A lead candidate functional single nucleotide polymorphism within the WARS2 gene associated with waist-hip-ratio does not alter RNA stability

Milan Mušo; Rebecca Dumbell; Sara Pulit; Nasa Sinnott-Armstrong; Samantha Laber; Louisa Zolkiewski; Liz Bentley; Melina Claussnitzer; Roger D Cox

doi:10.1016/j.bbagrm.2020.194640

A lead candidate functional single nucleotide polymorphism within the WARS2 gene associated with waist-hip-ratio does not alter RNA stability

Biochim Biophys Acta Gene Regul Mech. 2020 Nov;1863(11):194640. doi: 10.1016/j.bbagrm.2020.194640. Epub 2020 Sep 30.

Authors

Milan Mušo¹, Rebecca Dumbell¹, Sara Pulit², Nasa Sinnott-Armstrong³, Samantha Laber¹, Louisa Zolkiewski¹, Liz Bentley¹, Melina Claussnitzer⁴, Roger D Cox⁵

Affiliations

¹ MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK.
² Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands; Big Data Institute, Li Ka Shing Center for Health Information and Discovery, Oxford University, Oxford, UK; Program in Medical Population Genetics, Broad Institute, Cambridge, MA, USA.
³ The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
⁴ The Broad Institute of MIT and Harvard, Cambridge, MA, USA; Gerontology Division, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA; Institute of Nutritional Science, University of Hohenheim, Stuttgart, Germany.
⁵ MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire OX11 0RD, UK. Electronic address: r.cox@har.mrc.ac.uk.

Abstract

We have prioritised a single nucleotide polymorphism (SNP) rs2645294 as one candidate functional SNP in the TBX15-WARS2 waist-hip-ratio locus using posterior probability analysis. This SNP is located in the 3' untranslated region of the WARS2 (tryptophanyl tRNA synthetase 2, mitochondrial) gene with which it has an expression quantitative trait in subcutaneous white adipose tissue. We show that transcripts of the WARS2 gene in a human white adipose cell line, heterozygous for the rs2645294 SNP, showed allelic imbalance. We tested whether the rs2645294 SNP altered WARS2 RNA stability using three different methods: actinomycin-D inhibition and RNA decay, mature and nascent RNA analysis and luciferase reporter assays. We found no evidence of a difference in RNA stability between the rs2645294 alleles indicating that the allelic expression imbalance was likely due to transcriptional regulation.

Keywords: Adipose tissue; Allelic effect; EMSA; EQTL; GWAS; Luciferase assay; Nascent RNA; Posterior probability; RNA stability; RNA structure; RNA-binding protein; UTR region; Waist-to-hip ratio.

Publication types

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

MeSH terms

3' Untranslated Regions
Adipocytes, White / metabolism
Alleles
Cell Line, Tumor
Computational Biology / methods
Genes, Reporter
Genetic Association Studies*
Heterozygote
Humans
Nucleic Acid Conformation
Polymorphism, Single Nucleotide*
Quantitative Trait Loci
Quantitative Trait, Heritable*
RNA Stability
T-Box Domain Proteins / genetics*
Tryptophan-tRNA Ligase / genetics*
Waist-Hip Ratio

Substances

3' Untranslated Regions
T-Box Domain Proteins
TBX15 protein, human
Tryptophan-tRNA Ligase

Grants and funding

MC_U142661184/MRC_/Medical Research Council/United Kingdom