Human Hepatocyte Nuclear Factor 4-α Encodes Isoforms with Distinct Transcriptional Functions

HNF4 alpha is a nuclear receptor produced as 12 isoforms from two promoters by alternative splicing. To characterize the transcriptional capacities of all 12 HNF4 alpha isoforms, stable lines expressing each isoform were generated. The entire transcriptome associated with each isoform was analyzed as well as their respective interacting proteome. Major differences were noted in the transcriptional function of these isoforms. The alpha 1 and alpha 2 isoforms were the strongest regulators of gene expression whereas the alpha 3 isoform exhibited significantly reduced activity. The alpha 4, alpha 5, and alpha 6 isoforms, which use an alternative first exon, were characterized for the first time, and showed a greatly reduced transcriptional potential with an inability to recognize the consensus response element of HNF4 alpha. Several transcription factors and coregulators were identified as potential specific partners for certain HNF4 alpha isoforms. An analysis integrating the vast amount of omics data enabled the identification of transcriptional regulatory mechanisms specific to certain HNF4 alpha isoforms, hence demonstrating the importance of considering all isoforms given their seemingly diverse functions.