Chen Lab

Rods and cones are special neurons carrying out phototransduction that converts the light signal into neuronal signal. Rods are responsible for night vision, while cones are responsible for color vision and visual acuity. Both have a unique structure called Outer Segment (OS) where opsins, the visual pigments, are localized (Fig 1).

Fig 1: Rods and Cones in mammalian retina. A) A human retinal section showing three neuronal cell layers: outer nuclear layer (ONL) containing the nucleus of rods and cones; inner nuclear layer (INL) containing the nucleus of bipolar, horizontal and amacrine and Muller glial cells; ganglion cell layer (GCL). B) Diagram of rod and cone structure. C) Scanning EM showing the outer segments.  

The genetic program controlling rod/cone cell fate is referred as photoreceptor gene-regulatory-network (GRN), built on a set of specific transcription factors (TFs) (Fig 2, left panel) that bind to non-coding DNA regions so called cis-regulatory elements (CREs) (Fig 2, right panel) to determine where, when and how much each gene is expressed.

Key transcription factors (TFs)        ➨    Cis-Regulatory Elements (CREs)

Fig 2: Photoreceptor Gene-Regulatory-Network (GRN). Left: During development, key rod/cone TFs are activated in CRX-expressing cells (photoreceptor precursor) and act with CRX to specify rod versus cone cell fate. Right: Each target gene is regulated by interactions among TF-bound cis-regulatory elements (CREs). The chromatin containing these CREs/genes undergoes multiple levels of genomic organization in the nucleus as modeled in A-D: By forming gene loops, the promoter of a gene interacts with its proximal enhancer (A), distal enhancers (B), and additional long-range enhancers (C). The whole genome in the nucleus is further organized into distinct domains and active/silent compartments and territories (D). 

CRX is an otd/OTX-like homeodomain TF predominantly expressed in rods, cones (Fig 3A) and their precursors. CRX is essential for photoreceptor gene expression, development and maintenance. In Crx knockout mice (Crx^-/-), rods/cones fail to generate proper structure and function due to gene mis-regulation, leading to “blindness” and retinal degeneration. CRX has a N-terminal DNA-binding homeodomain and C-terminal trans-activation domains (Fig 3B). CRX acts by 1) binding to approximately six thousand CREs in the genome, 2) recruiting co-activators (epigenetic regulators) to a subset of CREs for local chromatin remodeling, and 3) activating transcription of target genes along with other TFs (Fig 3C).

Fig 3: CRX acts in rods/cones to regulate gene expression. (A) Immunostaining of a monkey retinal section, showing CRX (purple) is localized to the rod/cone nucleus (Blue-nucleus, Green-rod OS, Yellow-cone OS). (B) CRX contains two major functional domains and binds to a consensus DNA motif. (C) Model for CRX mechanism of action: CRX recruits epigenetic regulators, such as histone acetyltransferase (HAT), to configure an “open” chromatin at target genes, and activates transcription by interacting with other TFs and the RNA Pol II transcription machinery (adapted from Peng & Chen, 2007). CRX-mediated chromatin remodeling occurs at the level of DNA accessibility, histone modifications and long-range genomic interactions (Peng & Chen 2011; Ruzycki et al, 2018).      

Mutations in the human CRX gene are associated with autosomal dominant and de novo photoreceptor diseases varying in age onset and phenotype severity, including Leber congenital amaurosis (LCA), cone-rod dystrophy (CRD) and retinitis pigmentosa (RP).  Affected cones and rods show developmental abnormalities and degeneration. No treatment is currently available. Disease-causing mutations distribute along CRX protein and can be divided into four classes based on biochemical characteristics and pathogenic mechanisms of mutant proteins (Fig 4).

Fig 4: Four classes of disease-causing human CRX mutations and available animal models (adapted from Tran & Chen).