Orangutan Alu quiescence reveals possible source element: support for ancient backseat drivers

Jerilyn A Walker,Brygg Ullmer,Miriam K Konkel,Christopher P Monceaux,Robert Hubley,Oliver A Ryder,Mark A Batzer,Arian Fa Smit

doi:10.1186/1759-8753-3-8

Abstract

BackgroundSequence analysis of the orangutan genome revealed that recent proliferative activity of Alu elements has been uncharacteristically quiescent in the Pongo (orangutan) lineage, compared with all previously studied primate genomes. With relatively few young polymorphic insertions, the genomic landscape of the orangutan seemed like the ideal place to search for a driver, or source element, of Alu retrotransposition.ResultsHere we report the identification of a nearly pristine insertion possessing all the known putative hallmarks of a retrotranspositionally competent Alu element. It is located in an intronic sequence of the DGKB gene on chromosome 7 and is highly conserved in Hominidae (the great apes), but absent from Hylobatidae (gibbon and siamang). We provide evidence for the evolution of a lineage-specific subfamily of this shared Alu insertion in orangutans and possibly the lineage leading to humans. In the orangutan genome, this insertion contains three orangutan-specific diagnostic mutations which are characteristic of the youngest polymorphic Alu subfamily, AluYe5b5_Pongo. In the Homininae lineage (human, chimpanzee and gorilla), this insertion has acquired three different mutations which are also found in a single human-specific Alu insertion.ConclusionsThis seemingly stealth-like amplification, ongoing at a very low rate over millions of years of evolution, suggests that this shared insertion may represent an ancient backseat driver of Alu element expansion.

Highlights

Sequence analysis of the orangutan genome revealed that recent proliferative activity of Alu elements has been uncharacteristically quiescent in the Pongo lineage, compared with all previously studied primate genomes
Using the University of California Santa Cruz (UCSC) Genome Browser [18,19], it became evident that this insertion was not a recent event overlooked by our previous analyses, but was shared by the human and chimpanzee genomes, while absent from the rhesus macaque genome
This locus had been computationally filtered from our previous study of young orangutan-specific Alu insertions because it was present in the human genome

Summary

Introduction

Sequence analysis of the orangutan genome revealed that recent proliferative activity of Alu elements has been uncharacteristically quiescent in the Pongo (orangutan) lineage, compared with all previously studied primate genomes. With relatively few young polymorphic insertions, the genomic landscape of the orangutan seemed like the ideal place to search for a driver, or source element, of Alu retrotransposition. The amplification of Alu elements has been ongoing in primate genomes for about 65 million years [1,2]. They typically mobilize via a ‘copy and paste’ mechanism through an RNA intermediate, a process termed targetprimed reverse transcription (TPRT) [3]. Alu elements accumulate in an ‘identical by descent’ manner. This offspring element [4]. In the case of the orangutan, the landscape of relatively young elements is quite sparse [9]

Objectives

Methods

Results

Discussion

Conclusion