Alternative splicing is an FXRα loss-of-function mechanism and impacts energy metabolism in hepatocarcinoma cells.

Farnesoid X receptor α (FXRα) is a bile acid-activated nuclear receptor that sets the expression of glycolytic and lipogenic target genes by interacting with the 9-cis-retinoic acid receptor α (RXRα). Jointly with recruited cofactors, the current FXRα proteins reported so far in human and rodent have been described to regulate both isoform (α1-4)- and tissue-specific gene expression profiles in order to integrate energy balance and adapt metabolism. Here, we studied the biological functions of a FXRα naturally occurring spliced exon 5 isoform (FXRαse5) lacking the second zinc-binding module of the DNA Binding Domain (DBD). We show that the FXRαse5 is expressed in all FXRα-expressing tissues and cells from human and mouse, and that it is not able to either bind to its response element or activate FXRα dependent transcription. In parallel, this spliced variant displayed differential interaction capacities with its obligate heterodimer partner RXRα that may account for silencing of this permissive dimer for signal transduction. Finally, deletion of exon 5 by gene edition in HepG2 cells leads to FXRα loss-of-function, increased expression for LRH1 metabolic sensor and CD36 fatty acid transporter in conjunction with changes in glucose and triglycerides homeostasis. All together, these findings highlighted a novel mechanism by which alternative splicing may regulate FXRα gene function to fine-tune adaptive and/or metabolic responses. Taking this into account could deepen our understanding on how splicing events might hinder FXRα activity to regulate specific transcriptional programs and contribute to modify energy metabolism in normal tissues and metabolic diseases. To verify whether and to what extent the FXRαse5 isoform may modulate FXRα transcriptional network through specific binding to other FXRE DNA sequence motifs, we used RNA sequencing to explore the transcriptome of HepG2 overexpressing either FXRα1 or FXRαse5. By comparing genes regulated by these two FXRα isoforms with the empty control vector, we generated the heatmap and the Venn diagram of the RNAseq datasets