Abstract
BackgroundMammalian genomes are repositories of repetitive DNA sequences derived from transposable elements (TEs). Typically, TEs generate multiple, mostly inactive copies of themselves, commonly known as repetitive families or families of repeats. Recently, we proposed that families of TEs originate in small populations by genetic drift and that the origin of small subpopulations from larger populations can be fueled by biological innovations.ResultsWe report three distinct groups of repetitive families preserved in the human genome that expanded and declined during the three previously described periods of regulatory innovations in vertebrate genomes. The first group originated prior to the evolutionary separation of the mammalian and bird lineages and the second one during subsequent diversification of the mammalian lineages prior to the origin of eutherian lineages. The third group of families is primate-specific.ConclusionsThe observed correlation implies a relationship between regulatory innovations and the origin of repetitive families. Consistent with our previous hypothesis, it is proposed that regulatory innovations fueled the origin of new subpopulations in which new repetitive families became fixed by genetic drift.ReviewersEugene Koonin, I. King Jordan, Jürgen Brosius.
Highlights
Mammalian genomes are repositories of repetitive DNA sequences derived from transposable elements (TEs)
We report an additional 152 families of conserved repetitive elements (Additional file 1: Table S1, column F; consensus sequences to be released in Repbase), which were identified and reconstructed using the human genome sequence data
Using binomial and chi square statistics we identified 266 families that are significantly overrepresented in the conserved regions relative to the rest of the human genome, which are hereafter referred to as families of “conserved repeats”
Summary
Mammalian genomes are repositories of repetitive DNA sequences derived from transposable elements (TEs). Some TEs remain active for a limited period of time during which they produce mostly inactive copies of themselves known as families of interspersed repetitive elements, or repeats. The overall number of repetitive elements in the conserved genomic regions, relative to the total number of repeats in the entire genome, is expected to grow over time, primarily due to attrition of the repetitive DNA that didn’t assume any functional role in the genome. We use this process to identify ancient repetitive families of different age
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