Effect of the twelve isoforms of Hepatocyte nuclear factor 4 alpha on HCT116 cell line transcriptome

The nuclear receptor HNF4alpha is regulating a wide set of genes associated with development, cell differentiation, inflammation and metabolism. In human, 12 variants of HNF4a can be expressed by the use of two promoters and by alternative splicing. Until now, the characterization of this transcription factor has ignored this diversity and has remained confined to the study of a fraction of the isoforms. We therefore wanted to clarify the situation by specifically characterizing the transcriptional functions of the 12 isoforms of HNF4a. We have generated for this purpose stable lines expressing each isoform of HNF4a in HCT 116 cells. The expression of each isoform was then induced for 48 hours and the whole transcriptome was analyzed by RNA sequencing. The transcriptome associated with each specific isoform was then compared to empty control cells to determine the specific transcriptional functions of HNF4alpha's isoforms. Overall design: Stable HCT116 cell lines containing a single insertion of the different human HNF4alpha isoforms (1 to 12) fused to GFP at its C-terminal were generated through the Flp-In T-REx system. Expression of HNF4alpha isoforms was induced for 48 hours with 2.5 ug/ml of doxycycline before analyzing the transcriptome by RNA sequencing on Illumina NovaSeq 6000 system. Experiments were realized in triplicate for all isoforms of HNF4alpha and transcripts expression was compared to the one of the parental empty HCT116 cell line.