geno5mC: A Database to Explore the Association between Genetic Variation (SNPs) and CpG Methylation in the Human Genome

C Gómez-Martín; E Aparicio-Puerta; J M Medina; Guillermo Barturen; J L Oliver; M Hackenberg

doi:10.1016/j.jmb.2020.11.008

geno⁵mC: A Database to Explore the Association between Genetic Variation (SNPs) and CpG Methylation in the Human Genome

J Mol Biol. 2021 May 28;433(11):166709. doi: 10.1016/j.jmb.2020.11.008. Epub 2020 Nov 12.

Authors

C Gómez-Martín¹, E Aparicio-Puerta², J M Medina¹, Guillermo Barturen³, J L Oliver¹, M Hackenberg⁴

Affiliations

¹ Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain; Lab. de Bioinformática, Instituto de Biotecnología, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain.
² Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain; Lab. de Bioinformática, Instituto de Biotecnología, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain; Instituto de Investigación Biosanitaria (IBS) Granada, University Hospitals of Granada-University, Granada, Spain, Conocimiento s/n, 18100 Granada, Spain; Excellence Research Unit "Modeling Nature" (MNat), University of Granada, 18071 Granada, Spain.
³ Centro Pfizer-Universidad de Granada-Junta de Andalucía de Genómica e Investigación Oncológica, Genetics of Complex Diseases, 18016 Granada, Spain.
⁴ Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071 Granada, Spain; Lab. de Bioinformática, Instituto de Biotecnología, Centro de Investigación Biomédica, PTS, Avda. del Conocimiento s/n, 18100 Granada, Spain; Instituto de Investigación Biosanitaria (IBS) Granada, University Hospitals of Granada-University, Granada, Spain, Conocimiento s/n, 18100 Granada, Spain; Excellence Research Unit "Modeling Nature" (MNat), University of Granada, 18071 Granada, Spain. Electronic address: hackenberg@ugr.es.

PMID: 33188782
DOI: 10.1016/j.jmb.2020.11.008

Abstract

Genetic variation, gene expression and DNA methylation influence each other in a complex way. To study the impact of sequence variation and DNA methylation on gene expression, we generated geno⁵mC, a database that contains statistically significant SNP-CpG associations that are biologically classified either through co-localization with known regulatory regions (promoters and enhancers), or through known correlations with the expression levels of nearby genes. The SNP rs727563 can be used to illustrate the usefulness of this approach. This SNP has been associated with inflammatory bowel disease through GWAS, but it is not located near any gene related to this phenotype. However, geno⁵mC reveals that rs727563 is associated with the methylation state of several CpGs located in promoter regions of genes reported to be involved in inflammatory processes. This case exemplifies how geno⁵mC can be used to infer relevant and previously unknown interactions between described disease-associated SNPs and their functional targets.

Keywords: DNA methylation; SNPs; gene regulation.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

CpG Islands / genetics*
DNA Methylation / genetics*
Databases, Genetic*
Genome, Human*
Humans
Inflammatory Bowel Diseases / genetics
Polymorphism, Single Nucleotide / genetics*
Promoter Regions, Genetic
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