The role of retrotransposons in gene family expansions: insights from the mouse Abp gene family

Persistent Link:
http://hdl.handle.net/10150/610385
Title:
The role of retrotransposons in gene family expansions: insights from the mouse Abp gene family
Author:
Janousek, Vaclav; Karn, Robert; Laukaitis, Christina
Affiliation:
Department of Zoology, Faculty of Science, Charles University in Prague, Viničná 7, Prague 128 43, Czech Republic; Department of Medicine, College of Medicine, University of Arizona, Tucson, AZ, USA
Issue Date:
2013
Publisher:
BioMed Central
Citation:
Janoušek et al. BMC Evolutionary Biology 2013, 13:107 http://www.biomedcentral.com/1471-2148/13/107
Journal:
BMC Evolutionary Biology
Rights:
© 2013 Janoušek et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND:Retrotransposons have been suggested to provide a substrate for non-allelic homologous recombination (NAHR) and thereby promote gene family expansion. Their precise role, however, is controversial. Here we ask whether retrotransposons contributed to the recent expansions of the Androgen-binding protein (Abp) gene families that occurred independently in the mouse and rat genomes.RESULTS:Using dot plot analysis, we found that the most recent duplication in the Abp region of the mouse genome is flanked by L1Md_T elements. Analysis of the sequence of these elements revealed breakpoints that are the relicts of the recombination that caused the duplication, confirming that the duplication arose as a result of NAHR using L1 elements as substrates. L1 and ERVII retrotransposons are considerably denser in the Abp regions than in one Mb flanking regions, while other repeat types are depleted in the Abp regions compared to flanking regions. L1 retrotransposons preferentially accumulated in the Abp gene regions after lineage separation and roughly followed the pattern of Abp gene expansion. By contrast, the proportion of shared vs. lineage-specific ERVII repeats in the Abp region resembles the rest of the genome.CONCLUSIONS:We confirmed the role of L1 repeats in Abp gene duplication with the identification of recombinant L1Md_T elements at the edges of the most recent mouse Abp gene duplication. High densities of L1 and ERVII repeats were found in the Abp gene region with abrupt transitions at the region boundaries, suggesting that their higher densities are tightly associated with Abp gene duplication. We observed that the major accumulation of L1 elements occurred after the split of the mouse and rat lineages and that there is a striking overlap between the timing of L1 accumulation and expansion of the Abp gene family in the mouse genome. Establishing a link between the accumulation of L1 elements and the expansion of the Abp gene family and identification of an NAHR-related breakpoint in the most recent duplication are the main contributions of our study.
EISSN:
1471-2148
DOI:
10.1186/1471-2148-13-107
Keywords:
House mouse; Gene duplication; Androgen-binding protein; LINE1; ERVII; NAHR
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2148/13/107

Full metadata record

DC FieldValue Language
dc.contributor.authorJanousek, Vaclaven
dc.contributor.authorKarn, Roberten
dc.contributor.authorLaukaitis, Christinaen
dc.date.accessioned2016-05-20T09:05:37Z-
dc.date.available2016-05-20T09:05:37Z-
dc.date.issued2013en
dc.identifier.citationJanoušek et al. BMC Evolutionary Biology 2013, 13:107 http://www.biomedcentral.com/1471-2148/13/107en
dc.identifier.doi10.1186/1471-2148-13-107en
dc.identifier.urihttp://hdl.handle.net/10150/610385-
dc.description.abstractBACKGROUND:Retrotransposons have been suggested to provide a substrate for non-allelic homologous recombination (NAHR) and thereby promote gene family expansion. Their precise role, however, is controversial. Here we ask whether retrotransposons contributed to the recent expansions of the Androgen-binding protein (Abp) gene families that occurred independently in the mouse and rat genomes.RESULTS:Using dot plot analysis, we found that the most recent duplication in the Abp region of the mouse genome is flanked by L1Md_T elements. Analysis of the sequence of these elements revealed breakpoints that are the relicts of the recombination that caused the duplication, confirming that the duplication arose as a result of NAHR using L1 elements as substrates. L1 and ERVII retrotransposons are considerably denser in the Abp regions than in one Mb flanking regions, while other repeat types are depleted in the Abp regions compared to flanking regions. L1 retrotransposons preferentially accumulated in the Abp gene regions after lineage separation and roughly followed the pattern of Abp gene expansion. By contrast, the proportion of shared vs. lineage-specific ERVII repeats in the Abp region resembles the rest of the genome.CONCLUSIONS:We confirmed the role of L1 repeats in Abp gene duplication with the identification of recombinant L1Md_T elements at the edges of the most recent mouse Abp gene duplication. High densities of L1 and ERVII repeats were found in the Abp gene region with abrupt transitions at the region boundaries, suggesting that their higher densities are tightly associated with Abp gene duplication. We observed that the major accumulation of L1 elements occurred after the split of the mouse and rat lineages and that there is a striking overlap between the timing of L1 accumulation and expansion of the Abp gene family in the mouse genome. Establishing a link between the accumulation of L1 elements and the expansion of the Abp gene family and identification of an NAHR-related breakpoint in the most recent duplication are the main contributions of our study.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2148/13/107en
dc.rights© 2013 Janoušek et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.subjectHouse mouseen
dc.subjectGene duplicationen
dc.subjectAndrogen-binding proteinen
dc.subjectLINE1en
dc.subjectERVIIen
dc.subjectNAHRen
dc.titleThe role of retrotransposons in gene family expansions: insights from the mouse Abp gene familyen
dc.typeArticleen
dc.identifier.eissn1471-2148en
dc.contributor.departmentDepartment of Zoology, Faculty of Science, Charles University in Prague, Viničná 7, Prague 128 43, Czech Republicen
dc.contributor.departmentDepartment of Medicine, College of Medicine, University of Arizona, Tucson, AZ, USAen
dc.identifier.journalBMC Evolutionary Biologyen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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