The Fuchs corneal dystrophy-associated CTG repeat expansion in the TCF4 gene affects transcription from its alternative promoters

Alex Sirp,Jürgen Tuvikene,Kaja Nurm,Tõnis Timmusk,Mari Sepp,Kristian Leite

doi:10.1038/s41598-020-75437-3

Abstract

The CTG trinucleotide repeat (TNR) expansion in Transcription factor 4 (TCF4) intron 3 is the main cause of Fuchs’ endothelial corneal dystrophy (FECD) and may confer an increased risk of developing bipolar disorder (BD). Usage of alternative 5′ exons for transcribing the human TCF4 gene results in numerous TCF4 transcripts which encode for at least 18 N-terminally different protein isoforms that vary in their function and transactivation capability. Here we studied the TCF4 region containing the CTG TNR and characterized the transcription initiation sites of the nearby downstream 5′ exons 4a, 4b and 4c. We demonstrate that these exons are linked to alternative promoters and show that the CTG TNR expansion decreases the activity of the nearby downstream TCF4 promoters in primary cultured neurons. We confirm this finding using two RNA sequencing (RNA-seq) datasets of corneal endothelium from FECD patients with expanded CTG TNR in the TCF4 gene. Furthermore, we report an increase in the expression of various other TCF4 transcripts in FECD, possibly indicating a compensatory mechanism. We conclude that the CTG TNR affects TCF4 expression in a transcript-specific manner both in neurons and in the cornea.

Highlights

The CTG trinucleotide repeat (TNR) expansion in Transcription factor 4 (TCF4) intron 3 is the main cause of Fuchs’ endothelial corneal dystrophy (FECD) and may confer an increased risk of developing bipolar disorder (BD)
Analysis of GenBank data revealed that a total of 19 expressed sequence tags (EST-s) with 17 different transcription start sites (TSS)-s can be found between TCF4 internal exons 3 and 4 with none beginning downstream of exon 3 and upstream of the CTG TNR (Fig. 1C)
The CTG TNR was never present in the 5′ untranslated regions (UTR) of exon 4a, 4b and 4c transcripts since EST-s from GenBank and our 5′ rapid amplification of DNA ends (5′ RACE) revealed no TSS directly upstream of the TCF4 CTG TNR region (Fig. 1D, Supplementary Fig. S1)

Summary

Introduction

The CTG trinucleotide repeat (TNR) expansion in Transcription factor 4 (TCF4) intron 3 is the main cause of Fuchs’ endothelial corneal dystrophy (FECD) and may confer an increased risk of developing bipolar disorder (BD). We studied the TCF4 region containing the CTG TNR and characterized the transcription initiation sites of the nearby downstream 5′ exons 4a, 4b and 4c We demonstrate that these exons are linked to alternative promoters and show that the CTG TNR expansion decreases the activity of the nearby downstream TCF4 promoters in primary cultured neurons. An expansion of a CTG TNR, located in an alternative promoter region between TCF4 exons 3 and 4 (known as CTG 18.1), upstream of TCF4 5′ exons 4a, 4b and 4c causes Fuchs’ endothelial corneal dystrophy (FECD) and has been linked to Bipolar disorder (BD)[14,15]. AD activation domain, NLS nuclear localization domain, bHLH basic helix-loop-helix, FL full length, Δ lack of nuclear localization domain, EST expressed sequence tag, TSS transcription start site, FANTOM5 functional annotation of the mammalian genome, DPI decomposition-based peak identification, CAGE cap analysis of gene expression

Methods

Results

Conclusion