Functional Analysis of SNPs in the Regulation of CARM1 Expression and Plasma Homocysteine Levels
Background—Hyperhomocysteinemia is a risk factor for cardiovascular disease. Coactivator- associated arginine methyltransferase 1 (CARM1) participates in the synthesis of homocysteine, but whether the genetic variations regulate CARM1 expression and homocysteine levels remains unknown.
Methods and Results—Functional analyses combined with an association study were conducted to identify the causal variant for CARM1 expression and homocysteine levels. Based on functional annotations obtained from ENCODE, we selected four potentially functional single nucleotide polymorphisms (SNPs) in the CARM1 gene and investigated their effect on CARM1 transcription levels in vivo. rs117569851, located in the promoter region of CARM1, as well as rs12460421 and rs4804544, was associated with CARM1 expression levels, and the last two SNPs were discovered in high linkage disequilibrium (LD) with rs117569851 (r2=0.9 and r2=1.0) in our study sample. rs117569851 was further identified to be responsible for regulating CARM1 expression. The T allele disrupted the binding of early growth response-1 (Egr-1), which led to the downregulation of transcriptional activity in vitro and CARM1 mRNA levels in vivo. In addition, rs117569851 was associated with plasma homocysteine levels in a Chinese population (n=406), with a 2.16 μmol/L decrease per copy of T allele.
Conclusions—The present study suggests that a noncoding variant in the CARM1 promoter functions as a regulator of gene transcription and homocysteine levels.
- Received November 1, 2013.
- Revision received June 11, 2014.
- Accepted June 16, 2014.