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Evolutionary patterns of DNA base composition and correlation to polymorphisms in DNA repair systems.

Li X, Scanlon MJ, Yu J - Nucleic Acids Res. (2015)

Bottom Line: Individuals in the derived groups show an A&T-increase/G&C-decrease pattern compared with the basal groups.For three DNA repair genes (BRIP1, PMS2P3 and TTDN), ENCODE data provided evidence for interaction between genomic regions containing these genes and regions containing the significant SNPs.Our findings provide insights into the mechanisms of genome evolution.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, Iowa State University, Ames, IA 50011, USA.

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Related in: MedlinePlus

First genome-wide scan with a mixed model to identify genomic regions underlying variation in base composition. The upper panel displays the genomic regions (1 Mb) with five or more TASs detected by the mixed model using genome-wide [A] as trait values of 1092 humans. The middle pane shows the association signals detected by the mixed model between the genome-wide [A] values across polymorphic sites and individual SNPs. The dashed line indicates the threshold determined by Bonferroni correction to control for false positives. The lower panel shows the position and pathway information of known genes (red bars) from different DNA repair mechanisms that are flagged by TASs. MMR, mismatch excision repair; NER, nucleotide excision repair; BER, base excision repair; and HR, homologous recombination.
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Figure 3: First genome-wide scan with a mixed model to identify genomic regions underlying variation in base composition. The upper panel displays the genomic regions (1 Mb) with five or more TASs detected by the mixed model using genome-wide [A] as trait values of 1092 humans. The middle pane shows the association signals detected by the mixed model between the genome-wide [A] values across polymorphic sites and individual SNPs. The dashed line indicates the threshold determined by Bonferroni correction to control for false positives. The lower panel shows the position and pathway information of known genes (red bars) from different DNA repair mechanisms that are flagged by TASs. MMR, mismatch excision repair; NER, nucleotide excision repair; BER, base excision repair; and HR, homologous recombination.

Mentions: Although complex evolutionary history is challenging to study and multiple factors are likely to be involved, it should not deter us from making attempts to identify potential genomic regions that drive the divergence in base composition in humans. With this in mind, we first conducted a genome-wide scan with a mixed model controlling for both population structure (fixed effect) and relatedness (random effect) following established methods (27,28) (Figure 3). In this analysis, individual SNPs were tested for association with the genome-wide [A] values while controlling the population structure and relatedness. Given the strong divergence of base composition and the control for population structure, this set of identified genomic regions is more likely to underlie within-population variation in base composition.


Evolutionary patterns of DNA base composition and correlation to polymorphisms in DNA repair systems.

Li X, Scanlon MJ, Yu J - Nucleic Acids Res. (2015)

First genome-wide scan with a mixed model to identify genomic regions underlying variation in base composition. The upper panel displays the genomic regions (1 Mb) with five or more TASs detected by the mixed model using genome-wide [A] as trait values of 1092 humans. The middle pane shows the association signals detected by the mixed model between the genome-wide [A] values across polymorphic sites and individual SNPs. The dashed line indicates the threshold determined by Bonferroni correction to control for false positives. The lower panel shows the position and pathway information of known genes (red bars) from different DNA repair mechanisms that are flagged by TASs. MMR, mismatch excision repair; NER, nucleotide excision repair; BER, base excision repair; and HR, homologous recombination.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4402523&req=5

Figure 3: First genome-wide scan with a mixed model to identify genomic regions underlying variation in base composition. The upper panel displays the genomic regions (1 Mb) with five or more TASs detected by the mixed model using genome-wide [A] as trait values of 1092 humans. The middle pane shows the association signals detected by the mixed model between the genome-wide [A] values across polymorphic sites and individual SNPs. The dashed line indicates the threshold determined by Bonferroni correction to control for false positives. The lower panel shows the position and pathway information of known genes (red bars) from different DNA repair mechanisms that are flagged by TASs. MMR, mismatch excision repair; NER, nucleotide excision repair; BER, base excision repair; and HR, homologous recombination.
Mentions: Although complex evolutionary history is challenging to study and multiple factors are likely to be involved, it should not deter us from making attempts to identify potential genomic regions that drive the divergence in base composition in humans. With this in mind, we first conducted a genome-wide scan with a mixed model controlling for both population structure (fixed effect) and relatedness (random effect) following established methods (27,28) (Figure 3). In this analysis, individual SNPs were tested for association with the genome-wide [A] values while controlling the population structure and relatedness. Given the strong divergence of base composition and the control for population structure, this set of identified genomic regions is more likely to underlie within-population variation in base composition.

Bottom Line: Individuals in the derived groups show an A&T-increase/G&C-decrease pattern compared with the basal groups.For three DNA repair genes (BRIP1, PMS2P3 and TTDN), ENCODE data provided evidence for interaction between genomic regions containing these genes and regions containing the significant SNPs.Our findings provide insights into the mechanisms of genome evolution.

View Article: PubMed Central - PubMed

Affiliation: Department of Agronomy, Iowa State University, Ames, IA 50011, USA.

Show MeSH
Related in: MedlinePlus