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Polymorphism Analysis Reveals Reduced Negative Selection and Elevated Rate of Insertions and Deletions in Intrinsically Disordered Protein Regions.

Khan T, Douglas GM, Patel P, Nguyen Ba AN, Moses AM - Genome Biol Evol (2015)

Bottom Line: We also confirm previous findings that nonframeshifting indels are much more abundant in disordered regions relative to structured regions.We find that the rate of nonframeshifting indel polymorphism in intrinsically disordered regions resembles that of noncoding DNA and pseudogenes, and that large indels segregate in disordered regions in the human population.Our survey of polymorphism confirms patterns of evolution in disordered regions inferred based on longer evolutionary comparisons.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell & Systems Biology, University of Toronto, Ontario, Canada.

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— Polymorphism patterns and expression levels in yeast.(A) ThePa/Ps ratiodecreases for all three regions with increased protein expression levels.The difference in polymorphism ratio between the three regions remainsapproximately constant, independent of protein expression level. Disorderedregions (white) show higherPa/Ps ratiosacross the whole range of expression levels compared with Pfam domains(black) or other protein regions (white). Protein abundance estimates weremeasured in ppm (parts per million). (B) Similar resultsare found for the per gene estimates of thePa/Ps ratio.Error bars represent three times the standard error of the mean.
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evv105-F2: — Polymorphism patterns and expression levels in yeast.(A) ThePa/Ps ratiodecreases for all three regions with increased protein expression levels.The difference in polymorphism ratio between the three regions remainsapproximately constant, independent of protein expression level. Disorderedregions (white) show higherPa/Ps ratiosacross the whole range of expression levels compared with Pfam domains(black) or other protein regions (white). Protein abundance estimates weremeasured in ppm (parts per million). (B) Similar resultsare found for the per gene estimates of thePa/Ps ratio.Error bars represent three times the standard error of the mean.

Mentions: Yeast protein expression levels were obtained from PaxDB (Wang et al. 2012). Proteins were binned by proteinexpression levels and Pa/Psratios were calculated as above. Polymorphisms in proteins that had no expressioninformation were excluded from the analysis. P-value for the figure 2 was determined usingt-approximation for the distribution of the correlationcoefficient. A total of 96,373 yeast SNPs were found in the regions of interest andmore than 95% of yeast genes with SNPs had protein expression data from PaxDB(http://pax-db.org/#!species/4932, lastaccessed April 14, 2010). Fig. 1.


Polymorphism Analysis Reveals Reduced Negative Selection and Elevated Rate of Insertions and Deletions in Intrinsically Disordered Protein Regions.

Khan T, Douglas GM, Patel P, Nguyen Ba AN, Moses AM - Genome Biol Evol (2015)

— Polymorphism patterns and expression levels in yeast.(A) ThePa/Ps ratiodecreases for all three regions with increased protein expression levels.The difference in polymorphism ratio between the three regions remainsapproximately constant, independent of protein expression level. Disorderedregions (white) show higherPa/Ps ratiosacross the whole range of expression levels compared with Pfam domains(black) or other protein regions (white). Protein abundance estimates weremeasured in ppm (parts per million). (B) Similar resultsare found for the per gene estimates of thePa/Ps ratio.Error bars represent three times the standard error of the mean.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4494057&req=5

evv105-F2: — Polymorphism patterns and expression levels in yeast.(A) ThePa/Ps ratiodecreases for all three regions with increased protein expression levels.The difference in polymorphism ratio between the three regions remainsapproximately constant, independent of protein expression level. Disorderedregions (white) show higherPa/Ps ratiosacross the whole range of expression levels compared with Pfam domains(black) or other protein regions (white). Protein abundance estimates weremeasured in ppm (parts per million). (B) Similar resultsare found for the per gene estimates of thePa/Ps ratio.Error bars represent three times the standard error of the mean.
Mentions: Yeast protein expression levels were obtained from PaxDB (Wang et al. 2012). Proteins were binned by proteinexpression levels and Pa/Psratios were calculated as above. Polymorphisms in proteins that had no expressioninformation were excluded from the analysis. P-value for the figure 2 was determined usingt-approximation for the distribution of the correlationcoefficient. A total of 96,373 yeast SNPs were found in the regions of interest andmore than 95% of yeast genes with SNPs had protein expression data from PaxDB(http://pax-db.org/#!species/4932, lastaccessed April 14, 2010). Fig. 1.

Bottom Line: We also confirm previous findings that nonframeshifting indels are much more abundant in disordered regions relative to structured regions.We find that the rate of nonframeshifting indel polymorphism in intrinsically disordered regions resembles that of noncoding DNA and pseudogenes, and that large indels segregate in disordered regions in the human population.Our survey of polymorphism confirms patterns of evolution in disordered regions inferred based on longer evolutionary comparisons.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell & Systems Biology, University of Toronto, Ontario, Canada.

Show MeSH