CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors
Open accessAbstract
Approximately 98% of mammalian DNA is noncoding, yet we understand relatively little about the function of this enigmatic portion of the genome. The cis-regulatory elements that control gene expression reside in noncoding regions and can be identified by mapping the binding sites of tissue-specific transcription factors. Cone-rod homeobox (CRX) is a key transcription factor in photoreceptor differentiation and survival, but its in vivo targets are largely unknown. Here, we used chromatin immunoprecipitation with massively parallel sequencing (ChIP-seq) on CRX to identify thousands of cis-regulatory regions around photoreceptor genes in adult mouse retina. CRX directly regulates downstream photoreceptor transcription factors and their target genes via a network of spatially distributed regulatory elements around each locus. CRX-bound regions act in a synergistic fashion to activate transcription and contain multiple CRX binding sites which interact in a spacing- and orientation-dependent manner to fine-tune transcript levels. CRX ChIP-seq was also performed on Nrl(-/-) retinas, which represent an enriched source of cone photoreceptors. Comparison with the wild-type ChIP-seq data set identified numerous rod- and cone-specific CRX-bound regions as well as many shared elements. Thus, CRX combinatorially orchestrates the transcriptional networks of both rods and cones by coordinating the expression of photoreceptor genes including most retinal disease genes. In addition, this study pinpoints thousands of noncoding regions of relevance to both Mendelian and complex retinal disease.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
CRX is an essential transcription factor highly expressed in RPE and retinal ganglion cells.
“cone–rod homeobox (CRX), which is an essential transcription factor highly expressed in RPE and retinal ganglion cells (27).”
From Common variants near FRK/COL10A1 and VEGFA are associated with advanced age-related macular degeneration (2011) · cites this paper as [27]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Primer3 on the WWW for General Users and for Biologist Programmers
Rozen, S., & Skaletsky, H. (2003) · Humana Press eBooks · doi:10.1385/1-59259-192-2:365 · Cited by 14,952 · see citing works
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 4,408 · cited 2× · see citing works
“…for the Service Email Alerting click here.top right corner of the article or Receive free email alerts when new articles cite this article - sign up in the box at the http://genome.cshlp.org/subscriptions go to: Genome Research To subscribe to Copyright © 2010 by Cold Spring Harbor Laboratory Press”
MethodBioMart and Bioconductor: a powerful link between biological databases and microarray data analysis
Durinck, S., Moreau, Y., Kasprzyk, A., Davis, S. R., Moor, B. D., Brāzma, A., & Huber, W. K. (2005) · Computer applications in the biosciences · doi:10.1093/bioinformatics/bti525 · Cited by 2,327 · see citing works
The UCSC Genome Browser database: update 2011
Fujita, P. A., Rhead, B. L., Zweig, A. S., Hinrichs, A. S., Karolchik, D., Cline, M., Goldman, M. J., Barber, G. P., Clawson, H., Coelho, A., et al. (2010) · Nucleic Acids Research · doi:10.1093/nar/gkq963 · Cited by 1,836 · see citing works
The Major Cell Populations of the Mouse Retina
Jeon, C.-J., Strettoi, E., & Masland, R. H. (1998) · The Journal of Neuroscience · doi:10.1523/jneurosci.18-21-08936.1998 · Cited by 1,429 · see citing works
The DNA-encoded nucleosome organization of a eukaryotic genome
Kaplan, N., Moore, I. K., Fondufe-Mittendorf, Y., Gossett, A., Tillo, D., Field, Y., Leproust, E., Hughes, T., Lieb, J., Widom, J., et al. (2008) · Nature · doi:10.1038/nature07667 · Cited by 1,296 · see citing works
Sultan, M., Schulz, M. H., Richard, H., Magen, A., Klingenhoff, A., Scherf, M., Seifert, M., Borodina, T., Soldatov, A., Parkhomchuk, D., et al. (2008) · Science · doi:10.1126/science.1160342 · Cited by 1,293 · see citing works
Self-citationIn vivo enhancer analysis of human conserved non-coding sequences
Pennacchio, L. A., Ahituv, N., Moses, A. M., Prabhakar, S., Nobrega, M. A., Shoukry, M., Minovitsky, S., Dubchak, I., Holt, A., Lewis, K. D., et al. (2006) · Nature · doi:10.1038/nature05295 · Cited by 1,165 · see citing works
The Regulatory Genome: Gene Regulatory Networks In Development And Evolution
Davidson, E. H. (2006) · Thammasat University Digital Collections · Cited by 1,055 · see citing works
Nrl is required for rod photoreceptor development
Mears, A. J., Kondo, M., Swain, P. K., Takada, Y., Bush, R. A., Saunders, T. L., Sieving, P. A., & Swaroop, A. (2001) · Nature Genetics · doi:10.1038/ng774 · Cited by 912 · see citing works
Furukawa, T., Morrow, E. M., & Cepko, C. L. (1997) · Cell · doi:10.1016/s0092-8674(00)80439-0 · Cited by 901 · see citing works
Nuclear Architecture of Rod Photoreceptor Cells Adapts to Vision in Mammalian Evolution
Solovei, I. V., Kreysing, M., Lanctôt, C., Kösem, S., Peichl, L., Cremer, T. J., Guck, J. R., & Joffe, B. I. (2009) · Cell · doi:10.1016/j.cell.2009.01.052 · Cited by 785 · see citing works
An atlas of combinatorial transcriptional regulation in mouse and man
Ravasi, T., Suzuki, H., Cannistraci, C. V., Katayama, S., Bajic, V. B., Tan, K., Akalin, A., Schmeier, S., Kanamori-Katayama, M., Bertin, N., et al. (2010) · Cell · doi:10.1016/j.cell.2010.01.044 · Cited by 715 · see citing works
Chen, S., Wang, Q., Nie, Z., Sun, H., Lennon, G. G., Copeland, N. G., Gilbert, D. J., Jenkins, N. A., & Zack, D. J. (1997) · Neuron · doi:10.1016/s0896-6273(00)80394-3 · Cited by 712 · see citing works
Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data
Valouev, A., Johnson, D. S., Sundquist, A., Medina, C., Anton, E., Batzoglou, S., Myers, R. M., & Sidow, A. (2008) · Nature Methods · doi:10.1038/nmeth.1246 · Cited by 695 · see citing works
Otx2 homeobox gene controls retinal photoreceptor cell fate and pineal gland development
Nishida, A., Furukawa, A., Koike, C., Tano, Y., Aizawa, S., Matsuo, I., & Furukawa, T. (2003) · Nature Neuroscience · doi:10.1038/nn1155 · Cited by 607 · see citing works
(1998) · Cited by 601 · see citing works
Freund, C. L., Gregory, C. Y., Furukawa, T., Papaioannou, M. G., Looser, J., Ploder, L., Bellingham, J., Ng, D., Herbrick, J.-A., Duncan, A. M. V., et al. (1997) · Cell · doi:10.1016/s0092-8674(00)80440-7 · Cited by 564 · see citing works
A thyroid hormone receptor that is required for the development of green cone photoreceptors
Ng, L., Hurley, J. B., Dierks, B. D., Srinivas, M., Saltó, C., Vennström, B., Reh, T. A., & Forrest, D. (2001) · Nature Genetics · doi:10.1038/83829 · Cited by 561 · see citing works
Retinopathy and attenuated circadian entrainment in Crx-deficient mice
Furukawa, T., Morrow, E. M., Li, T., Davis, F. C., & Cepko, C. L. (1999) · Nature Genetics · doi:10.1038/70591 · Cited by 534 · see citing works
Phenotypic robustness conferred by apparently redundant transcriptional enhancers
Frankel, N., Davis, G. K., Vargas, D., Wang, S., Payre, F., & Stern, D. L. (2010) · Nature · doi:10.1038/nature09158 · Cited by 510 · see citing works
Transcription Factors Bind Thousands of Active and Inactive Regions in the Drosophila Blastoderm
Li, X., MacArthur, S., Bourgon, R., Nix, D. A., Pollard, D. A., Iyer, V. N., Hechmer, A., Simirenko, L., Stapleton, M., Hendriks, C. L. L., et al. (2008) · eScholarship (California Digital Library) · doi:10.1371/journal.pbio.0060027 · Cited by 479 · see citing works
Shadow enhancers as a source of evolutionary novelty
Hong, J.-W., Hendrix, D. A., & Levine, M. S. (2008) · Science · doi:10.1126/science.1160631 · Cited by 474 · see citing works
Combinatorial binding predicts spatio-temporal cis-regulatory activity
Zinzen, R. P., Girardot, C., Gagneur, J., Braun, M. M., & Furlong, E. E. M. (2009) · Nature · doi:10.1038/nature08531 · Cited by 397 · see citing works
The UCSC Genome Browser Database: update 2009
Kuhn, R. M., Karolchik, D., Zweig, A. S., Wang, T., Smith, K. E., Rosenbloom, K. R., Rhead, B. L., Raney, B. J., Pohl, A. A., Pheasant, M., et al. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn875 · Cited by 383 · see citing works
oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes
Sui, S. J. H. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki624 · Cited by 370 · see citing works
Akimoto, M., Cheng, H., Zhu, D., Brzezinski, J. A., Khanna, R., Filippova, E. V., Oh, E. C. T., Jing, Y., Linares, J., Brooks, M., et al. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0508214103 · Cited by 314 · see citing works
A conserved retina-specific gene encodes a basic motif/leucine zipper domain.
Swaroop, A., Xu, J. Z., Pawar, H., Jackson, A., Skolnick, C., & Agarwal, N. A. (1992) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.89.1.266 · Cited by 305 · see citing works
Analysis of combinatorial cis-regulation in synthetic and genomic promoters
Gertz, J., Siggia, E. D., & Cohen, B. A. (2009) · Nature · doi:10.1038/nature07521 · Cited by 304 · see citing works
Blackshaw, S., Fraioli, R. E., Furukawa, T., & Cepko, C. L. (2001) · Cell · doi:10.1016/s0092-8674(01)00574-8 · Cited by 303 · see citing works
De novo mutations in the CRX homeobox gene associated with Leber congenital amaurosis
Freund, C. L., Wang, Q., Chen, S., Muskat, B. L., Wiles, C. D., Sheffield, V. C., Jacobson, S. G., Mclnnes, R. R., Zack, D. J., & Stone, E. M. (1998) · Nature Genetics · doi:10.1038/ng0498-311 · Cited by 296 · see citing works
Chen, J., Rattner, A., & Nathans, J. (2005) · Journal of Neuroscience · doi:10.1523/jneurosci.3571-04.2005 · Cited by 286 · see citing works
Sohocki, M. M., Sullivan, L. S., Mintz-Hittner, H. A., Birch, D. G., Heckenlively, J. R., Freund, C. L., McInnes, R. R., & Daiger, S. P. (1998) · The American Journal of Human Genetics · doi:10.1086/302101 · Cited by 283 · see citing works
Regulatory logic of neuronal diversity: Terminal selector genes and selector motifs
Hobert, O. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0806070105 · Cited by 280 · see citing works
Microarray analysis of the transcriptional network controlled by the photoreceptor homeobox gene Crx
Livesey, F. J., Furukawa, T., Steffen, M. A., Church, G. M., & Cepko, C. L. (2000) · Current Biology · doi:10.1016/s0960-9822(00)00379-1 · Cited by 270 · see citing works
Swaroop, A., Chew, E. Y., Bowes Rickman, C., & Abecasis, G. R. (2009) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.9.081307.164350 · Cited by 270 · see citing works
G+C content dominates intrinsic nucleosome occupancy
Tillo, D., & Hughes, T. R. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-442 · Cited by 265 · see citing works
Molecular Genetics of Human Retinal Disease
Rattner, A., Sun, H., & Nathans, J. (1999) · Annual Review of Genetics · doi:10.1146/annurev.genet.33.1.89 · Cited by 228 · see citing works
The Leucine Zipper of NRL Interacts with the CRX Homeodomain
Mitton, K. P., Swain, P. K., Chen, S., Xu, S., Zack, D. J., & Swaroop, A. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m003658200 · Cited by 226 · see citing works
Akhmedov, N. B., Piriev, N. I., Chang, B., Rapoport, A. L., Hawes, N. L., Nishina, P. M., Nusinowitz, S., Heckenlively, J. R., Roderick, T. H., Kozak, C. A., et al. (2000) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.97.10.5551 · Cited by 221 · see citing works
A mutation in NRL is associated with autosomal dominant retinitis pigmentosa
Bessant, D. A. R., Payne, A. M., Mitton, K. P., Wang, Q.-L., Swain, P. K., Plant, C., Bird, A. C., Zack, D. J., Swaroop, A., & Bhattacharya, S. S. (1999) · Nature Genetics · doi:10.1038/7678 · Cited by 219 · see citing works
A Genetic Model for Interaction of the Homeodomain Recognition Helix with DNA
Hanes, S. D., & Brent, R. (1991) · Science · doi:10.1126/science.1671176 · Cited by 219 · see citing works
enoLOGOS: a versatile web tool for energy normalized sequence logos
Workman, C. T., Yin, Y., Corcoran, D. L., Ideker, T. E., Stormo, G. D., & Benos, P. V. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki439 · Cited by 214 · see citing works
Daniele, L. L., Lillo, C., Lyubarsky, A., Nikonov, S. S., Philp, N. J., Mears, A. J., Swaroop, A., Williams, D. S., & Pugh, E. N. (2005) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.04-1427 · Cited by 212 · see citing works
Zack, D. J., Bennett, J., Wang, Y., Davenport, C., Klaunberg, B. A., Gearhart, J. D., & Nathans, J. (1991) · Neuron · doi:10.1016/0896-6273(91)90355-4 · Cited by 203 · see citing works
Roberts, M. R., Hendrickson, A. E., McGuire, C. R., & Reh, T. A. (2005) · Investigative Ophthalmology & Visual Science · doi:10.1167/iovs.05-0093 · Cited by 202 · see citing works
Corbo, J. C., & Cepko, C. L. (2005) · PLoS Genetics · doi:10.1371/journal.pgen.0010011 · Cited by 174 · see citing works
Self-citationHigh Nucleosome Occupancy Is Encoded at Human Regulatory Sequences
Tillo, D., Kaplan, N., Moore, I. K., Fondufe‐Mittendorf, Y. N., Gossett, A. J., Field, Y., Lieb, J. D., Widom, J., Segal, E., & Hughes, T. R. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009129 · Cited by 169 · see citing works
Blimp1 controls photoreceptor versus bipolar cell fate choice during retinal development
Brzezinski, J. A., Lamba, D. A., & Reh, T. A. (2010) · Development · doi:10.1242/dev.043968 · Cited by 163 · see citing works
Gene Regulatory Networks for Development
Davidson, E. H. (2006) · Elsevier eBooks · doi:10.1016/b978-012088563-3.50022-5 · Cited by 154 · see citing works
The Cis-regulatory Logic of the Mammalian Photoreceptor Transcriptional Network
Hsiau, T. H.-C., Diaconu, C. I., Myers, C. A., Lee, J., Cepko, C. L., & Corbo, J. C. (2007) · PLoS ONE · doi:10.1371/journal.pone.0000643 · Cited by 141 · see citing works
Self-citationRothbächer, U., Bertrand, V., Lamy, C., & Lemaire, P. (2007) · Development · doi:10.1242/dev.010850 · Cited by 140 · see citing works
Oh, E. C. T., Cheng, H., Hong, H., Jia, L., Khan, N. W., & Swaroop, A. (2008) · Brain Research · doi:10.1016/j.brainres.2008.01.028 · Cited by 132 · see citing works
Holloway, M. (1994) · Scientific American · doi:10.1038/scientificamerican0894-76 · Cited by 127 · see citing works
Retinal degenerations with truncation mutations in the cone-rod homeobox (CRX) gene.
Jacobson, S. G., Cideciyan, A. V., Huang, Y., Hanna, D. B., Freund, C. L., Affatigato, L. M., Carr, R. E., Zack, D. J., Stone, E. M., & McInnes, R. R. (1998) · PubMed · Cited by 126 · see citing works
Cheng, H., Alemán, T. S., Cideciyan, A. V., Khanna, R., Jacobson, S. G., & Swaroop, A. (2006) · Human Molecular Genetics · doi:10.1093/hmg/ddl185 · Cited by 126 · see citing works
Multiple Phosphorylated Isoforms of NRL Are Expressed in Rod Photoreceptors
Swain, P. K., Hicks, D., Mears, A. J., Apel, I. J., Smith, J. E., John, S. K., Hendrickson, A. E., Milam, A. H., & Swaroop, A. (2001) · Journal of Biological Chemistry · doi:10.1074/jbc.m105855200 · Cited by 122 · see citing works
BETA2/NeuroD1 Null Mice: A New Model for Transcription Factor-Dependent Photoreceptor Degeneration
Pennesi, M. E., Cho, J.-H., Yang, Z. R., Wu, S. H., Zhang, J., Wu, S. M.-S., & Tsai, M. (2003) · Journal of Neuroscience · doi:10.1523/jneurosci.23-02-00453.2003 · Cited by 121 · see citing works
Enhancer identification through comparative genomics
Visel, A., Bristow, J. D., & Pennacchio, L. A. (2007) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2006.12.014 · Cited by 112 · see citing works
Transcriptional autoregulation in development
Crews, S. T., & Pearson, J. C. (2009) · Current Biology · doi:10.1016/j.cub.2009.01.015 · Cited by 112 · see citing works
Gene Regulatory Networks for DevelopmentWhat They Are, How They Work, and What They Mean
Davidson, E. H. (2006) · Elsevier eBooks · doi:10.1016/b978-012088563-3/50022-5 · Cited by 105 · see citing works
Davidson, E. H. (2006) · Cited by 105 · see citing works
Spacing ensures autonomous expression of different stripe enhancers in the even-skipped promoter
Small, S., Arnosti, D. N., & Levine, M. (1993) · Development · doi:10.1242/dev.119.3.767 · Cited by 103 · see citing works
Expression of Chx10 and Chx10-1 in the developing chicken retina
Chen, C.-M. A., & Cepko, C. L. (2000) · Mechanisms of Development · doi:10.1016/s0925-4773(99)00251-8 · Cited by 101 · see citing works
A typology of photoreceptor gene expression patterns in the mouse
Corbo, J. C., Myers, C. A., Lawrence, K. A., Jadhav, A. P., & Cepko, C. L. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0705465104 · Cited by 97 · see citing works
Self-citationFujieda, H., Bremner, R., Mears, A. J., & Sasaki, H. (2008) · Journal of Neurochemistry · doi:10.1111/j.1471-4159.2008.05739.x · Cited by 90 · see citing works
Makeev, V. J. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg799 · Cited by 89 · see citing works
Morabito, M. A., Yu, X., & Barnstable, C. J. (1991) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)92872-3 · Cited by 84 · see citing works
Furukawa, A., Koike, C., Lippincott, P., Cepko, C. L., & Furukawa, T. (2002) · Journal of Neuroscience · doi:10.1523/jneurosci.22-05-01640.2002 · Cited by 84 · see citing works
The orphan nuclear hormone receptor ERR β controls rod photoreceptor survival
Onishi, A., Peng, G.-H., Poth, E. M., Lee, D. A., Chen, J., Alexis, U., de Melo, J., Chen, S., & Blackshaw, S. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1000102107 · Cited by 81 · see citing works
Specific DNA Recognition and Intersite Spacing Are Critical for Action of the Bicoid Morphogen
Hanes, S. D., Riddihough, G., Ish‐Horowicz, D., & Brent, R. (1994) · Molecular and Cellular Biology · doi:10.1128/mcb.14.5.3364 · Cited by 75 · see citing works
Autoregulation of Eukaryotic Transcription Factors
Bateman, E. (1998) · Progress in nucleic acid research and molecular biology · doi:10.1016/s0079-6603(08)60892-2 · Cited by 73 · see citing works
Expression of the bZIP transcription factor gene Nrl in the developing nervous system.
Liu, Q., Ji, X., Breitman, M. L., et al. (1996) · PubMed · Cited by 70 · see citing works
RER, an Evolutionarily Conserved Sequence Upstream of the Rhodopsin Gene, Has Enhancer Activity
Nie, Z., Chen, S., Kumar, R., & Zack, D. J. (1996) · Journal of Biological Chemistry · doi:10.1074/jbc.271.5.2667 · Cited by 62 · see citing works
Qian, J. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki658 · Cited by 62 · see citing works
DeAngelis, M. M. (2002) · Archives of Ophthalmology · doi:10.1001/archopht.120.3.369 · Cited by 61 · see citing works
Chiu, M. I., & Nathans, J. (1994) · Visual Neuroscience · doi:10.1017/s0952523800003072 · Cited by 58 · see citing works
Chatelain, G., Fossat, N., Brun, G., & Lamonerie, T. (2006) · Journal of Molecular Medicine · doi:10.1007/s00109-006-0048-2 · Cited by 57 · see citing works
Chen, J., Tucker, C. L., Woodford, B. J., et al. (1994) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.91.7.2611 · Cited by 54 · see citing works
Mouse cone arrestin gene characterization: promoter targets expression to cone photoreceptors
Zhu, X., Ma, B., Babu, S., et al. (2002) · FEBS Letters · doi:10.1016/s0014-5793(02)03014-4 · Cited by 42 · see citing works
Lee, J., Myers, C., Williams, N. L., Abdelaziz, M., & Corbo, J. C. (2010) · Gene Therapy · doi:10.1038/gt.2010.77 · Cited by 40 · see citing works
Self-citationDevelopmentally important DNA elements within the bovine opsin upstream region.
DesJardin, L. E., & Hauswirth, W. W. (1996) · PubMed · Cited by 36 · see citing works
Specific DNA Recognition and Intersite Spacing Are Critical for Action of the Bicoid Morphogen
Hanes, S. D., Riddihough, G., Ish‐Horowicz, D., et al. (1994) · Molecular and Cellular Biology · doi:10.1128/mcb.14.5.3364-3375.1994 · Cited by 27 · see citing works
Shared Nuclear Protein Binding Sites in the Upstream Region of the Rat Opsin Gene
Yu, X., Chung, M., Morabito, M. A., et al. (1993) · Biochemical and Biophysical Research Communications · doi:10.1006/bbrc.1993.1186 · Cited by 25 · see citing works
Flexible promoter architecture requirements for coactivator recruitment
Chiang, D. Y., Nix, D. A., Shultzaberger, R. K., Gasch, A. P., & Eisen, M. B. (2006) · BMC Molecular Biology · doi:10.1186/1471-2199-7-16 · Cited by 21 · see citing works
CRX controls retinal expression of the X-linked juvenile retinoschisis (RS1) gene
Langmann, T., Lai, C. C.-L., Weigelt, K., Tam, B. M., Warneke-Wittstock, R., Moritz, O. L., & Weber, B. H. F. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn737 · Cited by 20 · see citing works
Self-citationSanuki, R., Omori, Y., Koike, C., Sato, S., & Furukawa, T. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.12.030 · Cited by 20 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
Evolution of Gene Regulatory Networks Controlling Body Plan Development
Peter, I. S., & Davidson, E. H. (2011) · Cell · doi:10.1016/j.cell.2011.02.017 · Cited by 417 · see citing works
Yu, Y., Bhangale, T. R., Fagerness, J., Ripke, S., Thorleifsson, G., Tan, P. L., Souied, E. H., Richardson, A. J., Merriam, J. E., Buitendijk, G. H. S., et al. (2011) · Human Molecular Genetics · doi:10.1093/hmg/ddr270 · Cited by 254 · see citing works
“Allelic change from T to C on this conserved region may disrupt a putative transcription factor-binding site for cone–rod homeobox (CRX), which is an essential transcription factor highly expressed in RPE and retinal ganglion cells (27).”
BackgroundKim, S.-Y., Yang, H.-J., Chang, Y.-S., Kim, J.-W., Brooks, M., Chew, E. Y., Wong, W. T., Fariss, R. N., Rachel, R. A., Cogliati, T., et al. (2014) · Investigative Opthalmology & Visual Science · doi:10.1167/iovs.14-15091 · Cited by 72 · see citing works
- Authors
- Corbo, J. C., Lawrence, K. A., Karlstetter, M., Myers, C. A., Abdelaziz, M., Dirkes, W., Weigelt, K., Seifert, M., Benes, V., Fritsche, L. G., Weber, B. H. F., & Langmann, T.
- Affiliations
- Washington University in St. Louis (US)
- Erasmus MC (NL)
- ORCID
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2010-08-06
- Volume
- 20
- Issue
- 11
- Pages
- 1512-1525
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC2963815
- OpenAlex
- W2114715558
- Cited by
- 219
- References
- 87
- Citations by year
- 2026: 6 · 2025: 12 · 2024: 16 · 2023: 16 · 2022: 14 · 2021: 15 · 2020: 16 · 2019: 7 · 2018: 12 · 2017: 8 · 2016: 12 · 2015: 15 · 2014: 22 · 2013: 16 · 2012: 11
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Digital Commons@Becker (Washington University School of Medicine) (submittedVersion)
- RePub (Erasmus University Rotterdam) (submittedVersion, other-oa)
- University of Regensburg Publication Server (University of Regensburg) (submittedVersion)
- HighWire Press Open Archive (submittedVersion)
- RePub (Erasmus University Rotterdam) (submittedVersion)
- Funders
- American Health Assistance Foundation
- Deutsche Forschungsgemeinschaft
- National Institutes of Health
- National Eye Institute (F32EY029571, R01EY018826, EY018826)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Retinal Development and Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Health Sciences › Medicine › Ophthalmology › Retinal Diseases and Treatments
- Keywords
- CRX, photoreceptors, cis-regulatory elements, transcription factor binding sites, non-coding genome, cone photoreceptors, rod photoreceptors, retinal disease genes, mouse retina
- MeSH terms
- Animals, Base Sequence, Binding Sites, Chromosome Mapping, Mice, Inbred C57BL, Molecular Sequence Data, Phylogeny, Protein Binding, Regulatory Sequences, Nucleic Acid, Sequence Homology, Nucleic Acid, Trans-Activators, Sequence Analysis, DNA, Retinal Cone Photoreceptor Cells, Mice, Knockout, Homeodomain Proteins, Chromatin Immunoprecipitation, Mice, High-Throughput Nucleotide Sequencing
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
