The SLC6A4 VNTR genotype determines transcription factor binding and epigenetic variation of this gene in response to cocaine in vitro

Abstract

We demonstrated that the genotype of the variable number tandem repeats (VNTRs) in the linked polymorphic region (LPR) of the 5' promoter and in the intron 2 (Stin2) transcriptional regulatory domains of the serotonin transporter SLC6A4 gene determined its promoter interactions with transcription factors and co-activators in response to cocaine in the JAr cell line. The LPR variants contain 14 (short, s) or 16 (long, l) copies of a 22-23 bp repeat element, whereas the Stin2 VNTR exists as three variants containing 9, 10 or 12 copies of a 16-17 bp repeat. We observed a differential effect of cocaine on the association of the promoter with the transcription factor CTCF, which bound to both LPR alleles prior to cocaine exposure but only to the l-allele following exposure. Significantly, this differential effect of cocaine was correlated with the binding of the transcriptional regulator MeCP2 specifically to the s-allele and recruiting the histone deacetylase complex (HDAC). Concurrently, cocaine increased the association of positive histone marks over the SLC6A4 gene locus. At the Stin2 domain, we lost binding of the transcription factor YB-1, while CTCF remained bound. Our biochemical data are consistent with differential reporter gene activity directed by the individual or dual domains in response to cocaine in an Epstein-Barr virus-based episome model of stable transfections. These observations suggest that exposure of JAr cells to cocaine may result in differential binding of transcription factors and activators based on a specific genotype that might alter epigenetic parameters affecting gene expression after the initial challenge.

Characterisation of the potential function of SVA retrotransposons to modulate gene expression patterns

“…The data on the central TR/VNTR indicated they support distinct transcriptional properties dependent on cell type. This is consistent with the action of VNTRs we have previously observed in the human serotonin and dopamine transporter genes [28,31,34]. We would expect that different complements of transcription factors present in both these cell lines are responsible for the activity of the reporter gene directed by the TR/VNTR.…”

“…SVAs contain large domains of repetitive DNA (VNTRs) similar in copy number and size of individual repeats to those, we and others, have found to direct differential tissue specific and stimulus inducible gene expression in many other genes [28-35]. This differential regulator property has been correlated with copy number of the VNTR in some genes [30,34-43].…”

Evaluation of Polymorphisms in the Sulfonamide Detoxification Genes CYB5A and CYB5R3 in Dogs with Sulfonamide Hypersensitivity

“…Sp transcription factors are known inducers of human CYB5A expression, so it is possible that this VNTR has functional relevance. Promoter VNTRs have been shown to affect the expression of several human genes, and VNTRs in the canine DRD4 gene have been associated with behavioral phenotypes in German Shepherds . Although we found no association between these VNTRs and sulfonamide hypersensitivity in the dogs in this study, the functional consequences of these VNTRs merit additional study.…”

An Evaluation of a SVA Retrotransposon in the FUS Promoter as a Transcriptional Regulator and Its Association to ALS

“…Although it is difficult to accurately predict the regulatory domains for a particular gene other than the proximal promoter (often 0.5 to 1 kb upstream of the transcriptional start site), our group and others have demonstrated important domains for gene regulation can reside in both the most evolutionary conserved regions (ECRs) which are non-coding [10]–[12] and the highly polymorphic and often rapidly evolving variable number tandem repeats (VNTRs) [13]–[19]. In both cases the ECR or VNTR can be tens of thousands of bases from the major transcriptional start of a gene [20].…”