The Role of SINE-VNTR-Alu (SVA) Retrotransposons in Shaping the Human Genome

Gianfrancesco, Olympia, Geary, Bethany, Savage, Abigail L ORCID: 0000-0002-2231-9800, Billingsley, Kimberley J, Bubb, Vivien J ORCID: 0000-0003-2763-7004 and Quinn, John P ORCID: 0000-0003-3551-7803 (2019) The Role of SINE-VNTR-Alu (SVA) Retrotransposons in Shaping the Human Genome. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES, 20 (23). E5977-.

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Official URL: http://dx.doi.org/10.3390/ijms20235977

Abstract

Retrotransposons can alter the regulation of genes both transcriptionally and post-transcriptionally, through mechanisms such as binding transcription factors and alternative splicing of transcripts. SINE-VNTR-Alu (SVA) retrotransposons are the most recently evolved class of retrotransposable elements, found solely in primates, including humans. SVAs are preferentially found at genic, high GC loci, and have been termed "mobile CpG islands". We hypothesise that the ability of SVAs to mobilise, and their non-random distribution across the genome, may result in differential regulation of certain pathways. We analysed SVA distribution patterns across the human reference genome and identified over-representation of SVAs at zinc finger gene clusters. Zinc finger proteins are able to bind to and repress SVA function through transcriptional and epigenetic mechanisms, and the interplay between SVAs and zinc fingers has been proposed as a major feature of genome evolution. We describe observations relating to the clustering patterns of both reference SVAs and polymorphic SVA insertions at zinc finger gene loci, suggesting that the evolution of this network may be ongoing in humans. Further, we propose a mechanism to direct future research and validation efforts, in which the interplay between zinc fingers and their epigenetic modulation of SVAs may regulate a network of zinc finger genes, with the potential for wider transcriptional consequences.

Item Type:	Article
Uncontrolled Keywords:	retrotransposon, SVA, polymorphism, primate, zinc finger protein, ZNF, evolution
Depositing User:	Symplectic Admin
Date Deposited:	12 Dec 2019 09:41
Last Modified:	19 Jan 2023 00:12
DOI:	10.3390/ijms20235977
Open Access URL:	https://doi.org/10.3390/ijms20235977
Related URLs:	Author Publisher
URI:	https://livrepository.liverpool.ac.uk/id/eprint/3066062