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.
Hsiau
Timothy H-C
TH
Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, United States of America.
Diaconu
Claudiu
C
Myers
Connie A
CA
Lee
Jongwoo
J
Cepko
Constance L
CL
Corbo
Joseph C
JC
D000465:Algorithms; D000818:Animals; D050976:Basic-Leucine Zipper Transcription Factors / Q000235:genetics; D001766:Blindness / Q000235:genetics; D016384:Consensus Sequence; D005136:Eye Proteins / Q000235:genetics; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D017403:In Situ Hybridization; D008322:Mammals; D020411:Oligonucleotide Array Sequence Analysis; D057093:Orphan Nuclear Receptors / Q000235:genetics; D020419:Photoreceptor Cells, Vertebrate / Q000473:pathology / Q000502:physiology*; D012045:Regulatory Sequences, Nucleic Acid; D012164:Retinal Diseases / Q000235:genetics*; D015534:Trans-Activators / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics; D014158:Transcription, Genetic
D050976:Basic-Leucine Zipper Transcription Factors; D005136:Eye Proteins; D018398:Homeodomain Proteins; C403073:NR2E3 protein, human; C490037:NRL protein, human; D057093:Orphan Nuclear Receptors; D015534:Trans-Activators; D014157:Transcription Factors; C109288:cone rod homeobox protein