ArticleProceedings of the National Academy of Sciences of the United States of America2001
Association between divergence and interspersed repeats in mammalian noncoding genomic DNA.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2001. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- The role of 3D genome organization in disease: From compartments to single nucleotides.Seminars in cell & developmental biology · 2019Review
- The effects of chromatin organization on variation in mutation rates in the genome.Nature reviews. Genetics · 2015Review
- A genome-wide view of mutation rate co-variation using multivariate analyses.Genome biology · 2011Article
- Structural and functional divergence of a 1-Mb duplicated region in the soybean (Glycine max) genome and comparison to an orthologous region from Phaseolus vulgaris.The Plant cell · 2010Article
- Conservation of human microsatellites across 450 million years of evolution.Genome biology and evolution · 2010Article
- Evolution of transcription factor binding sites in mammalian gene regulatory regions: handling counterintuitive results.Journal of molecular evolution · 2009Article
- Human-macaque comparisons illuminate variation in neutral substitution rates.Genome biology · 2008Article
- Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans.PLoS biology · 2007Article
- A survey of genomic properties for the detection of regulatory polymorphisms.PLoS computational biology · 2007Article
- Early history of mammals is elucidated with the ENCODE multiple species sequencing data.PLoS genetics · 2007Article
- Article
- A third approach to gene prediction suggests thousands of additional human transcribed regions.PLoS computational biology · 2006Article
- Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns.Genome biology · 2006Article
- Long homopurine*homopyrimidine sequences are characteristic of genes expressed in brain and the pseudoautosomal region.Nucleic acids research · 2006Article
- Organization of the MASP2 locus and its expression profile in mouse and rat.Mammalian genome : official journal of the International Mammalian Genome Society · 2004Article
- Patterns of insertions and their covariation with substitutions in the rat, mouse, and human genomes.Genome research · 2004Article
- Comparative analysis of vertebrate dystrophin loci indicate intron gigantism as a common feature.Genome research · 2003Article
- Analysis of primate genomic variation reveals a repeat-driven expansion of the human genome.Genome research · 2003Article
- Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution.Genome research · 2003Article
- Mosaic organization of orthologous sequences in grass genomes.Genome research · 2002Article
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Authors and funding
6 authors.
Funding
Abstract
The amount of noncoding genomic DNA sequence that aligns between human and mouse varies substantially in different regions of their genomes, and the amount of repetitive DNA also varies. In this report, we show that divergence in noncoding nonrepetitive DNA is strongly correlated with the amount of repetitive DNA in a region. We investigated aligned DNA in four large genomic regions with finished human sequence and almost or completely finished mouse sequence. These regions, totaling 5.89 Mb of DNA, are on different chromosomes and vary in their base composition. An analysis based on sliding windows of 10 kb shows that the fraction of aligned noncoding nonrepetitive DNA and the fraction of repetitive DNA are negatively correlated, both at the level of an entire region and locally within it. This conclusion is strongly supported by a randomization study, in which repetitive elements are removed and randomly relocated along the sequences. Thus, regions of noncoding genomic DNA that accumulated fewer point mutations since the primate-rodent divergence also suffered fewer retrotransposition events. These results indicate that some regions of the genome are more "flexible" over the time scale of mammalian evolution, being able to accommodate many point mutations and insertions, whereas other regions are more "rigid" and accumulate fewer changes. Stronger conservation is generally interpreted as indicating more extensive or more important function. The evidence presented here of correlated variation in the rates of different evolutionary processes across noncoding DNA must be considered in assessing such conservation for evidence of selection.
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