Search tips
Search criteria 


Logo of nihpaAbout Author manuscriptsSubmit a manuscriptHHS Public Access; Author Manuscript; Accepted for publication in peer reviewed journal;
J Neurochem. Author manuscript; available in PMC 2013 October 1.
Published in final edited form as:
PMCID: PMC3441145

NeuroD1 is required for survival of photoreceptors but not pinealocytes: Results from targeted gene deletion studies


NeuroD1 encodes a basic helix-loop-helix (bHLH) transcription factor involved in the development of neural and endocrine structures, including the retina and pineal gland. To determine the effect of NeuroD1 knockout in these tissues, a Cre/loxP recombination strategy was used to target a NeuroD1 floxed gene and generate NeuroD1 conditional knockout (cKO) mice. Tissue specificity was conferred using Cre recombinase expressed under the control of the promoter of Crx, which is selectively expressed in the pineal gland and retina. At two months of age NeuroD1 cKO retinas have a dramatic reduction in rod- and cone-driven electroretinograms and contain shortened and disorganized outer segments; by four months NeuroD1 cKO retinas are devoid of photoreceptors. In contrast, the NeuroD1 cKO pineal gland appears histologically normal. Microarray analysis of two-month-old NeuroD1 cKO retina and pineal gland identified a subset of genes that were affected 2- to 100-fold; in addition, a small group of genes exhibit altered differential night/day expression. Included in the down-regulated genes are Aipl1, which is necessary to prevent retinal degeneration, and Ankrd33, which is selectively expressed in the outer segments. These findings suggest that NeuroD1 may act through Aipl1 and other genes to maintain photoreceptor homeostasis.

Keywords: NeuroD1, microarray, retina, pineal gland, gene expression, transcriptome profiling


NeuroD1 is a basic helix-loop-helix (bHLH) transcription factor implicated in cell cycle regulation, retinal cell genesis, and neuronal development (Miyata et al. 1999, Schwab et al. 2000, Lee et al. 2000, Cai et al. 2000, Liu et al. 2000, Cherry et al. 2011, Ochocinska & Hitchcock, 2009). In the retina, NeuroD1 plays a role in terminal photoreceptor differentiation and survival of rod photoreceptors; loss of NeuroD1 results in progressive photoreceptor degeneration (Morrow et al. 1999, Pennesi et al. 2003). NeuroD1 also functions in cone photoreceptor patterning and mediates cone-specific expression through the regulation of thyroid hormone receptor β2 expression during development (Liu et al. 2008).

NeuroD1 mRNA is also highly abundant in the pineal gland and exhibits a developmental expression pattern similar to that of the retina (Bailey et al. 2009, Muñoz et al. 2007). This is consistent with the common evolutionary origin of pinealocytes and retinal photoreceptors (Klein 2006, Bailey et al. 2009, Donoso et al. 1985, Korf et al. 1985, Korf et al. 1992, Rodrigues et al. 1986, Reig et al. 1990, Schaad et al. 1991, Babila et al. 1992, Lolley et al. 1992). In contrast to the retina, the pineal gland is a relatively homogeneous structure, composed 95% of pinealocytes, which share some genetic features with photoreceptors. This makes the pineal gland a useful model for understanding elements of cell biology shared by both tissues.

Previous studies directed at understanding the role of NeuroD1 in the mouse retina have used a global knockout strategy that eliminates NeuroD1 expression in all tissues, including the pancreas and cerebellum (Morrow et al. 1999, Liu et al. 2008). The majority of these animals die shortly after birth, which limits efforts to study NeuroD1 function in the adult. Moreover, global knock out of NeuroD1 allows the possibility that the effects of this manipulation on the retina are mediated by non-retinal and non-pineal tissues.

To obviate this possibility in the current study, a Cre/loxP recombination strategy was used to limit gene deletion to the pineal gland and retina. Cre recombinase was selectively expressed in pinealocytes and retinal cells, including photoreceptors, by placing it under control of the Crx promoter, which is selectively expressed in both tissues late in gestation (Omori et al. 2012, Rath et al. 2006, Furukawa et al. 2002). Crx-cre mice were crossed with NeuroD1flox/flox mice (Goebbels et al. 2005) to generate NeuroD1flox/flox/Crx-cre+ (cKO) and NeuroD1flox/flox/Crx-cre control mice. The effects of NeuroD1 cKO on the retina and pineal gland were monitored histologically by immunofluorescence and transmission electron microscopy, and by microarray-based gene expression profiling. Retinal function was monitored using electroretinography. The findings of these studies are presented below.

Materials and Methods


All animal experiments and treatments were performed in accordance with the National Institutes of Health Guide for Care and Use of Laboratory Animals and the Animal Research: Reporting In Vivo Experiments (ARRIVE) guidelines. Mice were housed in a 12:12 Light-Dark Cycle with lights on at Zeitgeber time (ZT) 0 and food and water ad libitum. Both male and female mice were used for all experiments.

NeuroD1 cKO mice: A colony of mice was established on a C57BL/6J background using a male NeuroD1flox/flox animal in which exon 2 of the NeuroD1 gene, which includes the initiating codon, is flanked by two loxP sites (Goebbels et al. 2005). These animals were crossed with Crx-cre mice (Omori et al. 2012), which express Cre recombinase under the control of the 2-kb Crx promoter (Furukawa et al. 2002). See Fig. 1A and Supporting Information for further details.

Figure 1
Generation of NeuroD1 conditional knockout mice

Agr2−/− mice: A colony of Agr2 −/− mice was established by crossing a male Agr2+/− animal (Dr. David J. Erle, University of California, San Francisco) with a C57BL/6J female (Taconic Farms) to generate heterozygous progeny (Lewandoski et al. 1997, Park et al. 2009). These heterozygous progeny were used to generate Agr2 −/− (Agr2 KO) and age-matched wild type littermate control animals. See Supporting Information for further details.

Microarray analysis

Pineal glands and retinas from two-month-old NeuroD1 cKO and control mice were removed during the day at ZT6 and at night at ZT20; tissue was placed on solid CO2. Tail samples were collected in parallel for genotype confirmation. See Supporting Information for further details.

Total RNA (~200 ng/pineal gland and 1000 ng/retina) was prepared from pools of six pineal glands or retinas; three pools per organ and per genotype were analyzed at each sampling time. Published methods were used for total RNA isolation, quality control, and cDNA amplification (Rovsing et al, 2011). See Supporting Information for further details. Amplified cDNA was biotinylated using the Encore Biotin Module (NuGEN Technologies, Inc.). Biotinylated cDNA (20 ug) was fragmented and hybridized for 18 h at 45°C to the GeneChip Mouse Genome Array 430 2.0 (Affymetrix, Santa Clara, CA). This GeneChip contained 45,000 probe sets corresponding to 39,000 transcripts and variants from over 34,000 annotated mouse genes. The arrays were stained and washed as described in the Affymetrix protocols.

Data analysis

Affymetrix arrays were scanned using a GeneChip Scanner 3000 (Affymetrix). For each array, the raw signal intensity (.CEL) files were generated and analyzed with Genomatix ChipInspector V2.0 software (Munich, Germany). The following filters were used for all analyses: exhaustive matching, a false discovery rate (FDR) = 0, cut off = 1, region size = 300 bp and a minimum of 4 significant probes. Differences of p < 0.05 were considered to be statistically significant. See Supporting Information for further details. The microarray data are available at the NCBI Gene Expression Omnibus (

Promoter and transcription factor analyses were done using the following Genomatix Software Suite modules (Munich, Germany): Genes2Promoter, RegionMiner, and MatInspector. Briefly, the results from ChipInspector were loaded into the Genes2Promoter program to identify networks and pathways. RegionMiner was used to identify transcription factor module enrichment from the list of differentially expressed genes and MatInspector was used to inspect the relevant promoter regions.

Quantitative real time polymerase chain reaction (qRT-PCR)

Twenty differentially expressed transcripts (p<0.05) were validated by qRT-PCR using the LightCyclerR 480 Rapid Thermal Cycler System (Roche, Indianapolis, IN). The SPIA-amplified cDNA generated for the Microarrays was used as template for all qRT-PCR experiments. PCR reactions were performed in a 25 μL volume consisting of 0.5 μmol/L primers (Table 1), Real-Time SYBR® Green PCR Master Mix (SuperArray Bioscience, Frederick, MD), and cDNA as per the manufacturer’s instructions. Published methods were used for all assays (Muñoz et al., 2007). See Supporting Information for further details.

Table 1
Primers for genotyping and quantitative real-time PCR analysis.


All immunohistochemistry protocols were performed as previously described (Ochocinska & Hitchcock, 2009). Sections were stained with the following antisera: mouse monoclonal anti-Rho (Rho 4D2; Dr. Robert Molday, University of British Columbia, Vancouver, Canada) diluted 1:1000; rabbit polyclonal anti-M-opsin and antiS-opsin (Dr. Cheryl Craft, University of Southern California, Los Angeles), diluted 1:1000. Secondary antisera included goat anti-rabbit Alexa Fluor® 488 and goat anti-mouse Alexa Fluor® 555 (Invitrogen, Eugene, OR), diluted 1:200. The stained tissue sections were visualized under a LSM 510 META Laser Scanning Confocal Microscope (Carl Zeiss, Maple Grove, MN). See Supporting Information for further details.

Bromodeoxyuridine (BrdU) labeling

BrdU (Sigma, St. Louis, MO) was injected intraperitoneally (0.1mg BrdU/g body wt) at postnatal day 0 (P0) and at two months of age. The animals were sacrificed 4 hours post-injection. Three animals per genotype were analyzed (cKO, N=3; CON, N=3) at both ages.

Western Blot

Retina tissue was homogenized and 100 μg sample of retinal protein was separated by SDS-polyacrylamide gel electrophoresis (PAGE). Blots were incubated with a 1:5000 dilution of affinity-purified Rho 4D2 antiserum overnight at 4°C, followed by a 1- to 2-hour incubation with secondary Alexa Fluor® 680 goat anti-mouse IgG, diluted 1:15,000. Immunoreactive proteins were detected using the Odyssey Infrared Imaging System (Li-Cor; Lincoln, NE) and analyzed by video densitometry (Lynx software; Applied Imaging, Newcastle-upon-Tyne, UK). For semiquantitative analysis, blots were stripped and reprobed with a monoclonal antibody against beta-actin (Sigma, St. Louis, MO), diluted 1:1000, and Alexa Fluor® 800 goat anti-mouse IgG secondary antibody, diluted 1:5000. See Supporting Information for further details.

Transmission Electron Microscopy

Pineal glands were dissected and fixed (1 h at 4°C in 2.5% glutaraldehyde, made in 0.1M sodium cacodylate buffer, pH 7.4). Eyes were dissected and a slit was made in the superior cornea prior to fixation (2 h at 4°C in fixation mix). After the 2 h primary incubation, the superior cornea was cut away, the lens was removed and fixation was continued at 4°C overnight. Tissues were embedded and polymerized in 100% resin for 18 hours in a lab oven set at 70°C. Thin sections (50nm thick) were cut on a Reichert-Jung Ultracut-E ultramicrotome (Leica, Wetzlar, Germany) and collected on LuxFilm grids (Ted Pella, Inc., Redding, CA, Inc.; 30nm film thickness). The grids were post-stained with uranyl acetate and lead citrate and examined in a Tecnai G2 transmission electron microscope operating at 80kV (FEI, Hillsboro, OR). See Supporting Information for further details.


Published methods were used for electroretinography (Pang et al. 2005). See Supporting Information for further details.


Log2 transformed microarray data from control and NeuroD1 cKO groups, at ZT6 and ZT20, were compared using two-way ANOVA on GraphPad Prism V4 (GraphPad software). The statistical significance of the microarray, qRT-PCR, and Western blot results was determined by a Student’s two-tailed t-test with Welch’s correction (Armitage 2002). ERG results were compared using two-way ANOVA on GraphPad Prism V4 (GraphPad software) with p-values of < 0.05 considered statistically significant.


Morphological studies

The NeuroD1 cKO mouse retina has marked morphological changes

To characterize the retinal morphology of NeuroD1 cKO mice, retinal sections from three animals per genotype were analyzed (cKO, N=3; CON, N=3). Histological analysis revealed that the outer nuclear layer (ONL) in the NeuroD1 cKO retina is present at two months of age, although the observed thickness varies (Fig. 1B, middle panels). However, the ONL is absent at four months of age (Fig. 1B, right panels). The inner nuclear layer (INL), inner plexiform layer (IPL), and ganglion cell layer (GCL) are not affected in the NeuroD1 cKO retina based on histological evaluation via light microscopy (Fig. 1B) and transmission electron microscopy, comparing the cellular structures in all three retinal layers, including the ganglion cell layer, inner nuclear layer, and outer nuclear layer (data not shown). Specifically, we examined the morphology of the cells within the respective layers, the organelles within the cells including mitochondria and endoplasmic reticulum and the relationship between respective cells. Due to the absence of the ONL by four months of age, subsequent evaluation of cone and rod photoreceptors was limited to two-month-old retinas.

Cone receptors were examined using antisera against cell type-specific markers M-opsin (Opn1mw) and S-opsin (Opn1sw). M-opsin antisera labeled the outer segments of medium wavelength cone photoreceptors in control retinas. In contrast, in the cKO retina M-opsin immunoreactivity was nearly undetectable (compare Fig. 2A and Fig. 2B). The expression of M-opsin mRNA, was reduced by 80% in the cKO retina compared to controls (Fig. 2C). S-opsin antisera labeled cone outer segments in two-month-old control and NeuroD1 cKO retinas. However, the outer segments labeled with S-opsin were disorganized; in addition, the S-opsin protein was also mislocalized to the cell membrane and synapse (compare Fig. 2D and Fig. 2E). The expression level of S-opsin transcript, in the cKO and control retinas was similar (Fig. 2F).

Figure 2
Effect of NeuroD1 conditional knockout on photoreceptors

Rods were examined at two months of age using antisera against the rod-specific marker Rho. Retinal sections from three animals per genotype were analyzed (cKO, N=3; CON, N=3). The control retina showed a strong Rho signal (Fig. 2G). In contrast, the NeuroD1 cKO retina showed a weak Rho signal and the protein appeared to be partially mislocalized to the inner segments (Fig. 2H). The Rho-positive outer segments of the NeuroD1 cKO retina were also shortened and disorganized compared to the controls (Fig. 2H). The red label in the GCL of control and cKO retinas is consistent with the staining pattern of Müller glia end feet.

The immunohistological findings were confirmed by Western blot, which revealed that Rho protein in the two-month-old NeuroD1 cKO retina was significantly reduced relative to control (estimated by dilution analysis to be ~95%), (Fig. 2I). In contrast, Rho mRNA was reduced only 40% (Fig. 2J).

Ultrastructural analysis of retinal degeneration in two-month-old NeuroD1 cKO mice

Ultrastructural evaluation of retinas from conditional NeuroD1 cKO and control mice was performed using transmission electron microscopy (TEM). Retinal sections from three animals per genotype were analyzed (cKO, N=3; CON, N=3). No change in the inner nuclear layer and ganglion cell layer was apparent at the ultrastructural level (data not shown). In the NeuroD1 cKO retina, the outer segments were disorganized, shortened in length, and, in some regions, completely absent; the controls, in contrast, showed normal outer segments (compare Fig. 3A and C with Fig. 3B and D). The structural integrity of the outer segment discs appears altered and atypical whorls of membranous material (arrows in Fig. 3D) were present between the outer segments and the retinal pigment epithelium (RPE). This expansion of amorphous membranous material is also illustrated in Fig. 3E and at a higher magnification in Fig. 3F.

Figure 3
Changes in ultrastructure of NeuroD1 cKO retina at two months of age

Ultrastructural analysis of the pineal gland in two-month-old NeuroD1 cKO mice

To determine if there were any changes in pineal gland morphology between genotypes, pineal gland sections from three animals per genotype were analyzed (cKO, N=3; CON, N=3). In contrast to the striking photoreceptor degeneration phenotype observed in the NeuroD1 cKO retina, there was no obvious change in the morphology of the pineal gland body in NeuroD1 cKO compared to control mice at the light microscopy level (Fig. 4A and Fig. 4B). The pineal stalk was shorter and wider in the NeuroD1 cKO animals compared to controls (compare Fig. 4A with Fig. 4B). However, this observation could not be statistically quantified due to the variability in the pineal stalk morphology, and associated technical limitations.

Figure 4
Morphology and ultrastructure of two-month-old NeuroD1 cKO and control pineal gland

BrdU was used to label mitotically active cells (Wojtowicz & Kee 2006) with the intention of detecting differences between control and NeuroD1 cKO animals. Injections were performed at postnatal day zero and at two months of age. Brain sections from three animals per genotype and age group were analyzed (cKO, N=3; CON, N=3). BrdU labeling of the control and cKO pineal stalk at both developmental stages was not different (data not shown). This suggests that the pineal stalk phenotype observed in the NeuroD1 cKO animals is not associated with a difference in proliferation.

Ultrastructural evaluation of pineal glands from two-month-old NeuroD1 cKO and control mice was performed using TEM. Pineal gland sections from three animals per genotype were analyzed (cKO, N=3; CON, N=3). The morphology of pinealocytes and blood vessels in both groups was normal (Møller et al. 1978), as judged by examination of the relationship of pinealocytes to each other and to vascular elements and the appearance of cellular components including the nucleus, mitochondria, ER, membranes and vesicles(Fig. 4C and 4D).

Gene profiling studies

Deletion of NeuroD1 alters the retinal and pineal transcriptomes

The influence of NeuroD1 on the retina and pineal gland transcriptomes was assessed by Affymetrix microarray analysis in two-month-old control and NeuroD1 cKO mice. This revealed that NeuroD1 transcript abundance was reduced by >20-fold in both the retina and pineal gland, confirming the effectiveness of the KO strategy.

The microarray results identified several potential downstream target genes. In the retina, the expression of 55 genes was reduced >2-fold, including genes linked to transcription, phototransduction, and protein folding (Table 2). The most dramatically down-regulated genes included Ankrd33/Panky (7.8-fold), and Agr2 (7.9-fold), which are associated with retinal transcription (Sanuki et al. 2010) and protein folding (Persson et al. 2005), respectively. The following phototransduction-linked genes did not decrease more than 2-fold, including Rho, Gnat1, Rcvrn, Sag, Arr3, Pde6, and Grk1.

Table 2
Differentially expressed genes in two-month-old NeuroD1 cKO retina and pineal gland

In addition to down-regulated genes, it was observed that some genes were upregulated in the retina. The most highly up-regulated gene in the retina was the T cell marker Tal2 (11.8-fold); others include Gfap (5.4-fold), Prtg (5.7-fold), Edn2 (7.4-fold) and A2m (7.6-fold), all of which are associated with the immune response (Bucher et al. 2000, Kumar & Shamsuddin 2012, Takahashi et al. 2010, Rattner & Nathans 2005, Fan et al. 2010).

In the NeuroD1 cKO pineal gland, the expression of 16 genes was reduced > 2-fold (Table 2), including genes linked to transcription and calcium signaling. The most dramatically down-regulated genes included Agr2 (2.2-fold), S100a8 (3.3-fold) and S100a9 (3.1-fold). The most up-regulated gene in the pineal gland was Igl-V1 (9.1-fold), a member of the immunoglobulin family linked to the immune response (Das et al. 2011).

A set of 32 genes exhibited a night/day difference in expression in the control retina; 10 of these genes were also rhythmic in the NeuroD1 cKO retina. Eleven genes that were rhythmic in the NeuroD1 cKO retina did not show daily variations in the control retina at the time points studied (Table 3). In the control pineal gland, a set of 38 genes exhibited differential night/day expression; 28 of these genes also exhibited daily rhythms in the NeuroD1 cKO pineal gland. In addition, 14 genes were only rhythmic in the NeuroD1 cKO pineal gland (Table 3).

Table 3
Genes exhibiting a night/day rhythm in the control and/or NeuroD1 cKO retina and pineal gland

Microarray gene results were validated by qRT-PCR (Table 2). The transcripts examined were those that were most strongly impacted by the NeuroD1 deletion. In all cases, the results from qRT-PCR analysis qualitatively confirmed the changes observed. For some transcripts, the differences in expression detected by qRT-PCR were >4-fold greater than those revealed by microarray analysis.

In silico promoter analysis of genes affected in NeuroD1 cKO retina and pineal gland

The list of differentially regulated genes in the NeuroD1 cKO retina and pineal gland, shown in Table 2, was analyzed using the Genomatix Pathway System (GePS). Transcription factor binding sites were determined using RegionMiner, in Genomatix, which compares the promoter regions of the affected group of genes to promoters from the entire genome (Z-score >2, p<0.05). NeuroD1 binding sites were present in the promoters of several photoreceptor transduction genes including Opn1mw, Aipl1, Agr2, and Ankrd33 in the retina (Fig. 5A) and S100a8, S100a9, Per3, and Agr2 in the pineal gland (Fig. 5B). NeuroD1 dimerizes with its binding partner E47, a bHLH transcription factor, and forms a heterodimer NeuroD1/E47 to translocate to the nucleus and regulate transcription of target genes (Mehmood et al. 2011, Mehmood et al. 2009, Longo et al. 2008). Promoter analysis of the most affected genes using the MatInspector platform revealed that all of the down-regulated genes in the retina contain potential binding sites for the heterodimer NeuroD1/E47 (Fig. 5A). Only two down-regulated genes in the pineal gland, i.e. Agr2 and S100a9, contain putative binding sites for the NeuroD1/E47 complex (Fig. 5B).

Figure 5
In silico Promoter analysis of differentially expressed genes in the NeuroD1 cKO retina and pineal gland using Genomatix software

The list of genes with altered rhythmic expression on a night/day basis in the retina and pineal gland (Table 3) were analyzed using Genomatix software. To determine whether there was enrichment in specific transcription factor modules which included the NeuroD1/E47 binding site we used the transcription factor overrepresentation search in Genomatix. This analysis revealed that several transcription factor modules containing NeuroD1 were overrepresented in the genes with altered rhythms in both the retina and pineal gland with Z-scores > 4.0 (Table S1). The most overrepresented modules included the Krüppel-like transcription factor family in the retina (Z-score = 8.1) and the GATA binding factor family in the pineal gland (Z-score = 5.0).


Rod and cone ERGs are severely compromised in NeuroD1 cKO mice

The role of NeuroD1 in visual physiology was analyzed in NeuroD1 cKO mice by electoretinography. Rod- and cone-mediated ERGs were recorded to evaluate retinal function in NeuroD1 cKO mice. Four animals per genotype were analyzed (cKO, N=4; CON, N=4) at two and at four months of age. At two months of age, cKO mice showed significant reductions in rod-driven ERG responses compared to controls (Fig. 6A and Fig. 6C; *p<0.001). Cone ERG responses in cKO mice were reduced to undetectable levels at two months of age (Fig. 6B and Fig. 6D; *p<0.001). Rod and cone ERG responses in the cKO retina were undetectable at four months of age (data not shown).

Figure 6
Electroretinograms from NeuroD1 cKO mice compared to controls at two and four months of age

Cone and rod ERGs in the Agr2−/− mice are normal

The finding that selective knockout of NeuroD1 decreases the abundance of Agr2 transcripts raised the possibility that Agr2 deletion would cause retinal damage. To test this hypothesis, we examined rod and cone electroretinogram responses in Agr2−/− (KO) and control (CON) mice. Four animals per genotype were analyzed (KO, N=4; CON, N=4) at two and four months of age. Agr2−/− mice displayed normal rod and cone ERGs at both ages (Fig. 7A and Fig. 7B). Significant differences between the average rod and cone-driven b-wave amplitudes were not detected at these ages (Fig. 7C and Fig. 7D) or at six months of age (data not shown).

Figure 7
Electroretinograms from Agr2 KO mice compared to controls at two and four months of age


This is the first report on the effect of tissue-specific NeuroD1 knockout in the adult mouse retina and pineal gland. Analysis of NeuroD1 cKO retina and pineal gland revealed a marked reduction in NeuroD1 transcript and severely compromised photoreceptor function. This confirmed that the targeted knockout strategy was effective and establishes a useful model for studies of NeuroD1. The results of this study are discussed below from retinal and pineal perspectives, sequentially.

Role of NeuroD1 in retinal biology

The present study extends our understanding of the sequence of events involved in retinal degeneration induced by NeuroD1 deletion, which we view as a two stage process (Table 4). The first stage is characterized by marked reduction of photodetection as indicated by electroretinography, by changes in outer segments, and by a profound decrease in Rho. However, at this stage, the photoreceptor cell bodies appear to be histologically intact. In agreement, photodetector marker genes remain strongly expressed including transduction genes (e.g., Rho, Gnat1, Rcvrn, Sag, Arr3, Pde6, and Grk1) and transcription factor genes (e.g., Crx, Nrl, and Otx2). Moreover, the expression of thousands of other genes is also normal. This supports the interpretation that at this stage the cell bodies are not globally impacted by the loss of NeuroD1. However, a notable outstanding change observed is a 95% reduction in Rho. The second stage of photoreceptor deterioration is characterized by absence of photoreceptors, as observed by four months of age.

Table 4
The two stages of photoreceptor degeneration phenotype observed in the NeuroD1 cKO retina

The contrast between the marked change in ERG and the minor change in gene expression at two months suggests that one or all of the small number of genes that are most affected at this time play a critical role in the loss of photodetection and in disruption of outer segments without marked destruction of cell bodies. This group includes Aipl1, Ankyrd33/Panky, and Agr2. We suspect that the reduction in expression of one or more of these genes and their encoded proteins is critical for the initial deterioration of outer segments. Furthermore the presence of putative binding sites in the promoters of these affected genes suggests that NeuroD1 acts directly on these genes.

Aipl1 has been linked to Leber’s congenital amarousis, one of the earliest onset and the most severe forms of inherited retinopathy in humans (Ramamurthy et al. 2004). Experimental deletion of Aipl1 causes a retinal phenotype remarkably similar to the one described in the present study: compromised ERGs, altered structural integrity of the outer segment and the RPE boundary, and photoreceptor-specific degeneration (Ramamurthy et al. 2004, Dyer et al. 2004). Hence, the NeuroD1-Aipl1 link established in this study is of special interest because it raises the possibility that retinal pathologies could reflect a reduction in NeuroD1-dependent gene expression, leading to a reduction in Aipl1 expression, which leads to loss of phototransduction.

A second factor that might contribute to the observed effects of NeuroD1 cKO is Ankyrd33/Panky, which encodes a transcriptional cofactor that suppresses Crx-dependent photoreceptor genes (Sanuki et al. 2010). Accordingly, down-regulation of Ankrd33/Panky may remove suppression of a gene that has a negative influence on photoreceptor biology. An Ankyrd33/Panky knockout mouse model is not available but our expression data, as well as other gene profiling data, suggest that Ankyrd33 is a good retinal degeneration candidate gene (Geisert et al. 2009, Sanuki et al. 2010).

Decreased expression of Agr2 may also contribute to the loss of photoreceptor function through an effect on protein folding. This gene encodes a protein disulfide isomerase (Park et al. 2009, Persson et al. 2005); members of this family insure proper disulfide bonds are formed in newly synthesized proteins. Proper formation of disulfides is required for normal protein function; an example from the retina literature is Rho (McKibbin et al. 2007), misfolding of which prevents membrane insertion and proper function. Accordingly, it is possible that the decrease in Agr2 transcripts contributes to the observed effects because substrates of this enzyme, perhaps Rho, are incorrectly folded. However, the finding that Agr2−/− animals have normal ERG responses and relatively normal photoreceptor morphology indicates that loss of Agr2 alone does not explain the observed NeuroD1 cKO phenotype. Accordingly, it seems valuable to consider that Agr2 might contribute to photoreceptor physiology and that photoreceptor loss in the NeuroD1 cKO mouse reflects the impact of the partially reduced expression of it together with that of Aipl1 and Ankyrd33/Panky.

The observations in this study are consistent with the interpretation that the gradual loss of photoreceptor cell bodies may involve an immune response in which the initial deterioration of outer segments leads to destruction of photoreceptor cell bodies (Whitcup et al. 1998). This is consistent with the increased expression of genes associated with the immune response including Gfap, Prtg, Edn2, A2m, and Tal2. The most highly up-regulated (>11-fold) gene is T-cell acute lymphocytic leukemia 2 (Tal2), that encodes a bHLH transcription factor which functions as an oncogene whose activation can lead to T-cell leukemia, a cancer of the immune system (Bucher et al. 2000, Xia et al. 1994, Wadman et al. 1994).

NeuroD1 also plays a role in cone photoreceptor specification via regulation of thyroid hormone receptor beta2 (TRbeta2) expression (Liu et al. 2008). We found similar effects on cone photoreceptor specification but did not observe a change in expression of TRbeta2 at two months of age. However, the study by Liu et al., (2008) involved embryonic total NeuroD1 knockout and evaluated early postnatal retinal explants; in contrast, in the present study NeuroD1 was deleted late in gestation and adult tissue was evaluated. Therefore, it is possible that the differing results in the two studies reflect differences in the timing of the knockout and in the developmental stages examined.

Role of NeuroD1 in pineal biology

In contrast to the retina, deletion of NeuroD1 did not cause obvious pineal gland morphological effects, although shorter and wider pineal stalks were consistently observed. Deletion of NeuroD1 did not affect expression of phototransduction- or melatonin synthesis-related genes in the pineal gland, consistent with previous findings in neonatal mice (Muñoz et al. 2007). This suggests that NeuroD1 is not an essential regulator of the melatonin synthesis pathway, but does not eliminate the possibility that it is involved in modulating other aspects of pineal biology, including transcription and calcium signaling, processes which are linked to S100a8 and S100a9 (Ghavami et al. 2009); expression of which was suppressed in the NeuroD1 KO pineal gland.

Comparison of the results of the current study with the previous study on NeuroD1 deletion in neonatal mice reveals notable differences. Total knockout of NeuroD1 results in increased expression of Kif5c and Gad1 (Muñoz et al. 2007) in the neonatal pineal gland; this was not observed in the current study of the adult pineal gland in which the gene deletion occurs late in gestation, when Crx is first expressed. Accordingly the differences may reflect differences in the timing of NeuroD1 deletion and in the ages studied. It is likewise reasonable to suspect that NeuroD1 may play different roles during pineal development because NeuroD1 may control transcription in concert with other factors (Cherry et al. 2011); different combinations of which in the neonatal versus the adult pineal gland could have differential effects on gene expression.

Day-night analyses of the mouse pineal transcriptome have been previously published (Rovsing et al. 2011). Those analyses revealed significant differences in the abundance of rhythmic genes between species: In contrast to >600 genes found to be rhythmic in the rat pineal gland (Bailey et al. 2009), only 51 genes showed a day/night rhythm in 129sv mice (Rovsing et al. 2011). We compared the list of 51 genes that were rhythmically expressed in 129sv mice (Rovsing et al., 2011) with the list of 38 genes that were rhythmic in the NeuroD1 control pineal glands, which are on a C57BL/6J background. Of the 51 genes that were rhythmically expressed on a day-night basis in the 129sv control pineal glands only 15 were also rhythmic in the C57BL/6J; these included melatonin and signal transduction genes Aanat, Gng4, E2f8, Cpm, Nr1d1, and Nrxn3 (Rovsing et al., 2011). This indicates that there are notable strain differences in rhythmic gene expression in this tissue and perhaps others.

Concluding remarks

The findings of this report confirm that NeuroD1 is required for photoreceptor function and indicate that it may act through a small set of genes to promote retinal survival, specifically through the maintenance of photoreceptor outer segments, loss of which results in photoreceptor degeneration. NeuroD1 may also play a role in pinealocyte homeostasis. The advances from our study are summarized in Fig. 8, which describes the expression of NeuroD1 and its downstream targets in the photoreceptor and pinealocyte lineages. The absence of NeuroD1 and its downstream targets results in deterioration of outer segments and leads to the progressive degeneration of photoreceptor cell bodies (Table 5). The NeuroD1-Aipl1 link established in this study raises the possibility that retinal pathologies could in part reflect a reduction in NeuroD1-dependent gene expression, which in turn could suppress expression of Aipl1 and other genes required for photoreceptor homeostasis.

Figure 8
Schematic diagram illustrating NeuroD1 and its downstream targets in the photoreceptor and pinealocyte lineages

Supplementary Material

Supplementary Data


This research was supported by the Intramural Research Program of the National Institute of Child Health, NIH grants R01EY004864 and P30EY006360, and an unrestricted departmental grant from Research to Prevent Blindness, Inc. (RPB). PMI is a recipient of a Senior Scientific Investigator Award from RPB. We would like to thank members of the Klein laboratory, Dr. Morten Møller and Dr. James Russell for many helpful discussions, Dr. Cheryl Craft for the gift of S-opsin and M-opsin antisera, Dr. Robert Molday for the gift of the Rho (Rho 4D2) antiserum, Dr. David J. Erle for the gift of Agr2+/− mice, Chip Dye (NICHD Microscopy and Imaging Core) for his help with transmission electron microscopy, Dr. Anand Swaroop and members of the Neurobiology-Neurodegeneration and Repair Laboratory and Dr. Haohua Qian in the NEI Visual Function Core for assistance with electroretinography, and Daniel Abebe for his veterinary support.

Abbreviations used

basic helix-loop-helix
conditional knockout
Zeitgeber time
outer nuclear layer
inner nuclear layer
ganglion cell layer
retinal pigment epithelium
transmission electron microscopy


Any Conflict of Interest: None


  • Armitage P, Berry G, Matthews JNS. Statistical Methods in Medical Research. 4. Blackwell Science; Oxford: 2002.
  • Babila T, Schaad NC, Simonds WF, Shinohara T, Klein DC. Development of MEKA (phosducin), G beta, G gamma and S-antigen in the rat pineal gland and retina. Brain Res. 1992;585:141–148. [PubMed]
  • Bailey MJ, Coon SL, Carter DA, et al. Night/day changes in pineal expression of >600 genes: central role of adrenergic/cAMP signaling. J Biol Chem. 2009;284:7606–7622. [PubMed]
  • Bucher K, Sofroniew MV, Pannell R, et al. The T cell oncogene Tal2 is necessary for normal development of the mouse brain. Dev Biol. 2000;227:533–544. [PubMed]
  • Cai L, Morrow EM, Cepko CL. Misexpression of basic helix-loop-helix genes in the murine cerebral cortex affects cell fate choices and neuronal survival. Development. 2000;127:3021–3030. [PubMed]
  • Cherry TJ, Wang S, Bormuth I, Schwab M, Olson J, Cepko CL. NeuroD factors regulate cell fate and neurite stratification in the developing retina. J Neurosci. 2011;31:7365–7379. [PMC free article] [PubMed]
  • Das S, Hirano M, McCallister C, Tako R, Nikolaidis N. Comparative genomics and evolution of immunoglobulin-encoding loci in tetrapods. Adv Immunol. 2011;111:143–178. [PubMed]
  • Donoso LA, Merryman CF, Edelberg KE, Naids R, Kalsow C. S-antigen in the developing retina and pineal gland: a monoclonal antibody study. Invest Ophthalmol Vis Sci. 1985;26:561–567. [PubMed]
  • Dyer MA, Donovan SL, Zhang J, Gray J, Ortiz A, Tenney R, Kong J, Allikmets R, Sohocki MM. Retinal degeneration in Aipl1-deficient mice: a new genetic model of Leber congenital amaurosis. Brain Res Mol Brain Res. 2004;132:208–220. [PubMed]
  • Fan W, Li X, Wang W, Mo JS, Kaplan H, Cooper NG. Early Involvement of Immune/Inflammatory Response Genes in Retinal Degeneration in DBA/2J Mice. Ophthalmol Eye Dis. 2010;1:23–41. [PMC free article] [PubMed]
  • Furukawa A, Koike C, Lippincott P, Cepko CL, Furukawa T. The mouse Crx 5′-upstream transgene sequence directs cell-specific and developmentally regulated expression in retinal photoreceptor cells. J Neurosci. 2002;22:1640–1647. [PubMed]
  • Geisert EE, Lu L, Freeman-Anderson NE, Templeton JP, Nassr M, Wang X, Gu W, Jiao Y, Williams RW. Gene expression in the mouse eye: an online resource for genetics using 103 strains of mice. Mol Vis. 2009;15:1730–1763. [PMC free article] [PubMed]
  • Ghavami S, Chitayat S, Hashemi M, Eshraghi M, Chazin WJ, Halayko AJ, Kerkhoff C. S100A8/A9: a Janus-faced molecule in cancer therapy and tumorgenesis. Eur J Pharmacol. 2009;625:73–83. [PubMed]
  • Goebbels S, Bode U, Pieper A, Funfschilling U, Schwab MH, Nave KA. Cre/loxP-mediated inactivation of the bHLH transcription factor gene NeuroD/BETA2. Genesis. 2005;42:247–252. [PubMed]
  • Klein DC. Evolution of the vertebrate pineal gland: the AANAT hypothesis. Chronobiol Int. 2006;23:5–20. [PubMed]
  • Korf HW, Foster RG, Ekstrom P, Schalken JJ. Opsin-like immunoreaction in the retinae and pineal organs of four mammalian species. Cell Tissue Res. 1985;242:645–648. [PubMed]
  • Korf HW, White BH, Schaad NC, Klein DC. Recoverin in pineal organs and retinae of various vertebrate species including man. Brain Res. 1992;595:57–66. [PubMed]
  • Kumar A, Shamsuddin N. Retinal Muller glia initiate innate response to infectious stimuli via toll-like receptor signaling. PLoS One. 2012;7:e29830. [PMC free article] [PubMed]
  • Lee JK, Cho JH, Hwang WS, Lee YD, Reu DS, Suh-Kim H. Expression of neuroD/BETA2 in mitotic and postmitotic neuronal cells during the development of nervous system. Dev Dyn. 2000;217:361–367. [PubMed]
  • Lewandoski M, Meyers EN, Martin GR. Analysis of Fgf8 gene function in vertebrate development. Cold Spring Harb Symp Quant Biol. 1997;62:159–168. [PubMed]
  • Liu H, Etter P, Hayes S, Jones I, Nelson B, Hartman B, Forrest D, Reh TA. NeuroD1 regulates expression of thyroid hormone receptor 2 and cone opsins in the developing mouse retina. J Neurosci. 2008;28:749–756. [PubMed]
  • Liu M, Pereira FA, Price SD, et al. Essential role of BETA2/NeuroD1 in development of the vestibular and auditory systems. Genes Dev. 2000;14:2839–2854. [PubMed]
  • Lolley RN, Craft CM, Lee RH. Photoreceptors of the retina and pinealocytes of the pineal gland share common components of signal transduction. Neurochem Res. 1992;17:81–89. [PubMed]
  • Longo A, Guanga GP, Rose RB. Crystal structure of E47-NeuroD1/beta2 bHLH domain-DNA complex: heterodimer selectivity and DNA recognition. Biochemistry. 2008;47:218–229. [PubMed]
  • McKibbin C, Toye AM, Reeves PJ, Khorana HG, Edwards PC, Villa C, Booth PJ. Opsin stability and folding: the role of Cys185 and abnormal disulfide bond formation in the intradiscal domain. J Mol Biol. 2007;374:1309–1318. [PubMed]
  • Mehmood R, Yasuhara N, Fukumoto M, Oe S, Tachibana T, Yoneda Y. Cross-talk between distinct nuclear import pathways enables efficient nuclear import of E47 in conjunction with its partner transcription factors. Mol Biol Cell. 2011;22:3715–3724. [PMC free article] [PubMed]
  • Mehmood R, Yasuhara N, Oe S, Nagai M, Yoneda Y. Synergistic nuclear import of NeuroD1 and its partner transcription factor, E47, via heterodimerization. Exp Cell Res. 2009;315:1639–1652. [PubMed]
  • Miyata T, Maeda T, Lee JE. NeuroD is required for differentiation of the granule cells in the cerebellum and hippocampus. Genes Dev. 1999;13:1647–1652. [PubMed]
  • Møller M, van Deurs B, Westergaard E. Vascular permeability to proteins and peptides in the mouse pineal gland. Cell Tissue Res. 1978;195:1–15. [PubMed]
  • Morrow EM, Furukawa T, Lee JE, Cepko CL. NeuroD regulates multiple functions in the developing neural retina in rodent. Development. 1999;126:23–36. [PubMed]
  • Muñoz EM, Bailey MJ, Rath MF, Shi Q, Morin F, Coon SL, Møller M, Klein DC. NeuroD1: developmental expression and regulated genes in the rodent pineal gland. J Neurochem. 2007;102:887–899. [PubMed]
  • Nishida A, Furukawa A, Koike C, Tano Y, Aizawa S, Matsuo I, Furukawa T. Otx2 homeobox gene controls retinal photoreceptor cell fate and pineal gland development. Nat Neurosci. 2003;6:1255–1263. [PubMed]
  • Ochocinska MJ, Hitchcock PF. NeuroD regulates proliferation of photoreceptor progenitors in the retina of the zebrafish. Mech Dev. 2009;126:128–141. [PMC free article] [PubMed]
  • Omori Y, Araki F, Chaya T, Kajimura N, Irie S, Terada K, Muranishi Y, Tsujii T, Ueno S, Koyasu T, Tamaki Y, Kondo M, Amano S, Furukawa T. Presynaptic dystroglycan-pikachurin complex regulates the proper synaptic connection between retinal photoreceptor and bipolar cells. J Neurosci in press 2012 [PubMed]
  • Pang JJ, Chang B, Hawes NL, et al. Retinal degeneration 12 (rd12): a new, spontaneously arising mouse model for human Leber congenital amaurosis (LCA) Mol Vis. 2005;11:152–162. [PubMed]
  • Park SW, Zhen G, Verhaeghe C, Nakagami Y, Nguyenvu LT, Barczak AJ, Killeen N, Erle DJ. The protein disulfide isomerase AGR2 is essential for production of intestinal mucus. Proc Natl Acad Sci U S A. 2009;106:6950–6955. [PubMed]
  • Pennesi ME, Cho JH, Yang Z, Wu SH, Zhang J, Wu SM, Tsai MJ. BETA2/NeuroD1 null mice: a new model for transcription factor-dependent photoreceptor degeneration. J Neurosci. 2003;23:453–461. [PubMed]
  • Persson S, Rosenquist M, Knoblach B, Khosravi-Far R, Sommarin M, Michalak M. Diversity of the protein disulfide isomerase family: identification of breast tumor induced Hag2 and Hag3 as novel members of the protein family. Mol Phylogenet Evol. 2005;36:734–740. [PubMed]
  • Ramamurthy V, Niemi GA, Reh TA, Hurley JB. Leber congenital amaurosis linked to AIPL1: a mouse model reveals destabilization of cGMP phosphodiesterase. Proc Natl Acad Sci U S A. 2004;101:13897–13902. [PubMed]
  • Rath MF, Munoz E, Ganguly S, Morin F, Shi Q, Klein DC, Møller M. Expression of the Otx2 homeobox gene in the developing mammalian brain: embryonic and adult expression in the pineal gland. J Neurochem. 2006;97:556–566. [PubMed]
  • Rattner A, Nathans J. The genomic response to retinal disease and injury: evidence for endothelin signaling from photoreceptors to glia. J Neurosci. 2005;25:4540–4549. [PubMed]
  • Reig JA, Yu L, Klein DC. Pineal transduction. Adrenergic----cyclic AMP-dependent phosphorylation of cytoplasmic 33-kDa protein (MEKA) which binds beta gamma-complex of transducin. J Biol Chem. 1990;265:5816–5824. [PubMed]
  • Rodrigues MM, Hackett J, Gaskins R, Wiggert B, Lee L, Redmond M, Chader GJ. Interphotoreceptor retinoid-binding protein in retinal rod cells and pineal gland. Invest Ophthalmol Vis Sci. 1986;27:844–850. [PubMed]
  • Rovsing L, Clokie S, Bustos DM, Rohde K, Coon SL, Litman T, Rath MF, Møller M, Klein DC. Crx broadly modulates the pineal transcriptome. J Neurochem. 2011;119:262–274. [PMC free article] [PubMed]
  • Sanuki R, Omori Y, Koike C, Sato S, Furukawa T. Panky, a novel photoreceptor-specific ankyrin repeat protein, is a transcriptional cofactor that suppresses CRX-regulated photoreceptor genes. FEBS Lett. 2010;584:753–758. [PubMed]
  • Schaad NC, Shinohara T, Abe T, Klein DC. Photoneural control of the synthesis and phosphorylation of pineal MEKA (phosducin) Endocrinology. 1991;129:3289–3298. [PubMed]
  • Schwab MH, Bartholomae A, Heimrich B, et al. Neuronal basic helix-loop-helix proteins (NEX and BETA2/Neuro D) regulate terminal granule cell differentiation in the hippocampus. J Neurosci. 2000;20:3714–3724. [PubMed]
  • Takahashi KF, Kiyoshima T, Kobayashi I, et al. Protogenin, a new member of the immunoglobulin superfamily, is implicated in the development of the mouse lower first molar. BMC Dev Biol. 2010;10:115. [PMC free article] [PubMed]
  • Wadman I, Li J, Bash RO, Forster A, Osada H, Rabbitts TH, Baer R. Specific in vivo association between the bHLH and LIM proteins implicated in human T cell leukemia. EMBO J. 1994;13:4831–4839. [PubMed]
  • Whitcup SM, Vistica BP, Milam AH, Nussenblatt RB, Gery I. Recoverin-associated retinopathy: a clinically and immunologically distinctive disease. Am J Ophthalmol. 1998;126:230–237. [PubMed]
  • Wojtowicz JM, Kee N. BrdU assay for neurogenesis in rodents. Nat Protoc. 2006;1:1399–1405. [PubMed]
  • Xia Y, Hwang LY, Cobb MH, Baer R. Products of the TAL2 oncogene in leukemic T cells: bHLH phosphoproteins with DNA-binding activity. Oncogene. 1994;9:1437–1446. [PubMed]