Identification of Functional SNPs in the 5-prime Flanking Sequences of Human Genes

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2005 Feb 19

PMID 15717931

Citations 16

Authors

Salim Mottagui-Tabar

Mohammad A Faghihi

Yosuke Mizuno

Par G Engstrom

Boris Lenhard

Wyeth W Wasserman

Claes Wahlestedt

Affiliations

Soon will be listed here.

Abstract

Background: Over 4 million single nucleotide polymorphisms (SNPs) are currently reported to exist within the human genome. Only a small fraction of these SNPs alter gene function or expression, and therefore might be associated with a cell phenotype. These functional SNPs are consequently important in understanding human health. Information related to functional SNPs in candidate disease genes is critical for cost effective genetic association studies, which attempt to understand the genetics of complex diseases like diabetes, Alzheimer's, etc. Robust methods for the identification of functional SNPs are therefore crucial. We report one such experimental approach.

Results: Sequence conserved between mouse and human genomes, within 5 kilobases of the 5-prime end of 176 GPCR genes, were screened for SNPs. Sequences flanking these SNPs were scored for transcription factor binding sites. Allelic pairs resulting in a significant score difference were predicted to influence the binding of transcription factors (TFs). Ten such SNPs were selected for mobility shift assays (EMSA), resulting in 7 of them exhibiting a reproducible shift. The full-length promoter regions with 4 of the 7 SNPs were cloned in a Luciferase based plasmid reporter system. Two out of the 4 SNPs exhibited differential promoter activity in several human cell lines.

Conclusions: We propose a method for effective selection of functional, regulatory SNPs that are located in evolutionary conserved 5-prime flanking regions (5'-FR) regions of human genes and influence the activity of the transcriptional regulatory region. Some SNPs behave differently in different cell types.

Citing Articles

The Role of Genetic Polymorphisms in Diabetic Retinopathy: Narrative Review.

Sienkiewicz-Szlapka E, Fiedorowicz E, Krol-Grzymala A, Kordulewska N, Rozmus D, Cieslinska A Int J Mol Sci. 2023; 24(21).

PMID: 37958858 PMC: 10650381. DOI: 10.3390/ijms242115865.

Genetic mutations in NF-κB pathway genes were associated with the protection from hepatitis C virus infection among Chinese Han population.

Yue M, Tian T, Wang C, Fan H, Wu J, Wang J Sci Rep. 2019; 9(1):10830.

PMID: 31346215 PMC: 6658546. DOI: 10.1038/s41598-019-47058-y.

Effects of gene polymorphisms in the endoplasmic reticulum stress pathway on clinical outcomes of chemoradiotherapy in Chinese patients with nasopharyngeal carcinoma.

Guo X, Ma W, Liu L, Huang Y, Wang J, Huang L Acta Pharmacol Sin. 2017; 38(4):571-580.

PMID: 28216622 PMC: 5386314. DOI: 10.1038/aps.2016.148.

Regulatory Single-Nucleotide Variant Predictor Increases Predictive Performance of Functional Regulatory Variants.

Peterson T, Mort M, Cooper D, Radivojac P, Kann M, Mooney S Hum Mutat. 2016; 37(11):1137-1143.

PMID: 27406314 PMC: 6192032. DOI: 10.1002/humu.23049.

A novel type 2 diabetes risk allele increases the promoter activity of the muscle-specific small ankyrin 1 gene.

Yan R, Lai S, Yang Y, Shi H, Cai Z, Sorrentino V Sci Rep. 2016; 6:25105.

PMID: 27121283 PMC: 4848520. DOI: 10.1038/srep25105.

References

Kent W . BLAT--the BLAST-like alignment tool. Genome Res. 2002; 12(4):656-64. PMC: 187518. DOI: 10.1101/gr.229202. View

Stormo G . DNA binding sites: representation and discovery. Bioinformatics. 2000; 16(1):16-23. DOI: 10.1093/bioinformatics/16.1.16. View

Lenhard B, Wasserman W . TFBS: Computational framework for transcription factor binding site analysis. Bioinformatics. 2002; 18(8):1135-6. DOI: 10.1093/bioinformatics/18.8.1135. View

Ramensky V, Bork P, Sunyaev S . Human non-synonymous SNPs: server and survey. Nucleic Acids Res. 2002; 30(17):3894-900. PMC: 137415. DOI: 10.1093/nar/gkf493. View

Okazaki Y, Furuno M, Kasukawa T, Adachi J, Bono H, Kondo S . Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature. 2002; 420(6915):563-73. DOI: 10.1038/nature01266. View

Karolchik D, Baertsch R, Diekhans M, Furey T, Hinrichs A, Lu Y . The UCSC Genome Browser Database. Nucleic Acids Res. 2003; 31(1):51-4. PMC: 165576. DOI: 10.1093/nar/gkg129. View

Ponomarenko J, Merkulova T, Orlova G, Fokin O, Gorshkova E, Frolov A . rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation. Nucleic Acids Res. 2003; 31(1):118-21. PMC: 165559. DOI: 10.1093/nar/gkg112. View

Schwartz S, Kent W, Smit A, Zhang Z, Baertsch R, Hardison R . Human-mouse alignments with BLASTZ. Genome Res. 2003; 13(1):103-7. PMC: 430961. DOI: 10.1101/gr.809403. View

Sandelin A, Alkema W, Engstrom P, Wasserman W, Lenhard B . JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 2003; 32(Database issue):D91-4. PMC: 308747. DOI: 10.1093/nar/gkh012. View

10.

Lenhard B, Sandelin A, Mendoza L, Engstrom P, Jareborg N, Wasserman W . Identification of conserved regulatory elements by comparative genome analysis. J Biol. 2003; 2(2):13. PMC: 193685. DOI: 10.1186/1475-4924-2-13. View

11.

Fickett J . Quantitative discrimination of MEF2 sites. Mol Cell Biol. 1996; 16(1):437-41. PMC: 231020. DOI: 10.1128/MCB.16.1.437. View

12.

Tronche F, Ringeisen F, BLUMENFELD M, Yaniv M, Pontoglio M . Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome. J Mol Biol. 1997; 266(2):231-45. DOI: 10.1006/jmbi.1996.0760. View

13.

Duret L, Bucher P . Searching for regulatory elements in human noncoding sequences. Curr Opin Struct Biol. 1997; 7(3):399-406. DOI: 10.1016/s0959-440x(97)80058-9. View

14.

Fickett J . Predictive methods using nucleotide sequences. Methods Biochem Anal. 1998; 39:231-45. DOI: 10.1002/9780470110607.ch10. View

15.

Workman C, Stormo G . ANN-Spec: a method for discovering transcription factor binding sites with improved specificity. Pac Symp Biocomput. 2000; :467-78. DOI: 10.1142/9789814447331_0044. View

16.

Muller G . Towards 3D structures of G protein-coupled receptors: a multidisciplinary approach. Curr Med Chem. 2000; 7(9):861-88. DOI: 10.2174/0929867003374534. View

17.

Sherry S, Ward M, Kholodov M, Baker J, Phan L, Smigielski E . dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2000; 29(1):308-11. PMC: 29783. DOI: 10.1093/nar/29.1.308. View

18.

Pennacchio L, Rubin E . Genomic strategies to identify mammalian regulatory sequences. Nat Rev Genet. 2001; 2(2):100-9. DOI: 10.1038/35052548. View

19.

Sunyaev S, Ramensky V, Koch I, Lathe 3rd W, Kondrashov A, Bork P . Prediction of deleterious human alleles. Hum Mol Genet. 2001; 10(6):591-7. DOI: 10.1093/hmg/10.6.591. View

20.

Chasman D, ADAMS R . Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: structure-based assessment of amino acid variation. J Mol Biol. 2001; 307(2):683-706. DOI: 10.1006/jmbi.2001.4510. View