RESEARCH ARTICLE
Long Non-coding RNAs in the Human Genome Acquired by Horizontal Gene Transfer
Rian Pierneef, Frederick J. Clasen, Oliver K. I. Bezuidt, Oleg N. Reva*
Article Information
Identifiers and Pagination:
Year: 2018Volume: 11
First Page: 182
Last Page: 196
Publisher ID: TOBIOIJ-11-182
DOI: 10.2174/1875036201811010182
Article History:
Received Date: 25/5/2018Revision Received Date: 31/7/2018
Acceptance Date: 10/8/2018
Electronic publication date: 31/08/2018
Collection year: 2018
open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: (https://creativecommons.org/licenses/by/4.0/legalcode). This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Abstract
Background:
Horizontal gene transfer of mobile genetic elements is an essential component of prokaryotic evolution. These insertion events in eukaryotes and particularly in the human genome have been investigated by various methodologies with varying results.
Objective:
In this paper, we implement a sequence composition approach to investigate insertions of genomic islands in the human genome.
Methods:
A modified version of a prokaryotic GI identifier, SeqWord Gene Island Sniffer v.2.0, was used to predict genomic islands in the hg38 version of the human genome.
Results:
Predicted genomic islands were enriched with long non-coding RNAs and also contributed to the acquisition and modification of proteins associated with the immune system and gonad development, albeit to a lesser extent. The estimated rate of acquisition of these genomic islands in vertebrate genomes was non-linear with regards to species divergence times with an acceleration at the time of vertebrate land invasion and during the transition of prosimians to monkeys soon after the Cretaceous-Paleogene extinction.
Conclusion:
The rapid acquisition of non-conserved long non-coding RNAs in the human genome and probably in vertebrata genomes was facilitated by horizontal gene transfer. All predicted human genomic islands and supporting information are freely accessible from http://hislands.bi.up.ac.za.