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

Savage, Abigail L ORCID: 0000-0002-2231-9800, Bubb, Vivien J ORCID: 0000-0003-2763-7004, Breen, Gerome and Quinn, John P ORCID: 0000-0003-3551-7803 (2013) Characterisation of the potential function of SVA retrotransposons to modulate gene expression patterns. BMC EVOLUTIONARY BIOLOGY, 13 (1). 101-.

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Abstract

<h4>Background</h4>Retrotransposons are a major component of the human genome constituting as much as 45%. The hominid specific SINE-VNTR-Alus are the youngest of these elements constituting 0.13% of the genome; they are therefore a practical and amenable group for analysis of both their global integration, polymorphic variation and their potential contribution to modulation of genome regulation.<h4>Results</h4>Consistent with insertion into active chromatin we have determined that SVAs are more prevalent in genic regions compared to gene deserts. The consequence of which, is that their integration has greater potential to have affects on gene regulation. The sequences of SVAs show potential for the formation of secondary structure including G-quadruplex DNA. We have shown that the human specific SVA subtypes (E-F1) show the greatest potential for forming G-quadruplexes within the central tandem repeat component in addition to the 5' 'CCCTCT' hexamer. We undertook a detailed analysis of the PARK7 SVA D, located in the promoter of the PARK7 gene (also termed DJ-1), in a HapMap cohort where we identified 2 variable number tandem repeat domains and 1 tandem repeat within this SVA with the 5' CCCTCT element being one of the variable regions. Functionally we were able to demonstrate that this SVA contains multiple regulatory elements that support reporter gene expression in vitro and further show these elements exhibit orientation dependency.<h4>Conclusions</h4>Our data supports the hypothesis that SVAs integrate preferentially in to open chromatin where they could modify the existing transcriptional regulatory domains or alter expression patterns by a variety of mechanisms.

Item Type:	Article
Additional Information:	Savage, Abigail L Bubb, Vivien J Breen, Gerome Quinn, John P Journal article BMC evolutionary biology BMC Evol Biol. 2013 May 21;13(1):101.## TULIP Type: Articles/Papers (Journal) ##
Uncontrolled Keywords:	SVA, PARK7, DJ-1, Genetic variation, G-quadruplex DNA, Retrotransposon
Depositing User:	Symplectic Admin
Date Deposited:	21 Jan 2015 16:21
Last Modified:	16 Dec 2022 03:04
DOI:	10.1186/1471-2148-13-101
Publisher's Statement :	© 2013 Savage et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Related URLs:	Author Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/2005175