1
|
Functional Characterization of an In-Frame Deletion in the Basic Domain of the Retinal Transcription Factor ATOH7. Int J Mol Sci 2022; 23:ijms23031053. [PMID: 35162975 PMCID: PMC8834682 DOI: 10.3390/ijms23031053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/12/2022] [Accepted: 01/14/2022] [Indexed: 02/01/2023] Open
Abstract
Basic helix–loop–helix (bHLH) transcription factors are evolutionarily conserved and structurally similar proteins important in development. The temporospatial expression of atonal bHLH transcription factor 7 (ATOH7) directs the differentiation of retinal ganglion cells and mutations in the human gene lead to vitreoretinal and/or optic nerve abnormalities. Characterization of pathogenic ATOH7 mutations is needed to understand the functions of the conserved bHLH motif. The published ATOH7 in-frame deletion p.(Arg41_Arg48del) removes eight highly conserved amino acids in the basic domain. We functionally characterized the mutant protein by expressing V5-tagged ATOH7 constructs in human embryonic kidney 293T (HEK293T) cells for subsequent protein analyses, including Western blot, cycloheximide chase assays, Förster resonance energy transfer fluorescence lifetime imaging, enzyme-linked immunosorbent assays and dual-luciferase assays. Our results indicate that the in-frame deletion in the basic domain causes mislocalization of the protein, which can be rescued by a putative dimerization partner transcription factor 3 isoform E47 (E47), suggesting synergistic nuclear import. Furthermore, we observed (i) increased proteasomal degradation of the mutant protein, (ii) reduced protein heterodimerization, (iii) decreased DNA-binding and transcriptional activation of a reporter gene, as well as (iv) inhibited E47 activity. Altogether our observations suggest that the DNA-binding basic domain of ATOH7 has additional roles in regulating the nuclear import, dimerization, and protein stability.
Collapse
|
2
|
A transient decrease in mitochondrial activity contributes to establish the ganglion cell fate in retina adapted for high acuity vision. Dev Biol 2020; 469:96-110. [PMID: 33141037 DOI: 10.1016/j.ydbio.2020.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 10/05/2020] [Accepted: 10/06/2020] [Indexed: 12/17/2022]
Abstract
Although the plan of the retina is well conserved in vertebrates, there are considerable variations in cell type diversity and number, as well as in the organization and properties of the tissue. The high ratios of retinal ganglion cells (RGCs) to cones in primate fovea and bird retinas favor neural circuits essential for high visual acuity and color vision. The role that cell metabolism could play in cell fate decision during embryonic development of the nervous system is still largely unknown. Here, we describe how subtle changes of mitochondrial activity along the pathway converting uncommitted progenitors into newborn RGCs increase the recruitment of RGC-fated progenitors. ATOH7, a proneural protein dedicated to the production of RGCs in vertebrates, activates transcription of the Hes5.3 gene in pre-committed progenitors. The HES5.3 protein, in turn, regulates a transient decrease in mitochondrial activity via the retinoic acid signaling pathway few hours before cell commitment. This metabolic shift lengthens the progression of the ultimate cell cycle and is a necessary step for upregulating Atoh7 and promoting RGC differentiation.
Collapse
|
3
|
Chaudhary R, Gryder B, Woods WS, Subramanian M, Jones MF, Li XL, Jenkins LM, Shabalina SA, Mo M, Dasso M, Yang Y, Wakefield LM, Zhu Y, Frier SM, Moriarity BS, Prasanth KV, Perez-Pinera P, Lal A. Prosurvival long noncoding RNA PINCR regulates a subset of p53 targets in human colorectal cancer cells by binding to Matrin 3. eLife 2017; 6. [PMID: 28580901 PMCID: PMC5470874 DOI: 10.7554/elife.23244] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Accepted: 05/20/2017] [Indexed: 12/19/2022] Open
Abstract
Thousands of long noncoding RNAs (lncRNAs) have been discovered, yet the function of the vast majority remains unclear. Here, we show that a p53-regulated lncRNA which we named PINCR (p53-induced noncoding RNA), is induced ~100-fold after DNA damage and exerts a prosurvival function in human colorectal cancer cells (CRC) in vitro and tumor growth in vivo. Targeted deletion of PINCR in CRC cells significantly impaired G1 arrest and induced hypersensitivity to chemotherapeutic drugs. PINCR regulates the induction of a subset of p53 targets involved in G1 arrest and apoptosis, including BTG2, RRM2B and GPX1. Using a novel RNA pulldown approach that utilized endogenous S1-tagged PINCR, we show that PINCR associates with the enhancer region of these genes by binding to RNA-binding protein Matrin 3 that, in turn, associates with p53. Our findings uncover a critical prosurvival function of a p53/PINCR/Matrin 3 axis in response to DNA damage in CRC cells. DOI:http://dx.doi.org/10.7554/eLife.23244.001 Though DNA contains the information needed to build the proteins that keep cells alive, only 2% of the DNA in a human cell codes for proteins. The remaining 98% is referred to as non-coding DNA. The information in some of these non-coding regions can still be copied into molecules of RNA, including long molecules called lncRNAs. Little is known about what lncRNAs actually do, but growing evidence suggests that these molecules are important for a number of vital processes including cell growth and survival. When the DNA in an animal cell gets damaged, the cell needs to decide whether to pause growth and repair the damage, or to kill itself if the harm is too great. One of the best-studied proteins guiding this decision is the p53 protein, which increases the number of protein-coding genes needed to carry out either option in this decision. That is to say that, p53 regulates the genes needed to kill the cell and the genes needed to temporarily pause its growth and repair the damage, which instead keeps the cell alive. So, how does the p53 protein guide the decision, and are lncRNA molecules involved? Using human colon cancer cells, Chaudhary et al. now report that when DNA is damaged, the levels of a specific lncRNA increase 100-fold. Further experiments showed that this lncRNA – named PINCR, which refers to p53-induced noncoding RNA – promotes the survival of cells. Chaudhary et al. showed that PINCR molecules do this by recruiting a protein called Matrin 3 to a certain region in the DNA called an enhancer and then links it to promoter region in the DNA of specific genes that temporarily pause cell growth but keep the cell alive. This in turn activates these ‘pro-survival genes’. In further experiments, when the PINCR molecules were essentially deleted, p53 was not able to fully activate these genes and as a result more of the cells died. Together these findings increase our knowledge of how lncRNAs can work, especially in the context of DNA damage in cancer cells. A next important step will be to uncover other roles for the PINCR molecule in both cancer and healthy cells. DOI:http://dx.doi.org/10.7554/eLife.23244.002
Collapse
Affiliation(s)
- Ritu Chaudhary
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Berkley Gryder
- Oncogenomics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Wendy S Woods
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Murugan Subramanian
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Matthew F Jones
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Xiao Ling Li
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Lisa M Jenkins
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Svetlana A Shabalina
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, United States
| | - Min Mo
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Mary Dasso
- Laboratory of Gene Regulation and Development, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, United States
| | - Yuan Yang
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Lalage M Wakefield
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | - Yuelin Zhu
- Molecular Genetics Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| | | | - Branden S Moriarity
- Department of Pediatrics, Masonic Cancer Center, University of Minnesota, Twin Cities, United States
| | - Kannanganattu V Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Pablo Perez-Pinera
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Ashish Lal
- Regulatory RNAs and Cancer Section, Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States
| |
Collapse
|
4
|
Hanotel J, Bessodes N, Thélie A, Hedderich M, Parain K, Van Driessche B, Brandão KDO, Kricha S, Jorgensen MC, Grapin-Botton A, Serup P, Van Lint C, Perron M, Pieler T, Henningfeld KA, Bellefroid EJ. The Prdm13 histone methyltransferase encoding gene is a Ptf1a-Rbpj downstream target that suppresses glutamatergic and promotes GABAergic neuronal fate in the dorsal neural tube. Dev Biol 2013; 386:340-57. [PMID: 24370451 DOI: 10.1016/j.ydbio.2013.12.024] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 11/19/2013] [Accepted: 12/17/2013] [Indexed: 12/01/2022]
Abstract
The basic helix-loop-helix (bHLH) transcriptional activator Ptf1a determines inhibitory GABAergic over excitatory glutamatergic neuronal cell fate in progenitors of the vertebrate dorsal spinal cord, cerebellum and retina. In an in situ hybridization expression survey of PR domain containing genes encoding putative chromatin-remodeling zinc finger transcription factors in Xenopus embryos, we identified Prdm13 as a histone methyltransferase belonging to the Ptf1a synexpression group. Gain and loss of Ptf1a function analyses in both frog and mice indicates that Prdm13 is positively regulated by Ptf1a and likely constitutes a direct transcriptional target. We also showed that this regulation requires the formation of the Ptf1a-Rbp-j complex. Prdm13 knockdown in Xenopus embryos and in Ptf1a overexpressing ectodermal explants lead to an upregulation of Tlx3/Hox11L2, which specifies a glutamatergic lineage and a reduction of the GABAergic neuronal marker Pax2. It also leads to an upregulation of Prdm13 transcription, suggesting an autonegative regulation. Conversely, in animal caps, Prdm13 blocks the ability of the bHLH factor Neurog2 to activate Tlx3. Additional gain of function experiments in the chick neural tube confirm that Prdm13 suppresses Tlx3(+)/glutamatergic and induces Pax2(+)/GABAergic neuronal fate. Thus, Prdm13 is a novel crucial component of the Ptf1a regulatory pathway that, by modulating the transcriptional activity of bHLH factors such as Neurog2, controls the balance between GABAergic and glutamatergic neuronal fate in the dorsal and caudal part of the vertebrate neural tube.
Collapse
Affiliation(s)
- Julie Hanotel
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medicine, and ULB Neuroscience Institute, B-6041 Gosselies, Belgium
| | - Nathalie Bessodes
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medicine, and ULB Neuroscience Institute, B-6041 Gosselies, Belgium
| | - Aurore Thélie
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medicine, and ULB Neuroscience Institute, B-6041 Gosselies, Belgium
| | - Marie Hedderich
- Department of Developmental Biochemistry, Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University of Goettingen, 37077 Goettingen, Germany
| | - Karine Parain
- UPR CNRS 3294 Neurobiology and Development, Université Paris Sud, 91405 Orsay Cedex, France
| | - Benoit Van Driessche
- Laboratory of Molecular Virology, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medicine, B-6041 Gosselies, Belgium
| | - Karina De Oliveira Brandão
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medicine, and ULB Neuroscience Institute, B-6041 Gosselies, Belgium
| | - Sadia Kricha
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medicine, and ULB Neuroscience Institute, B-6041 Gosselies, Belgium
| | - Mette C Jorgensen
- DanStem, University of Copenhagen, 3B Blegdamsvej, DK-2200 Copenhagen N, Denmark
| | - Anne Grapin-Botton
- DanStem, University of Copenhagen, 3B Blegdamsvej, DK-2200 Copenhagen N, Denmark
| | - Palle Serup
- DanStem, University of Copenhagen, 3B Blegdamsvej, DK-2200 Copenhagen N, Denmark
| | - Carine Van Lint
- Laboratory of Molecular Virology, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medicine, B-6041 Gosselies, Belgium
| | - Muriel Perron
- UPR CNRS 3294 Neurobiology and Development, Université Paris Sud, 91405 Orsay Cedex, France
| | - Tomas Pieler
- Department of Developmental Biochemistry, Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University of Goettingen, 37077 Goettingen, Germany
| | - Kristine A Henningfeld
- Department of Developmental Biochemistry, Center for Nanoscale Microscopy and Molecular Physiology of the Brain (CNMPB), University of Goettingen, 37077 Goettingen, Germany
| | - Eric J Bellefroid
- Laboratory of Developmental Genetics, Université Libre de Bruxelles (ULB), Institute of Molecular Biology and Medicine, and ULB Neuroscience Institute, B-6041 Gosselies, Belgium.
| |
Collapse
|
5
|
Chiodini F, Matter-Sadzinski L, Rodrigues T, Skowronska-Krawczyk D, Brodier L, Schaad O, Bauer C, Ballivet M, Matter JM. A positive feedback loop between ATOH7 and a Notch effector regulates cell-cycle progression and neurogenesis in the retina. Cell Rep 2013; 3:796-807. [PMID: 23434507 DOI: 10.1016/j.celrep.2013.01.035] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 01/02/2013] [Accepted: 01/31/2013] [Indexed: 01/24/2023] Open
Abstract
The HES proteins are known Notch effectors and have long been recognized as important in inhibiting neuronal differentiation. However, the roles that they play in the specification of neuronal fate remain largely unknown. Here, we show that in the differentiating retinal epithelium, the proneural protein ATOH7 (ATH5) is required for the activation of the transcription of the Hes5.3 gene before the penultimate mitosis of progenitor cells. We further show that the HES5.3 protein slows down the cell-cycle progression of Atoh7-expressing cells, thereby establishing conditions for Atoh7 to reach a high level of expression in S phase and induce neuronal differentiation prior to the ultimate mitosis. Our study uncovers how a proneural protein recruits a protein known to be a component of the Notch signaling pathway in order to regulate the transition between an initial phase of selection among uncommitted progenitors and a later phase committing the selected progenitors to neuronal differentiation.
Collapse
Affiliation(s)
- Florence Chiodini
- Department of Biochemistry, Sciences II, University of Geneva, 1211 Geneva, Switzerland
| | | | | | | | | | | | | | | | | |
Collapse
|
6
|
Abstract
Within the developing vertebrate retina, particular subtypes of amacrine cells (ACs) tend to arise from progenitors expressing the basic helix-loop-helix (bHLH) transcription factor, Atoh7, which is necessary for the early generation of retinal ganglion cells (RGCs). All ACs require the postmitotic expression of the bHLH pancreas transcription factor Ptf1a; however, Ptf1a alone is not sufficient to give subtype identities. Here we use functional and in vivo time-lapse studies in the zebrafish retina to investigate on the developmental programs leading to ACs specification within the subsequent divisions of Atoh7-positive progenitors. We find evidences that the homeobox transcription factor Barhl2 is an AC subtype identity-biasing factor that turns on within Atoh7-positive descendants. In vivo lineage tracing reveals that particular modes of cell division tend to generate Barhl2-positive precursors from sisters of RGCs. Additionally, Atoh7 indirectly impacts these division modes to regulate the right number of barhl2-expressing cells. We finally find that Atoh7 itself influences the subtypes of Barhl2-dependent ACs. Together, the results from our study uncover lineage-related and molecular logic of subtype specification in the vertebrate retina, by showing that specific AC subtypes arise via a particular mode of cell division and a transcriptional network cascade involving the sequential expression of first atoh7 followed by ptf1a and then barhl2.
Collapse
|
7
|
Abstract
Neural basic helix-loop-helix (bHLH) transcription factors are crucial in regulating the differentiation and neuronal subtype specification of neurons. Precisely how these transcription factors direct such processes is largely unknown due to the lack of bona fide targets in vivo. Genetic evidence suggests that bHLH factors have shared targets in their common differentiation role, but unique targets with respect to their distinct roles in neuronal subtype specification. However, whether neuronal subtype-specific targets exist remains an unsolved question. To address this question, we focused on Atoh1 (Math1), a bHLH transcription factor that specifies distinct neuronal subtypes of the proprioceptive pathway in mammals including the dI1 (dorsal interneuron 1) population of the developing spinal cord. We identified transcripts unique to the Atoh1-derived lineage using microarray analyses of specific bHLH-sorted populations from mouse. Chromatin immunoprecipitation-sequencing experiments followed by enhancer reporter analyses identified five direct neuronal subtype-specific targets of Atoh1 in vivo along with their Atoh1-responsive enhancers. These targets, Klf7, Rab15, Rassf4, Selm, and Smad7, have diverse functions that range from transcription factors to regulators of endocytosis and signaling pathways. Only Rab15 and Selm are expressed across several different Atoh1-specified neuronal subtypes including external granule cells (external granule cell layer) in the developing cerebellum, hair cells of the inner ear, and Merkel cells. Our work establishes on a molecular level that neuronal differentiation bHLH transcription factors have distinct lineage-specific targets.
Collapse
|
8
|
Lelièvre EC, Lek M, Boije H, Houille-Vernes L, Brajeul V, Slembrouck A, Roger JE, Sahel JA, Matter JM, Sennlaub F, Hallböök F, Goureau O, Guillonneau X. Ptf1a/Rbpj complex inhibits ganglion cell fate and drives the specification of all horizontal cell subtypes in the chick retina. Dev Biol 2011; 358:296-308. [PMID: 21839069 DOI: 10.1016/j.ydbio.2011.07.033] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2010] [Revised: 07/19/2011] [Accepted: 07/25/2011] [Indexed: 11/18/2022]
Abstract
During development, progenitor cells of the retina give rise to six principal classes of neurons and the Müller glial cells found within the adult retina. The pancreas transcription factor 1 subunit a (Ptf1a) encodes a basic-helix-loop-helix transcription factor necessary for the specification of horizontal cells and the majority of amacrine cell subtypes in the mouse retina. The Ptf1a-regulated genes and the regulation of Ptf1a activity by transcription cofactors during retinogenesis have been poorly investigated. Using a retrovirus-mediated gene transfer approach, we reported that Ptf1a was sufficient to promote the fates of amacrine and horizontal cells from retinal progenitors and inhibit retinal ganglion cell and photoreceptor differentiation in the chick retina. Both GABAergic H1 and non-GABAergic H3 horizontal cells were induced following the forced expression of Ptf1a. We describe Ptf1a as a strong, negative regulator of Atoh7 expression. Furthermore, the Rbpj-interacting domains of Ptf1a protein were required for its effects on cell fate specification. Together, these data provide a novel insight into the molecular basis of Ptf1a activity on early cell specification in the chick retina.
Collapse
Affiliation(s)
- E C Lelièvre
- Centre de Recherche des Cordeliers, INSERM UMR S872, 75006 Paris, France
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
9
|
Nistor G, Seiler MJ, Yan F, Ferguson D, Keirstead HS. Three-dimensional early retinal progenitor 3D tissue constructs derived from human embryonic stem cells. J Neurosci Methods 2010; 190:63-70. [DOI: 10.1016/j.jneumeth.2010.04.025] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2009] [Revised: 04/22/2010] [Accepted: 04/26/2010] [Indexed: 11/30/2022]
|
10
|
Skowronska-Krawczyk D, Chiodini F, Ebeling M, Alliod C, Kundzewicz A, Castro D, Ballivet M, Guillemot F, Matter-Sadzinski L, Matter JM. Conserved regulatory sequences in Atoh7 mediate non-conserved regulatory responses in retina ontogenesis. Development 2009; 136:3767-77. [DOI: 10.1242/dev.033449] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The characterisation of interspecies differences in gene regulation is crucial to understanding the molecular basis of phenotypic diversity and evolution. The atonal homologue Atoh7 participates in the ontogenesis of the vertebrate retina. Our study reveals how evolutionarily conserved, non-coding DNA sequences mediate both the conserved and the species-specific transcriptional features of the Atoh7 gene. In the mouse and chick retina, species-related variations in the chromatin-binding profiles of bHLH transcription factors correlate with distinct features of the Atoh7 promoters and underlie variations in the transcriptional rates of the Atoh7 genes. The different expression kinetics of the Atoh7 genes generate differences in the expression patterns of a set of genes that are regulated by Atoh7 in a dose-dependent manner, including those involved in neurite outgrowth and growth cone migration. In summary, we show how highly conserved regulatory elements are put to use in mediating non-conserved functions and creating interspecies neuronal diversity.
Collapse
Affiliation(s)
| | - Florence Chiodini
- Department of Ophthalmology, School of Medicine, University of Geneva, 1211 Genève 4, Switzerland
| | - Martin Ebeling
- Bioinformatics, F. Hoffmann-La Roche, Basel 4070, Switzerland
| | - Christine Alliod
- Department of Biochemistry, Sciences II, University of Geneva, 1211 Genève 4, Switzerland
| | - Adam Kundzewicz
- Department of Biochemistry, Sciences II, University of Geneva, 1211 Genève 4, Switzerland
- Department of Ophthalmology, School of Medicine, University of Geneva, 1211 Genève 4, Switzerland
| | - Diogo Castro
- Division of Molecular Neurobiology, National Institute for Medical Research,The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Marc Ballivet
- Department of Biochemistry, Sciences II, University of Geneva, 1211 Genève 4, Switzerland
| | - François Guillemot
- Division of Molecular Neurobiology, National Institute for Medical Research,The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Lidia Matter-Sadzinski
- Department of Biochemistry, Sciences II, University of Geneva, 1211 Genève 4, Switzerland
- Department of Ophthalmology, School of Medicine, University of Geneva, 1211 Genève 4, Switzerland
| | - Jean-Marc Matter
- Department of Biochemistry, Sciences II, University of Geneva, 1211 Genève 4, Switzerland
- Department of Ophthalmology, School of Medicine, University of Geneva, 1211 Genève 4, Switzerland
| |
Collapse
|
11
|
Aerts S, Vilain S, Hu S, Tranchevent LC, Barriot R, Yan J, Moreau Y, Hassan BA, Quan XJ. Integrating computational biology and forward genetics in Drosophila. PLoS Genet 2009; 5:e1000351. [PMID: 19165344 PMCID: PMC2628282 DOI: 10.1371/journal.pgen.1000351] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Accepted: 12/19/2008] [Indexed: 11/18/2022] Open
Abstract
Genetic screens are powerful methods for the discovery of gene-phenotype associations. However, a systems biology approach to genetics must leverage the massive amount of "omics" data to enhance the power and speed of functional gene discovery in vivo. Thus far, few computational methods for gene function prediction have been rigorously tested for their performance on a genome-wide scale in vivo. In this work, we demonstrate that integrating genome-wide computational gene prioritization with large-scale genetic screening is a powerful tool for functional gene discovery. To discover genes involved in neural development in Drosophila, we extend our strategy for the prioritization of human candidate disease genes to functional prioritization in Drosophila. We then integrate this prioritization strategy with a large-scale genetic screen for interactors of the proneural transcription factor Atonal using genomic deficiencies and mutant and RNAi collections. Using the prioritized genes validated in our genetic screen, we describe a novel genetic interaction network for Atonal. Lastly, we prioritize the whole Drosophila genome and identify candidate gene associations for ten receptor-signaling pathways. This novel database of prioritized pathway candidates, as well as a web application for functional prioritization in Drosophila, called Endeavour-HighFly, and the Atonal network, are publicly available resources. A systems genetics approach that combines the power of computational predictions with in vivo genetic screens strongly enhances the process of gene function and gene-gene association discovery.
Collapse
Affiliation(s)
- Stein Aerts
- Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
- Department of Human Genetics, Katholieke Universiteit Leuven School of Medicine, Leuven, Belgium
| | - Sven Vilain
- Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
- Department of Human Genetics, Katholieke Universiteit Leuven School of Medicine, Leuven, Belgium
- Doctoral Program in Molecular and Developmental Genetics, Katholieke Universiteit Leuven School of Medicine, Leuven, Belgium
| | - Shu Hu
- Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
- Department of Human Genetics, Katholieke Universiteit Leuven School of Medicine, Leuven, Belgium
- Doctoral Program in Molecular and Developmental Genetics, Katholieke Universiteit Leuven School of Medicine, Leuven, Belgium
| | | | - Roland Barriot
- Department of Electrical Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jiekun Yan
- Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
- Department of Human Genetics, Katholieke Universiteit Leuven School of Medicine, Leuven, Belgium
| | - Yves Moreau
- Department of Electrical Engineering, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Bassem A. Hassan
- Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
- Department of Human Genetics, Katholieke Universiteit Leuven School of Medicine, Leuven, Belgium
- Doctoral Program in Molecular and Developmental Genetics, Katholieke Universiteit Leuven School of Medicine, Leuven, Belgium
| | - Xiao-Jiang Quan
- Laboratory of Neurogenetics, Department of Molecular and Developmental Genetics, Vlaams Instituut voor Biotechnologie, Leuven, Belgium
- Department of Human Genetics, Katholieke Universiteit Leuven School of Medicine, Leuven, Belgium
| |
Collapse
|
12
|
Mao CA, Wang SW, Pan P, Klein WH. Rewiring the retinal ganglion cell gene regulatory network: Neurod1 promotes retinal ganglion cell fate in the absence of Math5. Development 2008; 135:3379-88. [DOI: 10.1242/dev.024612] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Retinal progenitor cells (RPCs) express basic helix-loop-helix (bHLH)factors in a strikingly mosaic spatiotemporal pattern, which is thought to contribute to the establishment of individual retinal cell identity. Here, we ask whether this tightly regulated pattern is essential for the orderly differentiation of the early retinal cell types and whether different bHLH genes have distinct functions that are adapted for each RPC. To address these issues, we replaced one bHLH gene with another. Math5 is a bHLH gene that is essential for establishing retinal ganglion cell (RGC) fate. We analyzed the retinas of mice in which Math5 was replaced with Neurod1 or Math3, bHLH genes that are expressed in another RPC and are required to establish amacrine cell fate. In the absence of Math5, Math5Neurod1-KI was able to specify RGCs, activate RGC genes and restore the optic nerve, although not as effectively as Math5. By contrast, Math5Math3-KI was much less effective than Math5Neurod1-KI in replacing Math5. In addition, expression of Neurod1 and Math3 from the Math5Neurod1-KI/Math3-KIallele did not result in enhanced amacrine cell production. These results were unexpected because they indicated that bHLH genes, which are currently thought to have evolved highly specialized functions, are nonetheless able to adjust their functions by interpreting the local positional information that is programmed into the RPC lineages. We conclude that, although Neurod1 and Math3 have evolved specialized functions for establishing amacrine cell fate, they are nevertheless capable of alternative functions when expressed in foreign environments.
Collapse
Affiliation(s)
- Chai-An Mao
- Department of Biochemistry and Molecular Biology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Steven W. Wang
- Department of Ophthalmology and Visual Science, The University of Texas Houston Medical School, Houston, TX 77030, USA
| | - Ping Pan
- Department of Biochemistry and Molecular Biology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - William H. Klein
- Department of Biochemistry and Molecular Biology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
- Training Program in Genes and Development, The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA
| |
Collapse
|
13
|
Powell LM, Jarman AP. Context dependence of proneural bHLH proteins. Curr Opin Genet Dev 2008; 18:411-7. [PMID: 18722526 PMCID: PMC3287282 DOI: 10.1016/j.gde.2008.07.012] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2008] [Revised: 07/22/2008] [Accepted: 07/23/2008] [Indexed: 01/11/2023]
Abstract
A key point in neural development is the commitment of progenitor cells to a specific neural fate. In all animals studied, proneural proteins - transcription factors of the basic helix-loop-helix (bHLH) family - are central to this process. The function of these factors is strongly influenced by the spatial and temporal context in which they are expressed. It is important to understand the molecular mechanisms by which developmental context interacts with and modifies the intrinsic functions and properties of the proneural proteins. Recent insights have been obtained in Drosophila and vertebrates from analysis of how bHLH proteins interact with other transcription factors to regulate target genes.
Collapse
Affiliation(s)
- Lynn M Powell
- Centre for Integrative Physiology, University of Edinburgh, Edinburgh, United Kingdom.
| | | |
Collapse
|
14
|
Hernandez J, Matter-Sadzinski L, Skowronska-Krawczyk D, Chiodini F, Alliod C, Ballivet M, Matter JM. Highly Conserved Sequences Mediate the Dynamic Interplay of Basic Helix-Loop-Helix Proteins Regulating Retinogenesis. J Biol Chem 2007; 282:37894-905. [DOI: 10.1074/jbc.m703616200] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
|