Related Experiment Videos
Sporadic amplification of ID elements in rodents
D H Kass1, J Kim, P L Deininger
1Department of Biochemistry and Molecular Biology, Louisiana State University Medical Center, New Orleans 70112, USA.
Journal of Molecular Evolution
|January 1, 1996
Summary
Short interspersed elements (SINEs) like ID sequences show sporadic amplification across rodent genomes, varying greatly between species. This study investigates the copy number variations and potential drivers of ID element amplification in rodents.
Area of Science:
- Genomics
- Molecular Evolution
- Comparative Genomics
Background:
- ID sequences are a family of short interspersed elements (SINEs) found in the rodent genome.
- The copy number of individual ID elements varies significantly, up to three orders of magnitude, across different rodent species.
- This amplification pattern appears sporadic and does not correlate with established phylogenetic relationships within the order Rodentia.
Purpose of the Study:
- To quantify the copy number of ID elements in various rodent species.
- To investigate the evolutionary dynamics and potential mechanisms driving the observed variations in ID element amplification.
- To explore the role of BC1 genes in the amplification process.
Main Methods:
- Library screening and dot-blot analysis were employed to estimate ID element copy numbers.
- Sequence analysis of cloned ID elements was performed, particularly within the genus Peromyscus.
- Comparative sequence analysis of BC1 genes across different rodent species was conducted.
Main Results:
- ID element copy numbers varied widely, with estimates including 25,000 in deer mice, 1,500 in gerbils, 60,000 in squirrels, 150,000 in rats, 4,000 in mice, 1,000 in hamsters, and 200 in guinea pigs and nutrias.
- Rapid amplification events were identified after the divergence of rat and mouse, and also after the split of deer mouse and hamster lineages.
- No significant sequence variations in BC1 genes were found to explain the broad amplification differences, although species-group-specific variations in the ID core sequence of the BC1 gene were noted within Peromyscus.
Conclusions:
- The amplification of ID elements in rodents is a dynamic and sporadic process, not strictly following phylogenetic lines.
- BC1 genes are implicated as master genes in ID amplification, as suggested by sequence consensus between gerbil and deer mouse ID elements.
- Further research is needed to fully elucidate the mechanisms responsible for the substantial quantitative variations in ID element copy numbers across rodent species.