Modeling the asymmetric evolution of a mouse and rat-specific microRNA gene cluster intron 10 of the Sfmbt2 gene

BMC Genomics

Research Article

Frans C Schuit¹  Stefan Lehnert¹  Vladimir Kapitonov²  Pushpike J Thilakarathne³ 

[1] Gene Expression Unit, Department of Molecular Cell Biology, Katholieke Universiteit Leuven, Belgium;Genetic Information Research Institute, 1925 Landings Dr, 94043, Mountain View, CA, USA;Interuniversity Institute for Biostatistics and statistical Bioinformatics, Katholieke Universiteit Leuven, Belgium, and Universiteit Hasselt, Kapucijnenvoer 35, Blok D, bus 7001, B3000, Leuven, Belgium;

关键词: microRNA;    miRNA;    simple repeat;    SINE B1F3;    evolution;    gene conversion;   

DOI  :  10.1186/1471-2164-12-257

 received in 2010-12-23, accepted in 2011-05-23,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundThe total number of miRNA genes in a genome, expression of which is responsible for the miRNA repertoire of an organism, is not precisely known. Moreover, the question of how new miRNA genes arise during evolution is incompletely understood. Recent data in humans and opossum indicate that retrotranspons of the class of short interspersed nuclear elements have contributed to the growth of microRNA gene clusters.MethodWe studied a large miRNA gene cluster in intron 10 of the mouse Sfmbt2 gene using bioinformatic tools.ResultsMice and rats are unique to harbor a 55-65 Kb DNA sequence in intron 10 of the Sfmbt2 gene. This intronic region is rich in regularly repeated B1 retrotransposons together with inverted self-complementary CA/TG microsatellites. The smallest repeats unit, called MSHORT1 in the mouse, was duplicated 9 times in a tandem head-to-tail array to form 2.5 Kb MLONG1 units. The center of the mouse miRNA gene cluster consists of 13 copies of MLONG1. BLAST analysis of MSHORT1 in the mouse shows that the repeat unit is unique for intron 10 of the Sfmbt2 gene and suggest a dual phase model for growth of the miRNA gene cluster: arrangment of 10 MSHORT1 units into MLONG1 and further duplication of 13 head-to-tail MLONG1 units in the center of the miRNA gene cluster. Rats have a similar arrangment of repeat units in intron 10 of the Sfmbt2 gene. The discrepancy between 65 miRNA genes in the mouse cluster as compared to only 1 miRNA gene in the corresponding rat repeat cluster is ascribed to sequence differences between MSHORT1 and RSHORT1 that result in lateral-shifted, less-stable miRNA precursor hairpins for RSHORT1.ConclusionOur data provides new evidence for the emerging concept that lineage-specific retroposons have played an important role in the birth of new miRNA genes during evolution. The large difference in the number of miRNA genes in two closely related species (65 versus 1, mice versus rats) indicates that this species-specific evolution can be a rapid process.

【 授权许可】

Unknown   
© Lehnert et al; licensee BioMed Central Ltd. 2011. This article is published under license to 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), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.