Limits...
The cis-regulatory logic of the mammalian photoreceptor transcriptional network.

Hsiau TH, Diaconu C, Myers CA, Lee J, Cepko CL, Corbo JC - PLoS ONE (2007)

Bottom Line: Examination of these CREs permitted the definition of a simple cis-regulatory grammar rule associated with high-level expression.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America.

ABSTRACT
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.

Show MeSH

Related in: MedlinePlus

The transcription network controlled by Crx, Nrl, and Nr2e3.A, Venn diagram summarizing all genes dysregulated under high stringency criteria. A complete list of dysregulated genes is given in Table S2. The identity of all genes at points of intersection (including additional intersections not depicted here) are given in Table S7. B, Summary of rod-specific and cone-specific ISH patterns relative to a hematoxylin-eosin (H&E) stained section of retina. The scleral side of the retina is oriented up in all subsequent images. ONL = outer nuclear layer; INL = inner nuclear layer; GCL = ganglion cell layer. C-F, ISH with the indicated probes on four mutant and two wild-type backgrounds. Size bar (in C) = 100 µm G, Summary of transcription factors dysregulated in Crx-/-, Nrl-/-, and/or Nr2e3-/- under high stringency criteria. Green arrows indicate activation and red indicate repression. H and J, ISH with Crx and Prdm1 probes, respectively, on wild-type (CD-1) retinas at the indicated timepoints. J-L, ISH with the indicated probes on four mutant and two wild-type backgrounds. Note that all ISHs were performed on retinas from 6-9 week old animals with the exception of those on Crx-/- which derive from 4-5 week old animals.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC1916400&req=5

pone-0000643-g001: The transcription network controlled by Crx, Nrl, and Nr2e3.A, Venn diagram summarizing all genes dysregulated under high stringency criteria. A complete list of dysregulated genes is given in Table S2. The identity of all genes at points of intersection (including additional intersections not depicted here) are given in Table S7. B, Summary of rod-specific and cone-specific ISH patterns relative to a hematoxylin-eosin (H&E) stained section of retina. The scleral side of the retina is oriented up in all subsequent images. ONL = outer nuclear layer; INL = inner nuclear layer; GCL = ganglion cell layer. C-F, ISH with the indicated probes on four mutant and two wild-type backgrounds. Size bar (in C) = 100 µm G, Summary of transcription factors dysregulated in Crx-/-, Nrl-/-, and/or Nr2e3-/- under high stringency criteria. Green arrows indicate activation and red indicate repression. H and J, ISH with Crx and Prdm1 probes, respectively, on wild-type (CD-1) retinas at the indicated timepoints. J-L, ISH with the indicated probes on four mutant and two wild-type backgrounds. Note that all ISHs were performed on retinas from 6-9 week old animals with the exception of those on Crx-/- which derive from 4-5 week old animals.

Mentions: In order to elucidate the global architecture of transcriptional regulation in mouse photoreceptors, analyses of genes expressed in Crx-/- retinas at P21 were carried out on Affymetrix microarrays. These data were integrated with those of previous studies of Nrl-/- and Nr2e3-/- retinas [20], [25]. Using stringent criteria to define up- and downregulation, a total of 628 genes were identified as dysregulated in at least one of the three mutants (Fig. 1A; Tables S1, S2, S3, S4, S5 and S6). 179 genes were downregulated in Crx-/- (compared to 140 in Nrl-/- and 12 in Nr2e3-/-) whereas 93 genes were upregulated (compared to 297 in Nrl-/- and 55 in Nr2e3-/-). Our results accord well with two previous gene expression studies of the Crx mutant using cDNA microarrays and SAGE [9], [16]. The dysregulated genes comprise many known photoreceptor genes including numerous components of both rod and cone phototransduction cascades.


The cis-regulatory logic of the mammalian photoreceptor transcriptional network.

Hsiau TH, Diaconu C, Myers CA, Lee J, Cepko CL, Corbo JC - PLoS ONE (2007)

The transcription network controlled by Crx, Nrl, and Nr2e3.A, Venn diagram summarizing all genes dysregulated under high stringency criteria. A complete list of dysregulated genes is given in Table S2. The identity of all genes at points of intersection (including additional intersections not depicted here) are given in Table S7. B, Summary of rod-specific and cone-specific ISH patterns relative to a hematoxylin-eosin (H&E) stained section of retina. The scleral side of the retina is oriented up in all subsequent images. ONL = outer nuclear layer; INL = inner nuclear layer; GCL = ganglion cell layer. C-F, ISH with the indicated probes on four mutant and two wild-type backgrounds. Size bar (in C) = 100 µm G, Summary of transcription factors dysregulated in Crx-/-, Nrl-/-, and/or Nr2e3-/- under high stringency criteria. Green arrows indicate activation and red indicate repression. H and J, ISH with Crx and Prdm1 probes, respectively, on wild-type (CD-1) retinas at the indicated timepoints. J-L, ISH with the indicated probes on four mutant and two wild-type backgrounds. Note that all ISHs were performed on retinas from 6-9 week old animals with the exception of those on Crx-/- which derive from 4-5 week old animals.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC1916400&req=5

pone-0000643-g001: The transcription network controlled by Crx, Nrl, and Nr2e3.A, Venn diagram summarizing all genes dysregulated under high stringency criteria. A complete list of dysregulated genes is given in Table S2. The identity of all genes at points of intersection (including additional intersections not depicted here) are given in Table S7. B, Summary of rod-specific and cone-specific ISH patterns relative to a hematoxylin-eosin (H&E) stained section of retina. The scleral side of the retina is oriented up in all subsequent images. ONL = outer nuclear layer; INL = inner nuclear layer; GCL = ganglion cell layer. C-F, ISH with the indicated probes on four mutant and two wild-type backgrounds. Size bar (in C) = 100 µm G, Summary of transcription factors dysregulated in Crx-/-, Nrl-/-, and/or Nr2e3-/- under high stringency criteria. Green arrows indicate activation and red indicate repression. H and J, ISH with Crx and Prdm1 probes, respectively, on wild-type (CD-1) retinas at the indicated timepoints. J-L, ISH with the indicated probes on four mutant and two wild-type backgrounds. Note that all ISHs were performed on retinas from 6-9 week old animals with the exception of those on Crx-/- which derive from 4-5 week old animals.
Mentions: In order to elucidate the global architecture of transcriptional regulation in mouse photoreceptors, analyses of genes expressed in Crx-/- retinas at P21 were carried out on Affymetrix microarrays. These data were integrated with those of previous studies of Nrl-/- and Nr2e3-/- retinas [20], [25]. Using stringent criteria to define up- and downregulation, a total of 628 genes were identified as dysregulated in at least one of the three mutants (Fig. 1A; Tables S1, S2, S3, S4, S5 and S6). 179 genes were downregulated in Crx-/- (compared to 140 in Nrl-/- and 12 in Nr2e3-/-) whereas 93 genes were upregulated (compared to 297 in Nrl-/- and 55 in Nr2e3-/-). Our results accord well with two previous gene expression studies of the Crx mutant using cDNA microarrays and SAGE [9], [16]. The dysregulated genes comprise many known photoreceptor genes including numerous components of both rod and cone phototransduction cascades.

Bottom Line: Examination of these CREs permitted the definition of a simple cis-regulatory grammar rule associated with high-level expression.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America.

ABSTRACT
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.

Show MeSH
Related in: MedlinePlus