Retrotransposition of gene transcripts leads to structural variation in mammalian genomes

Ewing, Adam D., Ballinger, Tracy J., Earl, Dent, Harris, Christopher C., Ding, Li, Wilson, Richard K. and Haussler, David (2013) Retrotransposition of gene transcripts leads to structural variation in mammalian genomes. Genome Biology, 14 3: . doi:10.1186/gb-2013-14-3-r22

Author Ewing, Adam D.
Ballinger, Tracy J.
Earl, Dent
Harris, Christopher C.
Ding, Li
Wilson, Richard K.
Haussler, David
Title Retrotransposition of gene transcripts leads to structural variation in mammalian genomes
Journal name Genome Biology   Check publisher's open access policy
ISSN 1474-760X
Publication date 2013-03
Year available 2013
Sub-type Article (original research)
DOI 10.1186/gb-2013-14-3-r22
Open Access Status DOI
Volume 14
Issue 3
Total pages 14
Place of publication London, United Kingdom
Publisher BioMed Central
Language eng
Subject 1311 Genetics
1307 Cell Biology
1105 Dentistry
Formatted abstract
Retroposed processed gene transcripts are an important source of material for new gene formation on evolutionary timescales. Most prior work on gene retrocopy discovery compared copies in reference genome assemblies to their source genes. Here, we explore gene retrocopy insertion polymorphisms (GRIPs) that are present in the germlines of individual humans, mice, and chimpanzees, and we identify novel gene retrocopy insertions in cancerous somatic tissues that are absent from patient-matched non-cancer genomes.

Through analysis of whole-genome sequence data, we found evidence for 48 GRIPs in the genomes of one or more humans sequenced as part of the 1,000 Genomes Project and The Cancer Genome Atlas, but which were not in the human reference assembly. Similarly, we found evidence for 755 GRIPs at distinct locations in one or more of 17 inbred mouse strains but which were not in the mouse reference assembly, and 19 GRIPs across a cohort of 10 chimpanzee genomes, which were not in the chimpanzee reference genome assembly. Many of these insertions are new members of existing gene families whose source genes are highly and widely expressed, and the majority have detectable hallmarks of processed gene retrocopy formation. We estimate the rate of novel gene retrocopy insertions in humans and chimps at roughly one new gene retrocopy insertion for every 6,000 individuals.

We find that gene retrocopy polymorphisms are a widespread phenomenon, present a multi-species analysis of these events, and provide a method for their ascertainment.
Q-Index Code C1
Q-Index Status Provisional Code
Institutional Status Non-UQ

Document type: Journal Article
Sub-type: Article (original research)
Collection: Mater Research Institute-UQ (MRI-UQ)
Version Filter Type
Citation counts: TR Web of Science Citation Count  Cited 26 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 25 times in Scopus Article | Citations
Google Scholar Search Google Scholar
Created: Fri, 12 Dec 2014, 19:19:50 EST by System User on behalf of Mater Research Institute-UQ