Research Article: Presence of recombination hotspots throughout SLC6A3

Date Published: June 11, 2019

Publisher: Public Library of Science

Author(s): Juan Zhao, Yanhong Zhou, Nian Xiong, Hong Qing, Tao Wang, Zhicheng Lin, Jamuna Subramaniam.

http://doi.org/10.1371/journal.pone.0218129

Abstract

The human dopamine transporter gene SLC6A3 is involved in substance use disorders (SUDs) among many other common neuropsychiatric illnesses but allelic association results including those with its classic genetic markers 3’VNTR or Int8VNTR remain mixed and unexplainable. To better understand the genetics for reproducible association signals, we report the presence of recombination hotspots based on sequencing of the entire 5’ promoter regions in two small SUDs cohorts, 30 African Americans (AAs) and 30 European Americans (EAs). Recombination rate was the highest near the transcription start site (TSS) in both cohorts. In addition, each cohort carried 57 different promoter haplotypes out of 60 and no haplotypes were shared between the two ethnicities. A quarter of the haplotypes evolved in an ethnicity-specific manner. Finally, analysis of five hundred subjects of European ancestry, from the 1000 Genome Project, confirmed the promoter recombination hotspots and also revealed several additional ones in non-coding regions only. These findings provide an explanation for the mixed results as well as guidance for selection of effective markers to be used in next generation association validation (NGAV), facilitating the delineation of pathogenic variation in this critical neuropsychiatric gene.

Partial Text

By sequestering dopamine (DA) into presynaptic neurons, the dopamine transporter (DAT) regulates spatio-temporal components of DA transmission. As a critical regulator of DA transmission, DAT contributes to voluntary movement, reward and mnemonic functions of the brain and modulates the efficacy of therapeutic drugs targeted to this plasma membrane protein. DAT expression is highly circumscribed in discrete regions throughout the brain and the expression of the human DAT gene (SLC6A3) varies among subjects[1–5]. Thus DNA sequence variations in the regulatory regions specially the promoter of SLC6A3 may contribute to altered expressional patterns in the brain, dopamine-related individuality as well as diseases[6, 7]. The essential roles of DAT in brain function have mandated extensive studies of SLC6A3 associations with behaviors and diseases.

It is important to uncover novel, potentially functional polymorphisms and distinct haplotypes, and recombination hotspots because SLC6A3 activity can be haplotype-dependent partly due to cis-antagonism between 5’ and 3’ sides of SLC6A3[95]. The most significant findings from this deep-sequencing study included discovery of novel and selected polymorphisms and the presence of recombination hotspots throughout SLC6A3. Although association analysis of SUDs and SLC6A3 haplotypes was not a primary purpose here, five implications are highlighted as follows.

Extensive DNA sequence variations not only around the core promoter but also in other distal regulatory regions may work in concert or in haplotypes and influence dopamine-related individuality and diseases. Such genetic diversity of SLC6A3 may help explain the elusiveness of previous association findings with the classical markers in the 3’ side. The findings also lay a foundation for a better understanding of the roles that the polymorphic SLC6A3 plays in human brain.

 

Source:

http://doi.org/10.1371/journal.pone.0218129

 

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