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PLoS One. 2014 Oct 28;9(10):e109186. doi: 10.1371/journal.pone.0109186. eCollection 2014.

Longevity and plasticity of CFTR provide an argument for noncanonical SNP organization in hominid DNA.

Author information

1
Department of Computer and Information Sciences, University of Alabama at Birmingham, Birmingham, Alabama, United States of America.
2
Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America.
3
Department of Biostatistics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America.
4
Department of Computer and Information Sciences, University of Alabama at Birmingham, Birmingham, Alabama, United States of America; Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America.
5
Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America.
6
Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America; Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, United States of America.

Abstract

Like many other ancient genes, the cystic fibrosis transmembrane conductance regulator (CFTR) has survived for hundreds of millions of years. In this report, we consider whether such prodigious longevity of an individual gene--as opposed to an entire genome or species--should be considered surprising in the face of eons of relentless DNA replication errors, mutagenesis, and other causes of sequence polymorphism. The conventions that modern human SNP patterns result either from purifying selection or random (neutral) drift were not well supported, since extant models account rather poorly for the known plasticity and function (or the established SNP distributions) found in a multitude of genes such as CFTR. Instead, our analysis can be taken as a polemic indicating that SNPs in CFTR and many other mammalian genes may have been generated--and continue to accrue--in a fundamentally more organized manner than would otherwise have been expected. The resulting viewpoint contradicts earlier claims of 'directional' or 'intelligent design-type' SNP formation, and has important implications regarding the pace of DNA adaptation, the genesis of conserved non-coding DNA, and the extent to which eukaryotic SNP formation should be viewed as adaptive.

PMID:
25350658
PMCID:
PMC4211684
DOI:
10.1371/journal.pone.0109186
[Indexed for MEDLINE]
Free PMC Article

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