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Impact of non-LTR retrotransposons in the differentiation and evolution of anatomically modern humans

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  • Etienne Guichard
  • Valentina Peona
  • Guidantonio Malagoli Tagliazucchi
  • Lucia Abitante
  • Evelyn Jagoda
  • Margherita Musella
  • Marco Ricci
  • Alejandro Rubio-Roldan
  • Stefania Sarno
  • Donata Luiselli
  • Davide Pettener
  • Cristian Taccioli
  • Luca Pagani
  • Jose Luis Garcia-Perez
  • Alessio Boattini

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    Rights statement: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Original languageEnglish
Article number28
Number of pages19
JournalMobile DNA
Volume9
DOIs
Publication statusPublished - 15 Aug 2018

Abstract

Background: Transposable elements are biologically important components of eukaryote genomes. In particular, non-LTR retrotransposons (N-LTRrs) played a key role in shaping the human genome throughout evolution. In this study, we compared retrotransposon insertions differentially present in the genomes of Anatomically Modern Humans, Neanderthals, Denisovans and Chimpanzees, in order to assess the possible impact of retrotransposition in the differentiation of the human lineage.

Results: We first identified species-specific N-LTRrs and established their distribution in present day human populations. These analyses shortlisted a group of N-LTRr insertions that were found exclusively in Anatomically Modern Humans. These insertions are associated with an increase in the number of transcriptional/splicing variants of those genes they inserted in. The analysis of the functionality of genes containing human-specific N-LTRr insertions reflects changes that occurred during human evolution. In particular, the expression of genes containing the most recent N-LTRr insertions is enriched in the brain, especially in undifferentiated neurons, and these genes associate in networks related to neuron maturation and migration. Additionally, we identified candidate N-LTRr insertions that have likely produced new functional variants exclusive to modern humans, whose genomic loci show traces of positive selection.

Conclusions: Our results strongly suggest that N-LTRr impacted our differentiation as a species, most likely inducing an increase in neural complexity, and have been a constant source of genomic variability all throughout the evolution of the human lineage.

    Research areas

  • Non-LTR retrotranspososons, Human evolution, Ancient genomes, Chimpanzees, Generation of variability, Functional analyses, EMBRYONIC STEM-CELLS, TRANSPOSABLE ELEMENTS, L1 RETROTRANSPOSITION, GENOME EVOLUTION, HUMAN BRAIN, SOMATIC RETROTRANSPOSITION, REGULATORY NETWORKS, CARCINOMA-CELLS, SEQUENCE, PROMOTER

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