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Allele-specific transcription factor binding to common and rare variants associated with disease and gene expression.

Cavalli M, Pan G, Nord H, Wallerman O, Wallén Arzt E, Berggren O, Elvers I, Eloranta ML, Rönnblom L, Lindblad Toh K, Wadelius C - Hum. Genet. (2016)

Bottom Line: We found 9962 candidate regulatory SNPs, of which 16 % were rare and showed evidence of larger functional effect than common ones.Functionally rare variants may explain divergent GWAS results between populations and are candidates for a partial explanation of the missing heritability.Furthermore, by examining GWAS loci we found >400 allele-specific candidate SNPs, 141 of which were highly relevant in our cell types.

View Article: PubMed Central - PubMed

Affiliation: Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.

ABSTRACT
Genome-wide association studies (GWAS) have identified a large number of disease-associated SNPs, but in few cases the functional variant and the gene it controls have been identified. To systematically identify candidate regulatory variants, we sequenced ENCODE cell lines and used public ChIP-seq data to look for transcription factors binding preferentially to one allele. We found 9962 candidate regulatory SNPs, of which 16 % were rare and showed evidence of larger functional effect than common ones. Functionally rare variants may explain divergent GWAS results between populations and are candidates for a partial explanation of the missing heritability. The majority of allele-specific variants (96 %) were specific to a cell type. Furthermore, by examining GWAS loci we found >400 allele-specific candidate SNPs, 141 of which were highly relevant in our cell types. Functionally validated SNPs support identification of an SNP in SYNGR1 which may expose to the risk of rheumatoid arthritis and primary biliary cirrhosis, as well as an SNP in the last intron of COG6 exposing to the risk of psoriasis. We propose that by repeating the ChIP-seq experiments of 20 selected transcription factors in three to ten people, the most common polymorphisms can be interrogated for allele-specific binding. Our strategy may help to remove the current bottleneck in functional annotation of the genome.

No MeSH data available.


Related in: MedlinePlus

Functional effects of AS-SNPs in primary B cells. a Stimulation of B cells with the oligonucleotide ODN2216 increases the expression of TF EBF1. bTop rs909685 is a GWAS-SNP with AS behavior detected by EBF1 ChIP-seq reads. rs909685 is in LD with the eQTL SNP rs2069235 which is associated with the expression of the SYNGR1 gene. BottomSYNGR1 expression in an individual homozygous for the A- or T-allele, respectively, at rs909685, unstimulated (blue) or stimulated with ODN2216 (yellow). Middle motif for PITX3 at rs909685 which alters the TF-binding motif. cTop AS-SNP rs9603612 is located in an intron of COG6 and is in LD with the GWAS-SNP rs7993214. rs9603612 showed AS behavior with EBF1 ChIP-seq reads covering the SNP with significant difference. Bottom expression of COG6 in an individual homozygous for the C- and G-alleles, respectively, of rs9603612, unstimulated (blue) or stimulated with ODN2216 (yellow). Middle motif for CREB1 at rs9603612 which alters the TF-binding motif
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Fig4: Functional effects of AS-SNPs in primary B cells. a Stimulation of B cells with the oligonucleotide ODN2216 increases the expression of TF EBF1. bTop rs909685 is a GWAS-SNP with AS behavior detected by EBF1 ChIP-seq reads. rs909685 is in LD with the eQTL SNP rs2069235 which is associated with the expression of the SYNGR1 gene. BottomSYNGR1 expression in an individual homozygous for the A- or T-allele, respectively, at rs909685, unstimulated (blue) or stimulated with ODN2216 (yellow). Middle motif for PITX3 at rs909685 which alters the TF-binding motif. cTop AS-SNP rs9603612 is located in an intron of COG6 and is in LD with the GWAS-SNP rs7993214. rs9603612 showed AS behavior with EBF1 ChIP-seq reads covering the SNP with significant difference. Bottom expression of COG6 in an individual homozygous for the C- and G-alleles, respectively, of rs9603612, unstimulated (blue) or stimulated with ODN2216 (yellow). Middle motif for CREB1 at rs9603612 which alters the TF-binding motif

Mentions: Recently, rs909685 was associated with rheumatoid (Okada et al. 2014) and primary biliary cirrhosis (Liu et al. 2012). The eSNP rs2069235 is in high LD with the GWAS/AS-SNP rs909685 and associated with the expression of SYNGR1, coding for a membrane protein associated with presynaptic vesicles in neuronal cells and also expressed in B- and other immune cells. To validate the results from GM12878, we purified B cells from blood donors who had been genotyped using a 200 K ImmunoChip. The cells were either treated with medium only (mock) or stimulated with the oligonucleotide ODN2216 (see “Materials and methods”), which activated the TF EBF1 (Fig. 4a). ChIP-seq has shown that EBF1 binds to the regulatory element that harbors the GWAS/AS-SNP rs909685. B cells from donors who are homozygous, AA or TT for the alleles, respectively, at this locus showed significant difference in activity of SYNGR1 (Fig. 4b, lower panel). Stimulation with ODN2216, which increases the levels of EBF1, significantly decreased the expression of SYNGR1 for both genotypes (Fig. 4b, lower panel). rs909685 disrupts the motif for PITX3 which is known to interact with NURR1, a factor involved in the regulation of cortisol which suggests a link to inflammatory processes (Mages et al. 1994). This indicates that SYNGR1 is controlled by the regulatory element with the AS-SNP rs909685 giving an allelic difference in expression at basal conditions and that EBF1 acts as a repressor to decrease the expression from both alleles. Furthermore, it suggests that differential expression of SYNGR1 could mediate the genetic predisposition to rheumatoid arthritis and primary biliary cirrhosis at this locus.Fig. 4


Allele-specific transcription factor binding to common and rare variants associated with disease and gene expression.

Cavalli M, Pan G, Nord H, Wallerman O, Wallén Arzt E, Berggren O, Elvers I, Eloranta ML, Rönnblom L, Lindblad Toh K, Wadelius C - Hum. Genet. (2016)

Functional effects of AS-SNPs in primary B cells. a Stimulation of B cells with the oligonucleotide ODN2216 increases the expression of TF EBF1. bTop rs909685 is a GWAS-SNP with AS behavior detected by EBF1 ChIP-seq reads. rs909685 is in LD with the eQTL SNP rs2069235 which is associated with the expression of the SYNGR1 gene. BottomSYNGR1 expression in an individual homozygous for the A- or T-allele, respectively, at rs909685, unstimulated (blue) or stimulated with ODN2216 (yellow). Middle motif for PITX3 at rs909685 which alters the TF-binding motif. cTop AS-SNP rs9603612 is located in an intron of COG6 and is in LD with the GWAS-SNP rs7993214. rs9603612 showed AS behavior with EBF1 ChIP-seq reads covering the SNP with significant difference. Bottom expression of COG6 in an individual homozygous for the C- and G-alleles, respectively, of rs9603612, unstimulated (blue) or stimulated with ODN2216 (yellow). Middle motif for CREB1 at rs9603612 which alters the TF-binding motif
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Related In: Results  -  Collection

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Fig4: Functional effects of AS-SNPs in primary B cells. a Stimulation of B cells with the oligonucleotide ODN2216 increases the expression of TF EBF1. bTop rs909685 is a GWAS-SNP with AS behavior detected by EBF1 ChIP-seq reads. rs909685 is in LD with the eQTL SNP rs2069235 which is associated with the expression of the SYNGR1 gene. BottomSYNGR1 expression in an individual homozygous for the A- or T-allele, respectively, at rs909685, unstimulated (blue) or stimulated with ODN2216 (yellow). Middle motif for PITX3 at rs909685 which alters the TF-binding motif. cTop AS-SNP rs9603612 is located in an intron of COG6 and is in LD with the GWAS-SNP rs7993214. rs9603612 showed AS behavior with EBF1 ChIP-seq reads covering the SNP with significant difference. Bottom expression of COG6 in an individual homozygous for the C- and G-alleles, respectively, of rs9603612, unstimulated (blue) or stimulated with ODN2216 (yellow). Middle motif for CREB1 at rs9603612 which alters the TF-binding motif
Mentions: Recently, rs909685 was associated with rheumatoid (Okada et al. 2014) and primary biliary cirrhosis (Liu et al. 2012). The eSNP rs2069235 is in high LD with the GWAS/AS-SNP rs909685 and associated with the expression of SYNGR1, coding for a membrane protein associated with presynaptic vesicles in neuronal cells and also expressed in B- and other immune cells. To validate the results from GM12878, we purified B cells from blood donors who had been genotyped using a 200 K ImmunoChip. The cells were either treated with medium only (mock) or stimulated with the oligonucleotide ODN2216 (see “Materials and methods”), which activated the TF EBF1 (Fig. 4a). ChIP-seq has shown that EBF1 binds to the regulatory element that harbors the GWAS/AS-SNP rs909685. B cells from donors who are homozygous, AA or TT for the alleles, respectively, at this locus showed significant difference in activity of SYNGR1 (Fig. 4b, lower panel). Stimulation with ODN2216, which increases the levels of EBF1, significantly decreased the expression of SYNGR1 for both genotypes (Fig. 4b, lower panel). rs909685 disrupts the motif for PITX3 which is known to interact with NURR1, a factor involved in the regulation of cortisol which suggests a link to inflammatory processes (Mages et al. 1994). This indicates that SYNGR1 is controlled by the regulatory element with the AS-SNP rs909685 giving an allelic difference in expression at basal conditions and that EBF1 acts as a repressor to decrease the expression from both alleles. Furthermore, it suggests that differential expression of SYNGR1 could mediate the genetic predisposition to rheumatoid arthritis and primary biliary cirrhosis at this locus.Fig. 4

Bottom Line: We found 9962 candidate regulatory SNPs, of which 16 % were rare and showed evidence of larger functional effect than common ones.Functionally rare variants may explain divergent GWAS results between populations and are candidates for a partial explanation of the missing heritability.Furthermore, by examining GWAS loci we found >400 allele-specific candidate SNPs, 141 of which were highly relevant in our cell types.

View Article: PubMed Central - PubMed

Affiliation: Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.

ABSTRACT
Genome-wide association studies (GWAS) have identified a large number of disease-associated SNPs, but in few cases the functional variant and the gene it controls have been identified. To systematically identify candidate regulatory variants, we sequenced ENCODE cell lines and used public ChIP-seq data to look for transcription factors binding preferentially to one allele. We found 9962 candidate regulatory SNPs, of which 16 % were rare and showed evidence of larger functional effect than common ones. Functionally rare variants may explain divergent GWAS results between populations and are candidates for a partial explanation of the missing heritability. The majority of allele-specific variants (96 %) were specific to a cell type. Furthermore, by examining GWAS loci we found >400 allele-specific candidate SNPs, 141 of which were highly relevant in our cell types. Functionally validated SNPs support identification of an SNP in SYNGR1 which may expose to the risk of rheumatoid arthritis and primary biliary cirrhosis, as well as an SNP in the last intron of COG6 exposing to the risk of psoriasis. We propose that by repeating the ChIP-seq experiments of 20 selected transcription factors in three to ten people, the most common polymorphisms can be interrogated for allele-specific binding. Our strategy may help to remove the current bottleneck in functional annotation of the genome.

No MeSH data available.


Related in: MedlinePlus