title: Ribosomal RNA Genes Contribute to the Formation of Pseudogenes and Junk DNA in the Human Genome.
abstract: Approximately 35% of the human genome can be identified as sequence devoid of a selected-effect function, and not derived from transposable elements or repeated sequences. We provide evidence supporting a known origin for a fraction of this sequence. We show that: 1) highly degraded, but near full length, ribosomal DNA (rDNA) units, including both 45S and Intergenic Spacer (IGS), can be found at multiple sites in the human genome on chromosomes without rDNA arrays, 2) that these rDNA sequences have a propensity for being centromere proximal, and 3) that sequence at all human functional rDNA array ends is divergent from canonical rDNA to the point that it is pseudogenic. We also show that small sequence strings of rDNA (from 45S + IGS) can be found distributed throughout the genome and are identifiable as an "rDNA-like signal", representing 0.26% of the q-arm of HSA21 and ∼2% of the total sequence of other regions tested. The size of sequence strings found in the rDNA-like signal intergrade into the size of sequence strings that make up the full-length degrading rDNA units found scattered throughout the genome. We conclude that the displaced and degrading rDNA sequences are likely of a similar origin but represent different stages in their evolution towards random sequence. Collectively, our data suggests that over vast evolutionary time, rDNA arrays contribute to the production of junk DNA. The concept that the production of rDNA pseudogenes is a by-product of concerted evolution represents a previously under-appreciated process; we demonstrate here its importance.
authors.affiliation: Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada.
authors.forename: Brent M
authors.initials: BM
authors.lastname: Robicheau
authors.affiliation: Center for Comparative Genomics and Evolutionary Bioinformatics, Department of Mathematics and Statistics, Dalhousie University, Halifax, Nova Scotia, Canada.
authors.forename: Edward
authors.initials: E
authors.lastname: Susko
authors.affiliation: Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada.
authors.forename: Amye M
authors.initials: AM
authors.lastname: Harrigan
authors.affiliation: Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada.
authors.forename: Marlene
authors.initials: M
authors.lastname: Snyder
mesh_terms: D000818:Animals; D021901:DNA, Intergenic / Q000235:genetics*; D019143:Evolution, Molecular; D016678:Genome; D006801:Humans; D051379:Mice; D011544:Pseudogenes; D012335:RNA, Ribosomal / Q000235:genetics*
chemical_list: D021901:DNA, Intergenic; D012335:RNA, Ribosomal
keywords: concerted evolution; degraded rDNA; genome evolution; vestigial centromere