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Kikuta H, Laplante M, Navratilova P, Komisarczuk AZ, Engström PG, Fredman D, Akalin A, Caccamo M, Sealy I, Howe K, Ghislain J, Pezeron G, Mourrain P, Ellingsen S, Oates AC, Thisse C, Thisse B, Foucher I, Adolf B, Geling A, Lenhard B, Becker TS. Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res 2007; 17:545-55. [PMID: 17387144 PMCID: PMC1855176 DOI: 10.1101/gr.6086307] [Citation(s) in RCA: 282] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We report evidence for a mechanism for the maintenance of long-range conserved synteny across vertebrate genomes. We found the largest mammal-teleost conserved chromosomal segments to be spanned by highly conserved noncoding elements (HCNEs), their developmental regulatory target genes, and phylogenetically and functionally unrelated "bystander" genes. Bystander genes are not specifically under the control of the regulatory elements that drive the target genes and are expressed in patterns that are different from those of the target genes. Reporter insertions distal to zebrafish developmental regulatory genes pax6.1/2, rx3, id1, and fgf8 and miRNA genes mirn9-1 and mirn9-5 recapitulate the expression patterns of these genes even if located inside or beyond bystander genes, suggesting that the regulatory domain of a developmental regulatory gene can extend into and beyond adjacent transcriptional units. We termed these chromosomal segments genomic regulatory blocks (GRBs). After whole genome duplication in teleosts, GRBs, including HCNEs and target genes, were often maintained in both copies, while bystander genes were typically lost from one GRB, strongly suggesting that evolutionary pressure acts to keep the single-copy GRBs of higher vertebrates intact. We show that loss of bystander genes and other mutational events suffered by duplicated GRBs in teleost genomes permits target gene identification and HCNE/target gene assignment. These findings explain the absence of evolutionary breakpoints from large vertebrate chromosomal segments and will aid in the recognition of position effect mutations within human GRBs.
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Affiliation(s)
- Hiroshi Kikuta
- Sars Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
| | - Mary Laplante
- Sars Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
| | - Pavla Navratilova
- Sars Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
| | - Anna Z. Komisarczuk
- Sars Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
| | - Pär G. Engström
- Computational Biology Unit, University of Bergen, 5008 Bergen, Norway
- Programme for Genomics and Bioinformatics, Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - David Fredman
- Computational Biology Unit, University of Bergen, 5008 Bergen, Norway
| | - Altuna Akalin
- Computational Biology Unit, University of Bergen, 5008 Bergen, Norway
| | - Mario Caccamo
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Ian Sealy
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Kerstin Howe
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Julien Ghislain
- Biologie Moléculaire du Développement, INSERM U368, Ecole Normale Supérieure, Paris, 75230 Paris, Cedex 05 France
| | - Guillaume Pezeron
- Biologie Moléculaire du Développement, INSERM U368, Ecole Normale Supérieure, Paris, 75230 Paris, Cedex 05 France
| | - Philippe Mourrain
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Staale Ellingsen
- Sars Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
| | - Andrew C. Oates
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | | | - Bernard Thisse
- IGBMC, CNRS/INSERM/ULP, BP10142, 67404 Illkirch, Cedex, France
| | - Isabelle Foucher
- Unité de Génétique des Déficits Sensoriels, Institut Pasteur, F-75724 Paris Cedex 15, France
| | - Birgit Adolf
- Institute of Developmental Genetics, GSF Research Center, 85764 Neuherberg, Germany
| | - Andrea Geling
- Institute of Developmental Genetics, GSF Research Center, 85764 Neuherberg, Germany
| | - Boris Lenhard
- Sars Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
- Computational Biology Unit, University of Bergen, 5008 Bergen, Norway
| | - Thomas S. Becker
- Sars Centre for Marine Molecular Biology, University of Bergen, 5008 Bergen, Norway
- Corresponding author.E-mail ; fax 47-55584305
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Stigloher C, Ninkovic J, Laplante M, Geling A, Tannhäuser B, Topp S, Kikuta H, Becker TS, Houart C, Bally-Cuif L. Segregation of telencephalic and eye-field identities inside the zebrafish forebrain territory is controlled by Rx3. Development 2006; 133:2925-35. [PMID: 16818451 DOI: 10.1242/dev.02450] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Anteroposterior patterning of the vertebrate forebrain during gastrulation involves graded Wnt signaling, which segregates anterior fields (telencephalon and eye) from the diencephalon. How the telencephalic and retinal primordia are subsequently subdivided remains largely unknown. We demonstrate that at late gastrulation the Paired-like homeodomain transcription factor Rx3 biases cell specification choices towards the retinal fate within a population of bipotential precursors of the anterior forebrain: direct cell tracing demonstrates that retinal precursors acquire a telencephalic fate in embryos homozygous for the rx3-null allele ckh(ne2611), characterized by an enlarged telencephalon and a lack of eyes. Chimera analyses further indicate that this function of Rx3 is cell autonomous. Transfating of the eye field in the absence of Rx3 function correlates with a substantial posterior expansion of expression of the Wnt antagonist Tlc and the winged-helix transcription factor Foxg1. These results suggest that the process segregating the telencephalic and eye fields is isolated from diencephalic patterning, and is mediated by Rx3.
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Affiliation(s)
- Christian Stigloher
- Zebrafish Neurogenetics Junior Research Group, Institute of Virology, Technical University-Munich, Trogerstrasse 4b, D-81675, Munich, Germany
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Geling A, Plessy C, Rastegar S, Strähle U, Bally-Cuif L. Her5 acts as a prepattern factor that blocks neurogenin1 and coe2 expression upstream of Notch to inhibit neurogenesis at the midbrain-hindbrain boundary. Development 2004; 131:1993-2006. [PMID: 15056616 DOI: 10.1242/dev.01093] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Neurogenesis in both vertebrates and invertebrates is tightly controlled in time and space involving both positive and negative regulators. We report here that the bHLH factor Her5 acts as a prepattern gene to prevent neurogenesis in the anlage of the midbrain/hindbrain boundary in the zebrafish neural plate. This involves selective suppression of both neurogenin1(ngn1) and coe2 mRNA expression in a process that is independent of Notch signalling, and where inhibition of either ngn1or coe2 expression is sufficient to prevent neuronal differentiation across the midbrain-hindbrain boundary. A ngn1 transgene faithfully responds to Her5 and deletion analysis of the transgene identifies an E-box in a ngn1 upstream enhancer to be required for repression by Her5. Together our data demonstrate a role of Her5 as a prepattern factor in the spatial definition of proneural domains in the zebrafish neural plate, in a manner similar to its Drosophila homologue Hairy.
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Affiliation(s)
- Andrea Geling
- Zebrafish Neurogenetics Junior Research Group, Institute of Virology, Technical University-Munich, Trogerstrasse 4b, D-81675 Munich, Germany
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Geling A, Itoh M, Tallafuss A, Chapouton P, Tannhäuser B, Kuwada JY, Chitnis AB, Bally-Cuif L. bHLH transcription factor Her5 links patterning to regional inhibition of neurogenesis at the midbrain-hindbrain boundary. Development 2003; 130:1591-604. [PMID: 12620984 DOI: 10.1242/dev.00375] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The midbrain-hindbrain (MH) domain of the vertebrate embryonic neural plate displays a stereotypical profile of neuronal differentiation, organized around a neuron-free zone ('intervening zone', IZ) at the midbrain-hindbrain boundary (MHB). The mechanisms establishing this early pattern of neurogenesis are unknown. We demonstrate that the MHB is globally refractory to neurogenesis, and that forced neurogenesis in this area interferes with the continued expression of genes defining MHB identity. We further show that expression of the zebrafish bHLH Hairy/E(spl)-related factor Her5 prefigures and then precisely delineates the IZ throughout embryonic development. Using morpholino knock-down and conditional gain-of-function assays, we demonstrate that Her5 is essential to prevent neuronal differentiation and promote cell proliferation in a medial compartment of the IZ. We identify one probable target of this activity, the zebrafish Cdk inhibitor p27Xic1. Finally, although the her5 expression domain is determined by anteroposterior patterning cues, we show Her5 does not retroactively influence MH patterning. Together, our results highlight the existence of a mechanism that actively inhibits neurogenesis at the MHB, a process that shapes MH neurogenesis into a pattern of separate neuronal clusters and might ultimately be necessary to maintain MHB integrity. Her5 appears as a partially redundant component of this inhibitory process that helps translate early axial patterning information into a distinct spatiotemporal pattern of neurogenesis and cell proliferation within the MH domain.
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Affiliation(s)
- Andrea Geling
- Zebrafish Neurogenetics Junior Research Group, Institute of Virology, Technical University-Munich, Trogerstrasse 4b, D-81675 Munich, Germany
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Geling A, Steiner H, Willem M, Bally-Cuif L, Haass C. A gamma-secretase inhibitor blocks Notch signaling in vivo and causes a severe neurogenic phenotype in zebrafish. EMBO Rep 2002; 3:688-94. [PMID: 12101103 PMCID: PMC1084181 DOI: 10.1093/embo-reports/kvf124] [Citation(s) in RCA: 400] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Inhibition of amyloid beta-peptide (Abeta) production by blocking gamma-secretase activity is at present one of the most promising therapeutic strategies to slow progression of Alzheimer's disease pathology. gamma-secretase inhibitors apparently block Abeta generation via interference with presenilin (PS) function. Besides being an essential component of the gamma-secretase complex, PS itself may be an aspartyl protease with gamma-secretase activity, which is not only required for Abeta production but also for a similar proteolytic process involved in Notch signaling. Here we demonstrate that treatment of zebrafish embryos with a known gamma-secretase inhibitor affects embryonic development in a manner indistinguishable from Notch signaling deficiencies at morphological, molecular and biochemical levels. This indicates severe side-effects of gamma-secretase inhibitors in any Notch-dependent cell fate decision and demonstrates that the zebrafish is an ideal vertebrate system to validate compounds that selectively affect Abeta production, but not Notch signaling, under in vivo conditions.
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Affiliation(s)
- Andrea Geling
- Zebrafish Neurogenetics Junior Research Group, Institute for Virology, Technical University Munich, Trogerstrasse, Germany
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