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Quadruplex-single nucleotide polymorphisms (Quad-SNP) influence gene expression difference among individuals.

Baral A, Kumar P, Halder R, Mani P, Yadav VK, Singh A, Das SK, Chowdhury S - Nucleic Acids Res. (2012)

Bottom Line: Findings reveal significant association between quadruplex-SNPs and expression of the corresponding gene in individuals (P < 0.0001).The quadruplex motif, and not the disrupted-motif, enhanced transcription in human cell lines of different origin.Together, these findings build direct support for quadruplex-mediated transcription and suggest quadruplex-SNPs may play significant role in mechanistically understanding variations in gene expression among individuals.

View Article: PubMed Central - PubMed

Affiliation: Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India.

ABSTRACT
Non-canonical guanine quadruplex structures are not only predominant but also conserved among bacterial and mammalian promoters. Moreover recent findings directly implicate quadruplex structures in transcription. These argue for an intrinsic role of the structural motif and thereby posit that single nucleotide polymorphisms (SNP) that compromise the quadruplex architecture could influence function. To test this, we analysed SNPs within quadruplex motifs (Quad-SNP) and gene expression in 270 individuals across four populations (HapMap) representing more than 14,500 genotypes. Findings reveal significant association between quadruplex-SNPs and expression of the corresponding gene in individuals (P < 0.0001). Furthermore, analysis of Quad-SNPs obtained from population-scale sequencing of 1000 human genomes showed relative selection bias against alteration of the structural motif. To directly test the quadruplex-SNP-transcription connection, we constructed a reporter system using the RPS3 promoter-remarkable difference in promoter activity in the 'quadruplex-destabilized' versus 'quadruplex-intact' promoter was noticed. As a further test, we incorporated a quadruplex motif or its disrupted counterpart within a synthetic promoter reporter construct. The quadruplex motif, and not the disrupted-motif, enhanced transcription in human cell lines of different origin. Together, these findings build direct support for quadruplex-mediated transcription and suggest quadruplex-SNPs may play significant role in mechanistically understanding variations in gene expression among individuals.

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Promoter G-quadruplex motifs maintain the ancestral (chimpanzee) form. (A and B) Individual allele frequencies of Quad-SNP in the four HapMap populations—bar graph shows frequency of ancestral (chimpanzee) and derived allele for each SNP within a population (A) along with respective fractions of Quad-SNP that were either maintained with ancestral as major allele or flipped to the derived allele (B). (C) Categorization of stem/loop Quad-SNP with low (0–0.1), moderate (>0.1–0.5) or high (>0.5) derived allele frequencies shows stem SNP are significantly over-represented in the low category.
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gkr1258-F2: Promoter G-quadruplex motifs maintain the ancestral (chimpanzee) form. (A and B) Individual allele frequencies of Quad-SNP in the four HapMap populations—bar graph shows frequency of ancestral (chimpanzee) and derived allele for each SNP within a population (A) along with respective fractions of Quad-SNP that were either maintained with ancestral as major allele or flipped to the derived allele (B). (C) Categorization of stem/loop Quad-SNP with low (0–0.1), moderate (>0.1–0.5) or high (>0.5) derived allele frequencies shows stem SNP are significantly over-represented in the low category.

Mentions: Given the prevalence of PG4 motifs near promoters in addition to multiple studies showing role of the quadruplex motif in gene expression (12,13,17,19,20) we next analysed the region within 1 kb of transcription start sites (TSS) in 18 056 unique human promoters. We found 1184 validated Quad-SNP (see ‘Methods’ section) in this region (note: only 54 Quad-SNP that were significantly associated with gene expression as reported in (35) were analysed in the previous sections). Out of 1184, we first used 237 Quad-SNP, where both allele frequency and ancestral allele data were available for all four populations, for further study (‘Methods’ section). Figure 2A depicts the genotype frequency of Quad-SNPs in each population where each row represents a bar graph showing ancestral/derived allele frequency for a given SNP. In line with our earlier observation using 54 Quad-SNP, here we found that in 195 out of 237 (82.2%) ancestral allele was the common or major allele whereas in only 42 (17.7%) flipping was observed. The fraction of ancestral versus derived alleles in each population further confirmed the finding that ancestral alleles were mostly maintained among Quad-SNP (Figure 2B).Figure 2.


Quadruplex-single nucleotide polymorphisms (Quad-SNP) influence gene expression difference among individuals.

Baral A, Kumar P, Halder R, Mani P, Yadav VK, Singh A, Das SK, Chowdhury S - Nucleic Acids Res. (2012)

Promoter G-quadruplex motifs maintain the ancestral (chimpanzee) form. (A and B) Individual allele frequencies of Quad-SNP in the four HapMap populations—bar graph shows frequency of ancestral (chimpanzee) and derived allele for each SNP within a population (A) along with respective fractions of Quad-SNP that were either maintained with ancestral as major allele or flipped to the derived allele (B). (C) Categorization of stem/loop Quad-SNP with low (0–0.1), moderate (>0.1–0.5) or high (>0.5) derived allele frequencies shows stem SNP are significantly over-represented in the low category.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3351168&req=5

gkr1258-F2: Promoter G-quadruplex motifs maintain the ancestral (chimpanzee) form. (A and B) Individual allele frequencies of Quad-SNP in the four HapMap populations—bar graph shows frequency of ancestral (chimpanzee) and derived allele for each SNP within a population (A) along with respective fractions of Quad-SNP that were either maintained with ancestral as major allele or flipped to the derived allele (B). (C) Categorization of stem/loop Quad-SNP with low (0–0.1), moderate (>0.1–0.5) or high (>0.5) derived allele frequencies shows stem SNP are significantly over-represented in the low category.
Mentions: Given the prevalence of PG4 motifs near promoters in addition to multiple studies showing role of the quadruplex motif in gene expression (12,13,17,19,20) we next analysed the region within 1 kb of transcription start sites (TSS) in 18 056 unique human promoters. We found 1184 validated Quad-SNP (see ‘Methods’ section) in this region (note: only 54 Quad-SNP that were significantly associated with gene expression as reported in (35) were analysed in the previous sections). Out of 1184, we first used 237 Quad-SNP, where both allele frequency and ancestral allele data were available for all four populations, for further study (‘Methods’ section). Figure 2A depicts the genotype frequency of Quad-SNPs in each population where each row represents a bar graph showing ancestral/derived allele frequency for a given SNP. In line with our earlier observation using 54 Quad-SNP, here we found that in 195 out of 237 (82.2%) ancestral allele was the common or major allele whereas in only 42 (17.7%) flipping was observed. The fraction of ancestral versus derived alleles in each population further confirmed the finding that ancestral alleles were mostly maintained among Quad-SNP (Figure 2B).Figure 2.

Bottom Line: Findings reveal significant association between quadruplex-SNPs and expression of the corresponding gene in individuals (P < 0.0001).The quadruplex motif, and not the disrupted-motif, enhanced transcription in human cell lines of different origin.Together, these findings build direct support for quadruplex-mediated transcription and suggest quadruplex-SNPs may play significant role in mechanistically understanding variations in gene expression among individuals.

View Article: PubMed Central - PubMed

Affiliation: Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India.

ABSTRACT
Non-canonical guanine quadruplex structures are not only predominant but also conserved among bacterial and mammalian promoters. Moreover recent findings directly implicate quadruplex structures in transcription. These argue for an intrinsic role of the structural motif and thereby posit that single nucleotide polymorphisms (SNP) that compromise the quadruplex architecture could influence function. To test this, we analysed SNPs within quadruplex motifs (Quad-SNP) and gene expression in 270 individuals across four populations (HapMap) representing more than 14,500 genotypes. Findings reveal significant association between quadruplex-SNPs and expression of the corresponding gene in individuals (P < 0.0001). Furthermore, analysis of Quad-SNPs obtained from population-scale sequencing of 1000 human genomes showed relative selection bias against alteration of the structural motif. To directly test the quadruplex-SNP-transcription connection, we constructed a reporter system using the RPS3 promoter-remarkable difference in promoter activity in the 'quadruplex-destabilized' versus 'quadruplex-intact' promoter was noticed. As a further test, we incorporated a quadruplex motif or its disrupted counterpart within a synthetic promoter reporter construct. The quadruplex motif, and not the disrupted-motif, enhanced transcription in human cell lines of different origin. Together, these findings build direct support for quadruplex-mediated transcription and suggest quadruplex-SNPs may play significant role in mechanistically understanding variations in gene expression among individuals.

Show MeSH