Clustering, duplication and chromosomal distribution of mouse SINE retrotransposons.
We analyzed potential mechanisms determining chromosomal distributions of the mouse B1 and B2 non-LTR retrotransposons, also known as SINE elements. We report that young B1 and B2 SINEs are underrepresented on chromosome X relative to autosomes, which is consistent with their integration in male germ lines. As the age of the SINE elements progresses, their densities on chromosome X increase relative to autosomal densities, possibly due to differences in ectopic recombination rates between chromosome X and autosomes. Furthermore, unlike young human Alus that tend to be integrated outside Alu-dense regions, young B1 and B2 elements are found mostly in SINE-rich clusters. The B1- or B2-rich clusters are more likely to contain duplicated elements than B1- or B2-poor chromosomal regions. We also present evidence indicating potential association of B1 and B2 elements with intra-chromosomal segmental duplications. No such association was found with inter-chromosomal duplications. We propose that the accumulation of mouse SINE elements observed in GC-rich regions may be due to the excess of DNA duplications over deletions in gene-rich regions that tend to be GC rich.
Jurka
J
J
Genetic Information Research Institute, Mountain View, CA 94043, USA. jurka@girinst.org
Kohany
O
O
Pavlicek
A
A
Kapitonov
V V
VV
Jurka
M V
MV
D000818:Animals; D002874:Chromosome Mapping; D020440:Gene Duplication; D016678:Genome; D051379:Mice; D008957:Models, Genetic; D005810:Multigene Family; D018626:Retroelements; D020086:Short Interspersed Nucleotide Elements; D020079:Terminal Repeat Sequences
D018626:Retroelements