Structure and upstream region characterization of the human gene encoding rod photoreceptor cGMP phosphodiesterase alpha-subunit

A 350 bp region of the proximal promoter of Rds drives cell-type specific gene expression

RDS (retinal degeneration slow) is a photoreceptor-specific tetraspanin protein required for the biogenesis and maintenance of rod and cone outer segments. Mutations in the Rds gene are associated with multiple forms of rod- and cone-dominant retinal degeneration. To gain more insight into the mechanisms underlying the regulation of this gene, the identification of regulatory sequences within the promoter of Rds was undertaken. A 3.5 kb fragment of the 5' flanking region of the mouse Rds gene was isolated and binding sites for Crx, Otx2, Nr2e3, RXR family members, Mef2C, Esrrb, NF1, AP1, and SP1 in addition to several E-boxes, GC-boxes and GAGA-boxes were identified. Crx binding sequences were conserved in all mammalian species examined. Truncation expression analysis of the Rds promoter region in Y-79 retinoblastoma cells showed maximal activity in the 350 bp proximal promoter region. We also show that inclusion of more distal fragments reduced promoter activity to the basal level, and that the promoter activities are cell-type and direction specific. Co-transfection with Nrl increased promoter activity, suggesting that this gene positively regulates Rds expression. Based on these findings, a relatively small fragment of the Rds promoter may be useful in future gene transfer studies to drive gene expression in photoreceptors.

Data recovery and integration from public databases uncovers transformation-specific transcriptional downregulation of cAMP-PKA pathway-encoding genes

BACKGROUND

The integration of data from multiple genome-wide assays is essential for understanding dynamic spatio-temporal interactions within cells. Such integration, which leads to a more complete view of cellular processes, offers the opportunity to rationalize better the high amount of "omics" data freely available in several public databases.In particular, integration of microarray-derived transcriptome data with other high-throughput analyses (genomic and mutational analysis, promoter analysis) may allow us to unravel transcriptional regulatory networks under a variety of physio-pathological situations, such as the alteration in the cross-talk between signal transduction pathways in transformed cells.

RESULTS

Here we sequentially apply web-based and statistical tools to a case study: the role of oncogenic activation of different signal transduction pathways in the transcriptional regulation of genes encoding proteins involved in the cAMP-PKA pathway. To this end, we first re-analyzed available genome-wide expression data for genes encoding proteins of the downstream branch of the PKA pathway in normal tissues and human tumor cell lines. Then, in order to identify mutation-dependent transcriptional signatures, we classified cancer cells as a function of their mutational state. The results of such procedure were used as a starting point to analyze the structure of PKA pathway-encoding genes promoters, leading to identification of specific combinations of transcription factor binding sites, which are neatly consistent with available experimental data and help to clarify the relation between gene expression, transcriptional factors and oncogenes in our case study.

CONCLUSIONS

Genome-wide, large-scale "omics" experimental technologies give different, complementary perspectives on the structure and regulatory properties of complex systems. Even the relatively simple, integrated workflow presented here offers opportunities not only for filtering data noise intrinsic in high throughput data, but also to progressively extract novel information that would have remained hidden otherwise. In fact we have been able to detect a strong transcriptional repression of genes encoding proteins of cAMP/PKA pathway in cancer cells of different genetic origins. The basic workflow presented herein may be easily extended by incorporating other tools and can be applied even by researchers with poor bioinformatics skills.

Functional Analysis of the Rod Photoreceptor cGMP Phosphodiesterase α-Subunit Gene Promoter

To understand the factors controlling expression of the cGMP phosphodiesterase type 6 (PDE6) genes, we have characterized the promoter of the human PDE6A gene that encodes the catalytic alpha-subunit. In vivo DNase I hypersensitivity assays revealed two sites immediately upstream of the PDE6A core promoter region. Transient transfection assay in Y79 cells of constructs containing varying lengths of the promoter region showed a decrease in promoter activity with increasing length. The most active segment contained a 177-bp upstream sequence including apparent Crx and Nrl transcription factor binding sites. Both Crx and Nrl transactivated the PDE6A promoter in HEK293 cells and showed a >100-fold increase when coexpressed. Coexpression of a dominant negative inhibitor of Nrl abolished Nrl transactivation but had no effect on Crx. DNase I footprinting assays identified three potential Crx binding sites within a 55-bp segment beginning 29 bp upstream of the transcription start point. Mutation of two of these sites reduced reporter gene activity by as much as 69%. Gel shifts showed that all three Crx sites required a TAAT sequence for efficient binding. Consistent with a requirement for Crx and Nrl in Pde6a promoter activity, Pde6a mRNA is reduced by 87% in the retina of Crx(-/-) mice and is undetectable in Nrl(-/-) mice at postnatal day 10. These results establish that both Nrl and Crx are required for full transcriptional activity of the PDE6A gene.

A PDE6A promoter fragment directs transcription predominantly in the photoreceptor

Rod photoreceptor cGMP phosphodiesterase (PDE6) is a key enzyme in the phototransduction cascade. Lines of transgenic mice were established to determine the spatial expression pattern directed by an upstream fragment of the PDE6A gene. RT-PCR analysis showed that three of four lines analyzed transcribed the transgene predominantly in the retina and weakly in brain. The line showing no transgene transcription did not contain an intact transgene. Transcription of the transgene in the three lines was found in retina and weakly in brain, but not in heart, kidney, liver, or lung. Transcripts were most predominant in the photoreceptors of the retina. These results demonstrate that a short segment of the upstream region of the PDE6A gene comprises a functional promoter that is most active in photoreceptors.

Reproducible high efficiency gene transfer into Y79 retinoblastoma cells using adenofection

Several photoreceptor-specific genes are actively transcribed in Y79 retinoblastoma (Rb) cells, making this cell line potentially useful for the study of photoreceptor metabolism. The utility of these cells is limited because commonly used methods of gene transfer into Y79 cells are inefficient and lack reproducibility. In contrast, we found that adenovirus transduction yields high efficiency gene transfer, however, generation of recombinant adenovirus is lengthy and time consuming. Here, we show that adenofection, a method of coupling adenovirus to plasmid DNA for improved gene transfer, is efficient for gene delivery into Y79 cells. Recombinant adenovirus expressing bacterial lacZ was noncovalently complexed to GFP or luciferase reporter plasmids with polyethylenimine. Efficiency of plasmid gene delivery was determined by monitoring GFP fluorescence. For comparison, calcium phosphate-mediated or cationic lipid transfection was performed in Y79 and HEK293 cells using standard protocols. The adenofection protocol yielded significantly higher efficiencies in Y79 cells than that obtained in these cells with calcium phosphate or cationic lipids. This method will facilitate any experiment requiring reproducible high-level gene transfer. Here, we show that adenofection can be used to analyze activity of the rod photoreceptor PDE6A gene promoter.

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.

Cellular heterogeneity in cerebral cortex: a study of the morphology of pyramidal neurones in visual areas of the marmoset monkey

The morphological characteristics of the basal dendritic fields of layer III pyramidal neurones were determined in visual areas in the occipital, parietal, and temporal lobes of adult marmoset monkeys by means of intracellular iontophoretic injection of Lucifer yellow. Neurones in the primary visual area (V1) had the least extensive and least complex (as determined by Sholl analysis) dendritic trees, followed by those in the second visual area (V2). There was a progressive increase in size and complexity of dendritic trees with rostral progression from V1 and V2, through the "ventral stream," including the dorsolateral area (DL) and the caudal and rostral subdivisions of inferotemporal cortex (ITc and ITr, respectively). Neurones in areas of the dorsal stream, including the dorsomedial (DM), dorsoanterior (DA), middle temporal (MT), and posterior parietal (PP) areas, were similar in size and complexity but were larger and more complex than those in V1 and V2. Neurones in V1 had the lowest spine density, whereas neurones in V2, DM, DA, and PP had similar spine densities. Neurones in MT and inferotemporal cortex had relatively high spine densities, with those in ITr having the highest spine density of all neurones studied. Calculations based on the size, number of branches, and spine densities revealed that layer III pyramidal neurones in ITr have 7.4 times more spines on their basal dendritic fields than those in V1. The differences in the extent of, and the number of spines in, the basal dendritic fields of layer III pyramidal neurones in the different visual areas suggest differences in the ability of neurones to integrate excitatory and inhibitory inputs. The differences in neuronal morphology between visual areas, and the consistency in these differences across New World and Old World monkey species, suggest that they reflect fundamental organisational principles in primate visual cortical structure.