ArticlePLoS genetics2006
Genomic selective constraints in murid noncoding DNA.
Article in PLoS genetics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed.
- The position of the longest intron is related to biological functions in some human genes.Frontiers in genetics · 2022Article
- Insights Into the Molecular Evolution of AT-Hook Motif Nuclear Localization Genes inFrontiers in plant science · 2021Article
- Intron and gene size expansion during nervous system evolution.BMC genomics · 2020Article
- Drosophila Interspecific Hybridization Causes A Deregulation of the piRNA Pathway Genes.Genes · 2020Article
- Repeat associated mechanisms of genome evolution and function revealed by theGenome research · 2018Article
- Architecture and Distribution of Introns in Core Genes of FourG3 (Bethesda, Md.) · 2017Article
- Temperature-Related Reaction Norms of Gene Expression: Regulatory Architecture and Functional Implications.Molecular biology and evolution · 2015Article
- Using genomics to characterize evolutionary potential for conservation of wild populations.Evolutionary applications · 2014Article
- Natural selection on coding and noncoding DNA sequences is associated with virulence genes in a plant pathogenic fungus.Genome biology and evolution · 2014Article
- Transcription factor binding to Caenorhabditis elegans first introns reveals lack of redundancy with gene promoters.Nucleic acids research · 2014Article
- Article
- Association of intron loss with high mutation rate in Arabidopsis: implications for genome size evolution.Genome biology and evolution · 2013Article
- Dissecting the regulatory architecture of gene expression QTLs.Genome biology · 2012Article
- The evolution of intron size in amniotes: a role for powered flight?Genome biology and evolution · 2012Article
- A selection index for gene expression evolution and its application to the divergence between humans and chimpanzees.PloS one · 2012Article
- Methods to detect selection on noncoding DNA.Methods in molecular biology (Clifton, N.J.) · 2012Review
- Comparative analysis of teleost genome sequences reveals an ancient intron size expansion in the zebrafish lineage.Genome biology and evolution · 2011Article
- Long- and short-term selective forces on malaria parasite genomes.PLoS genetics · 2010Article
- In plants, expression breadth and expression level distinctly and non-linearly correlate with gene structure.Biology direct · 2009Article
- An overview of the introns-first theory.Journal of molecular evolution · 2009Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent work has suggested that there are many more selectively constrained, functional noncoding than coding sites in mammalian genomes. However, little is known about how selective constraint varies amongst different classes of noncoding DNA. We estimated the magnitude of selective constraint on a large dataset of mouse-rat gene orthologs and their surrounding noncoding DNA. Our analysis indicates that there are more than three times as many selectively constrained, nonrepetitive sites within noncoding DNA as in coding DNA in murids. The majority of these constrained noncoding sites appear to be located within intergenic regions, at distances greater than 5 kilobases from known genes. Our study also shows that in murids, intron length and mean intronic selective constraint are negatively correlated with intron ordinal number. Our results therefore suggest that functional intronic sites tend to accumulate toward the 5' end of murid genes. Our analysis also reveals that mean number of selectively constrained noncoding sites varies substantially with the function of the adjacent gene. We find that, among others, developmental and neuronal genes are associated with the greatest numbers of putatively functional noncoding sites compared with genes involved in electron transport and a variety of metabolic processes. Combining our estimates of the total number of constrained coding and noncoding bases we calculate that over twice as many deleterious mutations have occurred in intergenic regions as in known genic sequence and that the total genomic deleterious point mutation rate is 0.91 per diploid genome, per generation. This estimated rate is over twice as large as a previous estimate in murids.
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