A synonymous polymorphic variation in ACADM exon 11 affects splicing efficiency and may affect fatty acid oxidation

Area of Science:

• Genetics
• Molecular Biology
• Metabolic Disorders

Background:

• Genome-wide association studies linked a SNP upstream of the MCAD gene (ACADM) to altered medium-chain acylcarnitine levels.
• This suggests a potential impact on beta-oxidation of medium-chain fatty acids.

Purpose of the Study:

• To investigate the functional basis for the association between the upstream SNP and MCAD gene function.
• To determine if a synonymous variant within the ACADM gene explains the observed association.

Main Methods:

• Identified linkage between the upstream SNP (rs211718) and an intragenic synonymous SNP (c.1161A>G, rs1061337) in ACADM exon 11.
• Utilized minigene assays to assess the impact of the c.1161A>G variant on pre-mRNA splicing.
• Analyzed RNA-seq data to compare allele expression levels across tissues.
• Investigated the binding of splicing regulatory proteins (SRSF1 and hnRNP A1).

Main Results:

• The c.1161A allele was associated with exon 11 missplicing, while the c.1161G allele corrected this.
• The c.1161G allele appears to lead to increased production of full-length MCAD protein.
• Differential binding of splicing factors SRSF1 and hnRNP A1 was observed.
• RNA-seq data showed significantly higher expression of the c.1161G allele compared to c.1161A across tissues.

Conclusions:

• The synonymous SNP c.1161A>G is functional, impacting MCAD expression through altered splicing.
• Synonymous SNPs can significantly affect gene function by modulating splicing factor binding and pre-mRNA splicing.
• Changes in the balance of positive and negative splicing factors are crucial for sequence variations to exert functional effects.