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Allele-specific down-regulation of RPTOR expression induced by retinoids contributes to climate adaptations.

Sun C, Southard C, Witonsky DB, Kittler R, Di Rienzo A - PLoS Genet. (2010)

Bottom Line: The regulatory associated protein of MTOR encoded by the RPTOR gene is a key component of this pathway.A previous survey of candidate genes found that RPTOR contains multiple SNPs with strong correlations between allele frequencies and climate variables, consistent with the action of selective pressures that vary across environments.Our results show that signatures of genetic adaptations can identify variants with functional effects, consistent with the idea that selection signals may be used for SNP annotation.

View Article: PubMed Central - PubMed

Affiliation: Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

ABSTRACT
The mechanistic target of rapamycin (MTOR) pathway regulates cell growth, energy homeostasis, apoptosis, and immune response. The regulatory associated protein of MTOR encoded by the RPTOR gene is a key component of this pathway. A previous survey of candidate genes found that RPTOR contains multiple SNPs with strong correlations between allele frequencies and climate variables, consistent with the action of selective pressures that vary across environments. Using data from a recent genome scan for selection signals, we honed in on a SNP (rs11868112) 26 kb upstream to the transcription start site of RPTOR that exhibits the strongest association with temperature variables. Transcription factor motif scanning and mining of recently mapped transcription factor binding sites identified a binding site for POU class 2 homeobox 1 (POU2F1) spanning the SNP and an adjacent retinoid acid receptor (RAR) binding site. Using expression quantification, chromatin immunoprecipitation (ChIP), and reporter gene assays, we demonstrate that POU2F1 and RARA do bind upstream of the RPTOR gene to regulate its expression in response to retinoids; this regulation is affected by the allele status at rs11868112 with the derived allele resulting in lower expression levels. We propose a model in which the derived allele influences thermogenesis or immune response by altering MTOR pathway activity and thereby increasing fitness in colder climates. Our results show that signatures of genetic adaptations can identify variants with functional effects, consistent with the idea that selection signals may be used for SNP annotation.

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Enrichment of the region nearby rs11868112 in Anti-RAR ChIPed DNA relative to rabbit IgG ChIPed after AM580 and DMSO treatment.In HepG2 (A) and MCF-7 (B). Each bar indicates the average of three real time PCR technical replicates normalized by the input DNA and the error bar denotes standard deviation.
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pgen-1001178-g004: Enrichment of the region nearby rs11868112 in Anti-RAR ChIPed DNA relative to rabbit IgG ChIPed after AM580 and DMSO treatment.In HepG2 (A) and MCF-7 (B). Each bar indicates the average of three real time PCR technical replicates normalized by the input DNA and the error bar denotes standard deviation.

Mentions: To investigate the role of SNP rs11868112 in the regulation of RPTOR expression, we performed ChIP assays followed by quantitative PCR to determine whether RARA and/or POU2F1 bind the DNA near the SNP. First, we treated HepG2 and MCF-7 cells with AM580 and DSMO and performed a ChIP with antibodies against RARA followed by real time PCR quantification of the region spanning the RARA binding site detected by ChIP-chip [26]. We found a significant enrichment (P<0.02) of the putative RARA binding region for the chromatin immunoprecipitated DNA with the RARA antibody (Figure 4A and 4B), which confirms RARA binding to the region near rs11868112. This enrichment was observed in both DMSO and AM580 treated cells (Figure 4A and 4B), which is consistent with the model for the genomic actions of retinoic acid receptors [38].


Allele-specific down-regulation of RPTOR expression induced by retinoids contributes to climate adaptations.

Sun C, Southard C, Witonsky DB, Kittler R, Di Rienzo A - PLoS Genet. (2010)

Enrichment of the region nearby rs11868112 in Anti-RAR ChIPed DNA relative to rabbit IgG ChIPed after AM580 and DMSO treatment.In HepG2 (A) and MCF-7 (B). Each bar indicates the average of three real time PCR technical replicates normalized by the input DNA and the error bar denotes standard deviation.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2965758&req=5

pgen-1001178-g004: Enrichment of the region nearby rs11868112 in Anti-RAR ChIPed DNA relative to rabbit IgG ChIPed after AM580 and DMSO treatment.In HepG2 (A) and MCF-7 (B). Each bar indicates the average of three real time PCR technical replicates normalized by the input DNA and the error bar denotes standard deviation.
Mentions: To investigate the role of SNP rs11868112 in the regulation of RPTOR expression, we performed ChIP assays followed by quantitative PCR to determine whether RARA and/or POU2F1 bind the DNA near the SNP. First, we treated HepG2 and MCF-7 cells with AM580 and DSMO and performed a ChIP with antibodies against RARA followed by real time PCR quantification of the region spanning the RARA binding site detected by ChIP-chip [26]. We found a significant enrichment (P<0.02) of the putative RARA binding region for the chromatin immunoprecipitated DNA with the RARA antibody (Figure 4A and 4B), which confirms RARA binding to the region near rs11868112. This enrichment was observed in both DMSO and AM580 treated cells (Figure 4A and 4B), which is consistent with the model for the genomic actions of retinoic acid receptors [38].

Bottom Line: The regulatory associated protein of MTOR encoded by the RPTOR gene is a key component of this pathway.A previous survey of candidate genes found that RPTOR contains multiple SNPs with strong correlations between allele frequencies and climate variables, consistent with the action of selective pressures that vary across environments.Our results show that signatures of genetic adaptations can identify variants with functional effects, consistent with the idea that selection signals may be used for SNP annotation.

View Article: PubMed Central - PubMed

Affiliation: Department of Human Genetics, University of Chicago, Chicago, Illinois, United States of America.

ABSTRACT
The mechanistic target of rapamycin (MTOR) pathway regulates cell growth, energy homeostasis, apoptosis, and immune response. The regulatory associated protein of MTOR encoded by the RPTOR gene is a key component of this pathway. A previous survey of candidate genes found that RPTOR contains multiple SNPs with strong correlations between allele frequencies and climate variables, consistent with the action of selective pressures that vary across environments. Using data from a recent genome scan for selection signals, we honed in on a SNP (rs11868112) 26 kb upstream to the transcription start site of RPTOR that exhibits the strongest association with temperature variables. Transcription factor motif scanning and mining of recently mapped transcription factor binding sites identified a binding site for POU class 2 homeobox 1 (POU2F1) spanning the SNP and an adjacent retinoid acid receptor (RAR) binding site. Using expression quantification, chromatin immunoprecipitation (ChIP), and reporter gene assays, we demonstrate that POU2F1 and RARA do bind upstream of the RPTOR gene to regulate its expression in response to retinoids; this regulation is affected by the allele status at rs11868112 with the derived allele resulting in lower expression levels. We propose a model in which the derived allele influences thermogenesis or immune response by altering MTOR pathway activity and thereby increasing fitness in colder climates. Our results show that signatures of genetic adaptations can identify variants with functional effects, consistent with the idea that selection signals may be used for SNP annotation.

Show MeSH