title: Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes.
abstract: The rates at which human genomic DNA changes by neutral substitution and insertion of certain families of transposable elements covary in large, megabase-sized segments. We used the rat, mouse, and human genomic DNA sequences to examine these processes in more detail in comparisons over both shorter (rat-mouse) and longer (rodent-primate) times, and demonstrated the generality of the covariation. Different families of transposable elements show distinctive insertion preferences and patterns of variation with substitution rates. SINEs are more abundant in GC-rich DNA, but the regional GC preference for insertion (monitored in young SINEs) differs between rodents and humans. In contrast, insertions in the rodent genomes are predominantly LINEs, which prefer to insert into AT-rich DNA in all three mammals. The insertion frequency of repeats other than SINEs correlates strongly positively with the frequency of substitutions in all species. However, correlations with SINEs show the opposite effects. The correlations are explained only in part by the GC content, indicating that other factors also contribute to the inherent tendency of DNA segments to change over evolutionary time.
authors.affiliation: Department of Biochemistry and Molecular Biology, Center for Comparative Genomics and Bioinformatics, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
authors.forename: Shan
authors.initials: S
authors.lastname: Yang
authors.forename: Arian F
authors.initials: AF
authors.lastname: Smit
authors.forename: Scott
authors.initials: S
authors.lastname: Schwartz
authors.forename: Francesca
authors.initials: F
authors.lastname: Chiaromonte
authors.forename: Krishna M
authors.initials: KM
authors.lastname: Roskin
authors.forename: David
authors.initials: D
authors.lastname: Haussler
authors.forename: Webb
authors.initials: W
authors.lastname: Miller
authors.forename: Ross C
authors.initials: RC
authors.lastname: Hardison
mesh_terms: D000818:Animals; D019295:Computational Biology / Q000379:methods / Q000706:statistics & numerical data; D004251:DNA Transposable Elements / Q000235:genetics; D019143:Evolution, Molecular; D020862:GC Rich Sequence / Q000235:genetics; D014644:Genetic Variation / Q000235:genetics*; D016678:Genome; D015894:Genome, Human; D006801:Humans; D020084:Long Interspersed Nucleotide Elements / Q000235:genetics; D051379:Mice; D016254:Mutagenesis, Insertional / Q000235:genetics*; D051381:Rats; D016415:Sequence Alignment / Q000379:methods / Q000706:statistics & numerical data; D020086:Short Interspersed Nucleotide Elements / Q000235:genetics; D013045:Species Specificity
chemical_list: D004251:DNA Transposable Elements