A new mechanism for a familiar mutation – bovine DGAT1 K232A modulates gene expression through multi-junction exon splice enhancement

Abstract

Background: The DGAT1 gene encodes an enzyme responsible for catalysing the terminal reaction in mammary triglyceride synthesis, and underpins a well-known pleiotropic quantitative trait locus (QTL) with a large influence on milk composition phenotypes. Since first described over 15 years ago, a protein-coding variant K232A has been assumed as the causative variant underlying these effects, following in-vitro studies that demonstrated differing levels of triglyceride synthesis between the two protein isoforms. Results: We used a large RNAseq dataset to reexamine the underlying mechanisms of this large milk production QTL, and hereby report novel expression-based functions of the chr14 g.1802265AA > GC variant that encodes the DGAT1 K232A substitution. Using expression QTL (eQTL) mapping, we demonstrate a highly-significant mammary eQTL for DGAT1, where the K232A mutation appears as one of the top associated variants for this effect. By conducting in vitro expression and splicing experiments in bovine mammary cell culture, we further show modulation of splicing efficiency by this mutation, likely through disruption of an exon splice enhancer as a consequence of the allele encoding the 232A variant. Conclusions: The relative contributions of the enzymatic and transcription-based mechanisms now attributed to K232A remain unclear; however, these results suggest that transcriptional impacts contribute to the diversity of lactation effects observed at the DGAT1 locus.

Sequence-based genome-wide association study of individual milk mid-infrared wavenumbers in mixed-breed dairy cattle

“…The gene DGAT1 encodes diacylglycerol O-acyltransferase 1, which catalyses the final step in triglyceride production and which, given the substantial quantities of fat secreted during milk production, makes DGAT1 a well-demonstrated and straightforward candidate gene for this effect. The variant rs109234250 (K232A) reported here has been widely ascribed to the effects of the DGAT1 gene on milk production, with a recent study showing that these effects may be due in part to an expression-based mechanism [ 64 ].…”

Association of DGAT1 With Cattle, Buffalo, Goat, and Sheep Milk and Meat Production Traits

“…The SNP (rs109421300) has A and G alleles, while G allele was associated with antagonistic pleiotropy for positive fat yield and negative milk and protein yields in U.S. Holstein cattle. It was reported in a recent study that the variant DGAT1 K232A modulates the expression of DGAT1 gene in the mammary gland of dairy cattle (19).…”

“…The allelic frequency and the influence of the DGAT1 K232A polymorphism have been illustrated in dairy cattle populations in different countries including New Zealand (12,19,21,50), Israel (13), the Netherlands (51,52), Germany (53,54), Poland (55,56), China (57)(58)(59), France (60), India (45), and Sweden (47).…”

“…The important role of DGAT1 in the metabolism of milk fat makes DGAT1 gene an interesting candidate for the genetic variation of milk characteristics in milk goats (107). DGAT1 also plays an essential function in physiological processes that include the synthesis of TAG, such as the absorption of intestinal fat (22,36), the development of adipose tissue, and mammals' lactation (12,19).…”

“…Several studies have targeted the bovine quantitative trait loci (QTLs) on chromosome 14 for their association with milk production traits (12)(13)(14)(15)(16)(17)(18)(19)(20). Acyl CoA:diacylglycerol acyltransferase (DGAT1) gene at chromosome 14 has been documented as a candidate marker for the QTLs associated with milk production traits through cattle genome and linkage mapping studies (21,22).…”