat protein Function, Refinement, Annotation and Classification of Topologies
Appears in collections:	Publikationen Life Sciences und Facility Management

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Apsley, A. T., Domico, E. R., Verbiest, M. A., Brogan, C. A., Buck, E. R., Burich, A. J., Cardone, K. M., Stone, W. J., Anisimova, M., & Vandenbergh, D. J. (2023). A novel hypervariable variable number tandem repeat in the dopamine transporter gene (SLC6A3). Life Science Alliance, 6(4), e202201677. https://doi.org/10.26508/lsa.202201677

Apsley, A.T. et al. (2023) ‘A novel hypervariable variable number tandem repeat in the dopamine transporter gene (SLC6A3)’, Life Science Alliance, 6(4), p. e202201677. Available at: https://doi.org/10.26508/lsa.202201677.

A. T. Apsley et al., “A novel hypervariable variable number tandem repeat in the dopamine transporter gene (SLC6A3),” Life Science Alliance, vol. 6, no. 4, p. e202201677, Apr. 2023, doi: 10.26508/lsa.202201677.

APSLEY, Abner T., Emma R. DOMICO, Max A. VERBIEST, Carly A. BROGAN, Evan R. BUCK, Andrew J. BURICH, Kathleen M. CARDONE, Wesley J. STONE, Maria ANISIMOVA und David J. VANDENBERGH, 2023. A novel hypervariable variable number tandem repeat in the dopamine transporter gene (SLC6A3). Life Science Alliance. April 2023. Bd. 6, Nr. 4, S. e202201677. DOI 10.26508/lsa.202201677

Apsley, Abner T., Emma R. Domico, Max A. Verbiest, Carly A. Brogan, Evan R. Buck, Andrew J. Burich, Kathleen M. Cardone, Wesley J. Stone, Maria Anisimova, and David J. Vandenbergh. 2023. “A Novel Hypervariable Variable Number Tandem Repeat in the Dopamine Transporter Gene (SLC6A3).” Life Science Alliance 6 (4): e202201677. https://doi.org/10.26508/lsa.202201677.

Apsley, Abner T., et al. “A Novel Hypervariable Variable Number Tandem Repeat in the Dopamine Transporter Gene (SLC6A3).” Life Science Alliance, vol. 6, no. 4, Apr. 2023, p. e202201677, https://doi.org/10.26508/lsa.202201677.