Transcriptional precision in photoreceptor development and diseases - Lessons from 25 years of CRX research

Abstract

The vertebrate retina is made up of six specialized neuronal cell types and one glia that are generated from a common retinal progenitor. The development of these distinct cell types is programmed by transcription factors that regulate the expression of specific genes essential for cell fate specification and differentiation. Because of the complex nature of transcriptional regulation, understanding transcription factor functions in development and disease is challenging. Research on the Cone-rod homeobox transcription factor CRX provides an excellent model to address these challenges. In this review, we reflect on 25 years of mammalian CRX research and discuss recent progress in elucidating the distinct pathogenic mechanisms of four CRX coding variant classes. We highlight how in vitro biochemical studies of CRX protein functions facilitate understanding CRX regulatory principles in animal models. We conclude with a brief discussion of the emerging systems biology approaches that could accelerate precision medicine for CRX-linked diseases and beyond.

Keywords: CRX; dominant diseases; gene regulation; homeodomain; inherited retinopathy; molecular genetics; pathogenic mechanisms.

FIGURE 1

Multiple sequence alignment of human and mouse CRX and OTX2 protein sequences. Multiple sequence alignment is generated by the EMBL-EBI Clustal Omega program with default parameters. Selected amino acids are highlighted: golden: aromatic residues and Leucine; pink: acidic residues; blue: basic residues. Refseq protein sequence accession numbers: hCRX: NP_000545.1 (hg38); mCRX: NP_031796.1 (mml0); hOTX2: NP_068374.1 (hg38); mOTX2: NP_659090.1 (mml0).

FIGURE 2

Distribution of human CRX coding variants and their predicted pathogenic classes. (A) Schematic showing full-length human CRX protein and its major domains, (B) Schematic showing the amino acid composition of full-length CRX protein. Acid, basic, aromatic, and Leucine residues are highlighted, (C) Bar chart showing the number of unique variants at each amino acid position, (D) Heatmap showing the type of protein sequence change reported at each amino acid position, (E) Diagram showing the predicted pathogenic classes based on the categorical approach. The complete list of curated CRX coding variants and accompanying references can be found in Supplementary Table 1. (F) Established animal models carrying different Crx variants. The labels are organized to match the relative amino acid positions of the CRX variants, and their colors match that of their pathogenic classes, (G) Diagrams comparing the amino acid composition of part of human CRX (UniProt: 043186) transcription effector domain (aa. 229–299) and selected variants predicted to create extended C-terminus with altered residue composition. Numbers accompanying each diagram represent the extended CRX protein length. Filled triangles above each diagram indicate the frameshift residue positions.

FIGURE 3

Summary of human CRX coding variants and their predicted pathogenic mechanisms in knock-in mouse models. (A) Diagrams depicting chromatin remodeling at CRX-dependent accessible sites in WT and Crx KO mouse retinas during post-natal development. P2, P14, P21: post-natal day 2, 14, 21. (B–E) Schematics highlighting the molecular mechanisms of human CRX coding variants in four pathogenic classes. We provide the type of variants for each class, the representative animal models, and associated phenotypes in humans, panels (B,C) depict models for missense variants of the CRX homeodomain (DNA binding domain), panels (D,E) depict models for frameshift and nonsense variants of the CRX transcription effector domain. +1 and +2 indicate the reading frame is shifted 1 or 2 bp 3′ to the original reading frame.