Pericentromeric Duplications in the Laboratory Mouse

Abstract

Duplications have long been postulated to be an important mechanism by which genomes evolve. Interspecies genomic comparisons are one method by which the origin and molecular mechanism of duplications can be inferred. By comparative mapping in human, mouse, and rat, we previously found evidence for a recent chromosome-fission event that occurred in the mouse lineage. Cytogenetic mapping revealed that the genomic segments flanking the fission site appeared to be duplicated, with copies residing near the centromere of multiple mouse chromosomes. Here we report the mapping and sequencing of the regions of mouse chromosomes 5 and 6 involved in this chromosome-fission event as well as the results of comparative sequence analysis with the orthologous human and rat genomic regions. Our data indicate that the duplications associated with mouse chromosomes 5 and 6 are recent and that the resulting duplicated segments share significant sequence similarity with a series of regions near the centromeres of the mouse chromosomes previously identified by cytogenetic mapping. We also identified pericentromeric duplicated segments shared between mouse chromosomes 5 and 1. Finally, novel mouse satellite sequences as well as putative chimeric transcripts were found to be associated with the duplicated segments. Together, these findings demonstrate that pericentromeric duplications are not restricted to primates and may be a common mechanism for genome evolution in mammals.

Human, Mouse, and Rat Genome Large-Scale Rearrangements: Stability Versus Speciation

“…This indicates that the centromeric regions of mouse chromosomes are very active for interchromosomal rearrangements, consistent with a study reporting that numerous Robertsonian fusions have resulted in six distinct chromosomal races (e.g., 2N = 20, 2N = 22, etc., instead of the normal 2N = 40) in the wild populations of M. musculus found in Maderia (BrittonDavidian et al 2000). The M5/M6 fission was previously identified by cytogenetic studies; recent duplications associated with this event were found in the pericentromeric regions of multiple mouse chromosomes, and two novel mouse satellite repeats were identified Thomas et al 2003a). To determine whether other fissions in Table 3 also involve such duplications and repeats, we performed a preliminary study of the sequences flanking these breakpoints in each lineage.…”

“…Except for the gene phosphatidylserine decarboxylase (encoded in 30 Mb of H22) that is partially duplicated in M11 (tip), M17 (6Mb), and M5 (31Mb) (the gene is partial in M11 and M17, but complete in M5), as well as the gene Notch3 (encoded in 15 Mb of H19) that is partially duplicated in M10 (78 Mb, partial) and M17 (31.8 Mb,complete), no other significant duplications were found. The 27-bp novel mouse satellites described by Thomas et al (2003a) have been identified in a tandem, head-to-tail fashion in the chromosomal tip of M17 (52 copies at 3.06 Mb and 103 copies at 3.07 Mb), M2 (15 copies at 3 Mb), and M4 (57 copies at 3.35 Mb). The 36-bp satellites are less frequent; beside what have been described by Thomas et al (2003a), no significant amounts were found in other places, except 13 copies at M4 3.27 Mb and five copies at M7 3.06 Mb.…”

“…The 27-bp novel mouse satellites described by Thomas et al (2003a) have been identified in a tandem, head-to-tail fashion in the chromosomal tip of M17 (52 copies at 3.06 Mb and 103 copies at 3.07 Mb), M2 (15 copies at 3 Mb), and M4 (57 copies at 3.35 Mb). The 36-bp satellites are less frequent; beside what have been described by Thomas et al (2003a), no significant amounts were found in other places, except 13 copies at M4 3.27 Mb and five copies at M7 3.06 Mb.…”

The Rice Nuclear Genome Continuously Integrates, Shuffles, and Eliminates the Chloroplast Genome to Cause Chloroplast–Nuclear DNA Flux

“…A 620-kb mitochondrial DNA insertion was observed in the pericentromeric region of Arabidopsis thaliana chromosome 2 (Stupar et al, 2001). Furthermore, the pericentromeric regions of mammalian genomes contain large segments of interchromosomal duplications (International Human Genome Sequencing Consortium, 2001;Bailey et al, 2002;Thomas et al, 2003). Incorporation of large DNA fragments into the pericentromeric region may be a strategy of genomic evolution conserved between plants and animals.…”

Chromosome Evolution in Cyperales

“…These insights include the number and location of genes involved in the differences between species (Bernacchi and Tanksley 1997; Bradshaw et al 1998;Westerbergh and Doebley 2002), the number and interactions of genes involved in reproductive isolation (Rieseberg et al 1996;Wu and Hollocher 1998), and synteny between diverse genera that reveals a surprising amount of structural conservation (Tanksley et al 1988(Tanksley et al , 1992Paterson et al 1996;Gale and Devos 1998;Ku et al 2000). Extending this research to chromosomal structural changes represents one aspect of genomics that can be considered in its infancy (Nadeau and Snakoff 1998;Paterson et al 2000;Song et al 2001), but is providing tantalizing insights into the link between genome structural evolution and genome function (The Rice Chromosome 10 Sequencing Consortium 2003; Thomas et al 2003). Applying a genomics approach to chromosome changes will provide an avenue to test new models for reproductive isolation arising from genic factors associated with karyotypic alterations that Noor et al (2001) and Rieseberg (2001) have formulated.…”