A cis-acting element, T alpha-1, in the upstream region of rod alpha-transducin gene that binds a developmentally regulated retina-specific nuclear factor

The cis-regulatory logic of the mammalian photoreceptor transcriptional network

The photoreceptor cells of the retina are subject to a greater number of genetic diseases than any other cell type in the human body. The majority of more than 120 cloned human blindness genes are highly expressed in photoreceptors. In order to establish an integrative framework in which to understand these diseases, we have undertaken an experimental and computational analysis of the network controlled by the mammalian photoreceptor transcription factors, Crx, Nrl, and Nr2e3. Using microarray and in situ hybridization datasets we have produced a model of this network which contains over 600 genes, including numerous retinal disease loci as well as previously uncharacterized photoreceptor transcription factors. To elucidate the connectivity of this network, we devised a computational algorithm to identify the photoreceptor-specific cis-regulatory elements (CREs) mediating the interactions between these transcription factors and their target genes. In vivo validation of our computational predictions resulted in the discovery of 19 novel photoreceptor-specific CREs near retinal disease genes. Examination of these CREs permitted the definition of a simple cis-regulatory grammar rule associated with high-level expression. To test the generality of this rule, we used an expanded form of it as a selection filter to evolve photoreceptor CREs from random DNA sequences in silico. When fused to fluorescent reporters, these evolved CREs drove strong, photoreceptor-specific expression in vivo. This study represents the first systematic identification and in vivo validation of CREs in a mammalian neuronal cell type and lays the groundwork for a systems biology of photoreceptor transcriptional regulation.

Genomic organization of the human rod photoreceptor cGMP-gated cation channel beta-subunit gene

We previously reported that the CNGB1 locus encoding the rod photoreceptor cGMP-gated channel beta-subunit is complex, comprising non-overlapping transcription units that give rise to at least six transcripts (Ardell, M.D., Aragon, I., Oliveira, L., Porche, G.E., Burke, E., Pittler, S.J., 1996. The beta subunit of human rod photoreceptor cGMP-gated cation channel is generated from a complex transcription unit. FEBS Lett. 389, 213-218). To further understand the transcriptional regulation of this extraordinarily complex locus, and to develop a screen for defects in the gene in patients with hereditary disease, we determined its genomic organization and DNA sequence. The CNGB1 locus consists of 33 exons, which span approximately 100kb of genomic DNA on chromosome 16. The beta-subunit comprises two domains, an N-terminal glutamic acid-rich segment (GARP), and a C-terminal channel-like portion. Two additional exons encoding a short GARP transcript and a truncated channel-like transcript have been identified. A major transcription start point was identified 79bp upstream of the initiator ATG. To begin analysis of the basis for the generation of multiple transcripts, and to identify promoters driving expression in retina, approximately 2.5kb of the upstream region were sequenced. Putative cis-elements, which can bind the retina-specific transcription factors Crx and Erx, were found immediately upstream of the transcription start point, and may be important for gene expression in this tissue. From our analysis, a model is reported to account for at least four of the retinal transcripts.

Rod outer segment membrane guanylate cyclase type 1 (ROS-GC1) gene: structure, organization and regulation by phorbol ester, a protein kinase C activator

At present there are two recognized members of the ROS-GC subfamily of membrane guanylate cyclases. They are ROS-GC1 and ROS-GC2. A distinctive feature of this family is that its members are not switched on by the extracellular peptide hormones; instead, they are modulated by intracellular Ca2+ signals, consistent to their linkage with phototransduction. An intriguing feature of ROS-GC1, which distinguishes it from ROS-GC2, is that it has two Ca2+ switches. One switch inhibits the enzyme at micromolar concentrations of Ca2+, as in phototransduction; the other, stimulates. The stimulatory switch, most likely, is linked to retinal synaptic activity. Thus, ROS-GC1 is linked to both phototransduction and the synaptic activity. The present study describes (1) the almost complete structural identity of 18.5 kb ROS-GC1 gene; (2) its structural organization: the gene is composed of 20 exons and 19 introns with classical GT/AG boundaries; (3) the activity of the ROS-GC1 promoter assayed through luciferase reporter in COS cells; and (4) induction of the gene by phorbol ester, a protein kinase C (PKC) activator. The co-presence of PKC and ROS-GC1 in photoreceptors suggests that regulation of the ROS-GC1 gene by PKC might be a physiologically relevant phenomenon.

Transcriptional regulation of cellular retinaldehyde-binding protein in the retinal pigment epithelium. A role for the photoreceptor consensus element

Cellular retinaldehyde-binding protein (CRALBP) is abundantly expressed in the retinal pigment epithelium (RPE) and Muller cells of the retina, where it is thought to function in retinoid metabolism and visual pigment regeneration. Mutations in human CRALBP that destroy retinoid binding have been linked to autosomal recessive retinitis pigmentosa. To identify the DNA elements that regulate expression of the human CRALBP gene in the RPE, transient transfection studies were carried out with three CRALBP-expressing human RPE cell culture systems. The regions from -2089 to -1539 base pairs and from -243 to +80 base pairs demonstrated positive regulatory activity. Similar activity was not observed with cultured human breast, liver, or skin cells. Since sequence analysis of the -243 to +80 region identified the presence of two photoreceptor consensus element-1 (PCE-1) sites, elements that have been implicated in photoreceptor gene regulation, the role of these sequences in RPE expression was examined. Mutation of either PCE-1 site significantly reduced reporter activity, and mutation or deletion of both sites dramatically reduced activity. Electrophoretic mobility shift analysis with RPE nuclear extracts revealed two complexes that required intact PCE-1 sites. These studies also identified two identical sequences (GCAGGA) flanking PCE-1, termed the binding CRALBP element (BCE), that are also important for complex formation. Southwestern analysis with PCE-1/BCEcontaining probes identified species with apparent masses near 90-100 and 31 kDa. These results begin to identify the regulatory regions required for RPE expression of CRALBP and suggest that PCE-1-binding factor(s) may play a role in regulating RPE as well as photoreceptor gene expression.

The bovine guanylate cyclase GC-E gene and 5' flanking region

The gene encoding the bovine guanylate cyclase isoform E (GC-E) was isolated as a single 18 kb genomic clone and shown to have 20 exons and 19 introns. Comparison of the structure of the GC-E gene with structures of other membrane guanylate cyclase genes indicates that the GC-E is most closely related to the subfamily of sensory guanylate cyclases. Comparison of the GC-E structure with that of the more distantly related guanylate cyclase isoform A (GC-A) gene shows the most divergence in the extracellular and C-terminal regions, but general conservation of introns and exons in the intracellular kinase-like and catalytic domains. RT-PCR from several bovine tissues shows that GC-E is expressed only in the retina. Consistent with this pattern of expression, elements for the retinal-specific transcription factors RET-1, RET-2 and Talpha-1 are located in the 5' flanking promoter region.

Structural and developmental analysis of the mouse peripherin/rds gene

Mutations in the peripherin/rds gene have been reported to be associated with different forms of human autosomal dominant retinitis pigmentosa (ADRP) and macular degeneration (MD). To better understand the disruptive role of these mutations, knowledge of the structure-function relationship of the peripherin/rds gene is needed. To facilitate that, genomic clones encoding the mouse gene were isolated using bovine cDNA sequences as probes. Sequence analysis of clone lambda 6-1-1, that contained the entire coding sequence for the mouse peripherin/rds, yielded the exon-intron organization of the gene. The gene is composed of three exons (581, 247, and 213 bp) and two introns with the first and second introns 8.6 kb and 3.7 kb in size, respectively. Two major (1.6 and 2.7 kb) and three minor (4.0, 5.5, 6.5 kb) transcripts were detected on RNA blots. The major transcripts first appeared in the brain at embryonic day 13 and in the retina at postnatal day 1. Transcripts were missing in brain and eye of mice at embryonic day 15. Several transcription start sites were mapped within 26 nucleotides approximately 200 bp upstream from the translation initiation site. However, transcripts varied in the lengths of their 3' untranslated portion as a result of the utilization of different polyadenylation signals.

Characterization of the Xenopus rhodopsin gene

The abundant Xenopus rhodopsin gene and cDNA have been cloned and characterized. The gene is composed of five exons spanning 3.5 kilobase pairs of genomic DNA and codes for a protein 82% identical to the bovine rhodopsin. The cDNA was expressed in COS1 cells and regenerated with 11-cis-retinal, forming a light-sensitive pigment with maximal absorbance at 500 nm. Both Southern blots and polymerase chain reaction amplification of intron 1 revealed multiple products, indicating more than one allele for the rhodopsin gene. Comparisons with other vertebrate rhodopsin 5 upstream sequences showed significant nucleotide homologies in the 200 nucleotides proximal to the transcription initiation site. This homology included the TATA box region, Ret 1/PCE1 core sequence (CCAATTA), and surrounding nucleotides. To functionally characterize the rhodopsin promoter, transient embryo transfections were used to assay transcriptional control elements in the 5 upstream region using a luciferase reporter. DNA sequences encompassing -5500 to +41 were able to direct luciferase expression in embryo heads. Reporter gene expression was also observed in embryos microinjected with reporter plasmids during early blastomere stages. These results locate transcriptional control elements upstream of the Xenopus rhodopsin gene and show the feasibility of embryo transfections for promoter analysis of rod-specific genes.

RER, an evolutionarily conserved sequence upstream of the rhodopsin gene, has enhancer activity

Previous transgenic mouse experiments localized the mammalian rhodopsin gene promoter to a region just upstream of the mRNA start site, and also suggested the existence of a second more distal regulatory region. A highly conserved 100-base pair (bp) sequence which is homologous to the red and green opsin locus control region is located 1.5-2 kilobases upstream of the rhodopsin gene (depending on the species). In order to test the activity of this 100-bp region, transgenic mice were generated with bovine rhodopsin promoter/lacZ constructs which differed only by the presence or absence of the sequence. Of 11 lines generated, all demonstrated photoreceptor-specific expression of the transgene, but the lines with the putative regulatory region showed significantly higher expression. Additional transgenic lines in which the region was fused to a minimal heterologous promoter did not show transgene expression in the retina. Gel mobility shift and DNase I footprint assays demonstrated that bovine retinal nuclear extracts contain retina-specific as well as ubiquitously expressed factors that interact with the putative regulatory region in a sequence-specific manner. These results indicate that the 100-bp sequence can indeed function in vivo as a rhodopsin enhancer region.

Mash-1 is expressed during ROD photoreceptor differentiation and binds an E-box, E(opsin)-1 in the rat opsin gene

It has been shown previously that the transcription factor Mash-1 plays a significant role in mammalian neurogenesis. In the present study we show that Mash-1 is expressed during rat retinal development and that it interacts specifically with an E-box identified in the promoter of the opsin gene during rod photoreceptor differentiation. We propose that opsin may be one of the downstream neuronal genes regulated by Mash-1 during neurogenesis in the central nervous system.

A single cis-acting element in a short promoter segment of the gene encoding the interphotoreceptor retinoid-binding protein confers tissue-specific expression

Interphotoreceptor retinoid-binding protein (IRBP) is the major protein component of the interphotoreceptor matrix. IRBP has a highly restricted tissue-specific expression in retinal photoreceptor cells and in a subgroup of pinealocytes. With the purpose of understanding how transcriptional regulation contributes to the expression of human IRBP, we have studied a short promoter fragment (from -123 to +18, relative to the transcription start site). We demonstrate, by analysis of the expression of the lacZ reporter gene fused to this short promoter fragment in transgenic mice, that it is sufficient to confer tissue-specific expression in retinal photoreceptors and in pinealocytes. DNA/protein binding assays, performed to identify binding sites for tissue-specific trans-acting factors, have shown that an element between -45 and -58 binds a factor present only in nuclear extracts of retinoblastoma-derived cell lines, which express IRBP. An element further upstream, between -86 and -106, binds apparently ubiquitous factors. Site-directed mutagenesis was performed to disrupt a GATTAA motif included in the -45 to -58 binding site and a second inverted GATTAA motif present shortly upstream. In transgenic mice bearing the mutated version of the promoter fragment, the expression of the reporter gene was completely abolished, thus suggesting that this element is essential for tissue-specific expression. A GATTAA motif appears in the 5'-flanking regions of several photoreceptor-specific genes, suggesting that this could be the recognition site for a photoreceptor-specific factor.

Characterization and regulation of the protein binding to a cis-acting element, RET 1, in the rat opsin promoter

RET 1 is a binding site for retinal nuclear proteins located at -136 to -110 bp in the rat opsin promoter, as defined by DNase protection assays. A similar sequence is found in the upstream flanking regions of many other photoreceptor genes in mammals and other species, including Drosophila. A 7-base consensus sequence, CAATTAG, is found in these genes and has the binding activity of the longer RET 1 element. A 40-kDa protein that binds to RET 1 has been purified over 2 x 10(5)-fold to apparent homogeneity by affinity chromatography. The RET 1 binding activity is first detectable at E18 and increases during the first two postnatal weels, At embryonic ages the retarded bands show an altered mobility and at early postnatal ages two bands are detected, with the adult band increasing and the embryonic band decreasing in intensity. Treatment of early postnatal retinas with bFGF increased the binding activity in nuclear extracts and caused a shift in migration of the retarded band to a position characteristic of the embryonic form of the complex. The results support the hypothesis that RET 1-like elements play an important role in rod photoreceptor development.