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Kim YI, O'Rourke R, Sagerström CG. scMultiome analysis identifies embryonic hindbrain progenitors with mixed rhombomere identities. eLife 2023; 12:e87772. [PMID: 37947350 PMCID: PMC10662952 DOI: 10.7554/elife.87772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 11/09/2023] [Indexed: 11/12/2023] Open
Abstract
Rhombomeres serve to position neural progenitors in the embryonic hindbrain, thereby ensuring appropriate neural circuit formation, but the molecular identities of individual rhombomeres and the mechanism whereby they form has not been fully established. Here, we apply scMultiome analysis in zebrafish to molecularly resolve all rhombomeres for the first time. We find that rhombomeres become molecularly distinct between 10hpf (end of gastrulation) and 13hpf (early segmentation). While the embryonic hindbrain transiently contains alternating odd- versus even-type rhombomeres, our scMultiome analyses do not detect extensive odd versus even molecular characteristics in the early hindbrain. Instead, we find that each rhombomere displays a unique gene expression and chromatin profile. Prior to the appearance of distinct rhombomeres, we detect three hindbrain progenitor clusters (PHPDs) that correlate with the earliest visually observed segments in the hindbrain primordium that represent prospective rhombomere r2/r3 (possibly including r1), r4, and r5/r6, respectively. We further find that the PHPDs form in response to Fgf and RA morphogens and that individual PHPD cells co-express markers of multiple mature rhombomeres. We propose that the PHPDs contain mixed-identity progenitors and that their subdivision into individual rhombomeres requires the resolution of mixed transcription and chromatin states.
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Affiliation(s)
- Yong-Il Kim
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical SchoolAuroraUnited States
| | - Rebecca O'Rourke
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical SchoolAuroraUnited States
| | - Charles G Sagerström
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical SchoolAuroraUnited States
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Leino SA, Constable SCJ, Streit A, Wilkinson DG. Zbtb16 mediates a switch between Fgf signalling regimes in the developing hindbrain. Development 2023; 150:dev201319. [PMID: 37642135 PMCID: PMC10508701 DOI: 10.1242/dev.201319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 08/22/2023] [Indexed: 08/31/2023]
Abstract
Developing tissues are sequentially patterned by extracellular signals that are turned on and off at specific times. In the zebrafish hindbrain, fibroblast growth factor (Fgf) signalling has different roles at different developmental stages: in the early hindbrain, transient Fgf3 and Fgf8 signalling from rhombomere 4 is required for correct segmentation, whereas later, neuronal Fgf20 expression confines neurogenesis to specific spatial domains within each rhombomere. How the switch between these two signalling regimes is coordinated is not known. We present evidence that the Zbtb16 transcription factor is required for this transition to happen in an orderly fashion. Zbtb16 expression is high in the early anterior hindbrain, then gradually upregulated posteriorly and confined to neural progenitors. In mutants lacking functional Zbtb16, fgf3 expression fails to be downregulated and persists until a late stage, resulting in excess and more widespread Fgf signalling during neurogenesis. Accordingly, the spatial pattern of neurogenesis is disrupted in Zbtb16 mutants. Our results reveal how the distinct stage-specific roles of Fgf signalling are coordinated in the zebrafish hindbrain.
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Affiliation(s)
- Sami A. Leino
- Neural Development Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London SE1 1UL, UK
| | - Sean C. J. Constable
- Neural Development Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Andrea Streit
- Centre for Craniofacial and Regenerative Biology, Faculty of Dentistry, Oral and Craniofacial Sciences, King's College London, London SE1 1UL, UK
| | - David G. Wilkinson
- Neural Development Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
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3
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Kim YI, O’Rourke R, Sagerström CG. scMultiome analysis identifies embryonic hindbrain progenitors with mixed rhombomere identities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.27.525932. [PMID: 36747868 PMCID: PMC9900950 DOI: 10.1101/2023.01.27.525932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Rhombomeres serve to position neural progenitors in the embryonic hindbrain, thereby ensuring appropriate neural circuit formation, but the molecular identities of individual rhombomeres and the mechanism whereby they form have not been fully established. Here we apply scMultiome analysis in zebrafish to molecularly resolve all rhombomeres for the first time. We find that rhombomeres become molecularly distinct between 10hpf (end of gastrulation) and 13hpf (early segmentation). While the mature hindbrain consists of alternating odd- versus even-type rhombomeres, our scMultiome analyses do not detect extensive odd versus even characteristics in the early hindbrain. Instead, we find that each rhombomere displays a unique gene expression and chromatin profile. Prior to the appearance of distinct rhombomeres, we detect three hindbrain progenitor clusters (PHPDs) that correlate with the earliest visually observed segments in the hindbrain primordium and that represent prospective rhombomere r2/r3 (possibly including r1), r4 and r5/r6, respectively. We further find that the PHPDs form in response to Fgf and RA morphogens and that individual PHPD cells co-express markers of multiple mature rhombomeres. We propose that the PHPDs contain mixed-identity progenitors and that their subdivision into individual mature rhombomeres requires resolution of mixed transcription and chromatin states.
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Affiliation(s)
| | | | - Charles G. Sagerström
- Section of Developmental Biology, Department of Pediatrics, University of Colorado Medical School, 12801 E. 17th Avenue, Aurora, CO 80045
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Qiu Y, Fung L, Schilling TF, Nie Q. Multiple morphogens and rapid elongation promote segmental patterning during development. PLoS Comput Biol 2021; 17:e1009077. [PMID: 34161317 PMCID: PMC8259987 DOI: 10.1371/journal.pcbi.1009077] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 07/06/2021] [Accepted: 05/13/2021] [Indexed: 12/21/2022] Open
Abstract
The vertebrate hindbrain is segmented into rhombomeres (r) initially defined by distinct domains of gene expression. Previous studies have shown that noise-induced gene regulation and cell sorting are critical for the sharpening of rhombomere boundaries, which start out rough in the forming neural plate (NP) and sharpen over time. However, the mechanisms controlling simultaneous formation of multiple rhombomeres and accuracy in their sizes are unclear. We have developed a stochastic multiscale cell-based model that explicitly incorporates dynamic morphogenetic changes (i.e. convergent-extension of the NP), multiple morphogens, and gene regulatory networks to investigate the formation of rhombomeres and their corresponding boundaries in the zebrafish hindbrain. During pattern initiation, the short-range signal, fibroblast growth factor (FGF), works together with the longer-range morphogen, retinoic acid (RA), to specify all of these boundaries and maintain accurately sized segments with sharp boundaries. At later stages of patterning, we show a nonlinear change in the shape of rhombomeres with rapid left-right narrowing of the NP followed by slower dynamics. Rapid initial convergence improves boundary sharpness and segment size by regulating cell sorting and cell fate both independently and coordinately. Overall, multiple morphogens and tissue dynamics synergize to regulate the sizes and boundaries of multiple segments during development. In segmental pattern formation, chemical gradients control gene expression in a concentration-dependent manner to specify distinct gene expression domains. Despite the stochasticity inherent to such biological processes, precise and accurate borders form between segmental gene expression domains. Previous work has revealed synergy between gene regulation and cell sorting in sharpening borders that are initially rough. However, it is still poorly understood how size and boundary sharpness of multiple segments are regulated in a tissue that changes dramatically in its morphology as the embryo develops. Here we develop a stochastic multiscale cell-base model to investigate these questions. Two novel strategies synergize to promote accurate segment formation, a combination of long- and short-range morphogens plus rapid tissue convergence, with one responsible for pattern initiation and the other enabling pattern refinement.
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Affiliation(s)
- Yuchi Qiu
- Department of Mathematics, University of California, Irvine, California, United States of America
| | - Lianna Fung
- Department of Developmental and Cell Biology, University of California, Irvine, California, United States of America
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California, United States of America
| | - Thomas F. Schilling
- Department of Developmental and Cell Biology, University of California, Irvine, California, United States of America
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California, United States of America
- * E-mail: (TFS); (QN)
| | - Qing Nie
- Department of Mathematics, University of California, Irvine, California, United States of America
- Department of Developmental and Cell Biology, University of California, Irvine, California, United States of America
- The NSF-Simons Center for Multiscale Cell Fate Research, University of California, Irvine, California, United States of America
- * E-mail: (TFS); (QN)
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Meserve JH, Nelson JC, Marsden KC, Hsu J, Echeverry FA, Jain RA, Wolman MA, Pereda AE, Granato M. A forward genetic screen identifies Dolk as a regulator of startle magnitude through the potassium channel subunit Kv1.1. PLoS Genet 2021; 17:e1008943. [PMID: 34061829 PMCID: PMC8195410 DOI: 10.1371/journal.pgen.1008943] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 06/11/2021] [Accepted: 05/04/2021] [Indexed: 11/19/2022] Open
Abstract
The acoustic startle response is an evolutionarily conserved avoidance behavior. Disruptions in startle behavior, particularly startle magnitude, are a hallmark of several human neurological disorders. While the neural circuitry underlying startle behavior has been studied extensively, the repertoire of genes and genetic pathways that regulate this locomotor behavior has not been explored using an unbiased genetic approach. To identify such genes, we took advantage of the stereotypic startle behavior in zebrafish larvae and performed a forward genetic screen coupled with whole genome analysis. We uncovered mutations in eight genes critical for startle behavior, including two genes encoding proteins associated with human neurological disorders, Dolichol kinase (Dolk), a broadly expressed regulator of the glycoprotein biosynthesis pathway, and the potassium Shaker-like channel subunit Kv1.1. We demonstrate that Kv1.1 and Dolk play critical roles in the spinal cord to regulate movement magnitude during the startle response and spontaneous swim movements. Moreover, we show that Kv1.1 protein is mislocalized in dolk mutants, suggesting they act in a common genetic pathway. Combined, our results identify a diverse set of eight genes, all associated with human disorders, that regulate zebrafish startle behavior and reveal a previously unappreciated role for Dolk and Kv1.1 in regulating movement magnitude via a common genetic pathway.
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Affiliation(s)
- Joy H. Meserve
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jessica C. Nelson
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kurt C. Marsden
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jerry Hsu
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Fabio A. Echeverry
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Roshan A. Jain
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Marc A. Wolman
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Alberto E. Pereda
- Dominick P. Purpura Department of Neuroscience, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Michael Granato
- Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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Lang I, Virk G, Zheng DC, Young J, Nguyen MJ, Amiri R, Fong M, Arata A, Chadaideh KS, Walsh S, Weiser DC. The Evolution of Duplicated Genes of the Cpi-17/Phi-1 ( ppp1r14) Family of Protein Phosphatase 1 Inhibitors in Teleosts. Int J Mol Sci 2020; 21:ijms21165709. [PMID: 32784920 PMCID: PMC7460850 DOI: 10.3390/ijms21165709] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Accepted: 08/07/2020] [Indexed: 11/29/2022] Open
Abstract
The Cpi-17 (ppp1r14) gene family is an evolutionarily conserved, vertebrate specific group of protein phosphatase 1 (PP1) inhibitors. When phosphorylated, Cpi-17 is a potent inhibitor of myosin phosphatase (MP), a holoenzyme complex of the regulatory subunit Mypt1 and the catalytic subunit PP1. Myosin phosphatase dephosphorylates the regulatory myosin light chain (Mlc2) and promotes actomyosin relaxation, which in turn, regulates numerous cellular processes including smooth muscle contraction, cytokinesis, cell motility, and tumor cell invasion. We analyzed zebrafish homologs of the Cpi-17 family, to better understand the mechanisms of myosin phosphatase regulation. We found single homologs of both Kepi (ppp1r14c) and Gbpi (ppp1r14d) in silico, but we detected no expression of these genes during early embryonic development. Cpi-17 (ppp1r14a) and Phi-1 (ppp1r14b) each had two duplicate paralogs, (ppp1r14aa and ppp1r14ab) and (ppp1r14ba and ppp1r14bb), which were each expressed during early development. The spatial expression pattern of these genes has diverged, with ppp1r14aa and ppp1r14bb expressed primarily in smooth muscle and skeletal muscle, respectively, while ppp1r14ab and ppp1r14ba are primarily expressed in neural tissue. We observed that, in in vitro and heterologous cellular systems, the Cpi-17 paralogs both acted as potent myosin phosphatase inhibitors, and were indistinguishable from one another. In contrast, the two Phi-1 paralogs displayed weak myosin phosphatase inhibitory activity in vitro, and did not alter myosin phosphorylation in cells. Through deletion and chimeric analysis, we identified that the difference in specificity for myosin phosphatase between Cpi-17 and Phi-1 was encoded by the highly conserved PHIN (phosphatase holoenzyme inhibitory) domain, and not the more divergent N- and C- termini. We also showed that either Cpi-17 paralog can rescue the knockdown phenotype, but neither Phi-1 paralog could do so. Thus, we provide new evidence about the biochemical and developmental distinctions of the zebrafish Cpi-17 protein family.
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Affiliation(s)
- Irene Lang
- Department of Biological Sciences, University of the Pacific, Stockton, CA 98211, USA; (I.L.); (G.V.); (D.C.Z.); (J.Y.); (M.J.N.); (R.A.); (M.F.); (A.A.); (K.S.C.)
| | - Guneet Virk
- Department of Biological Sciences, University of the Pacific, Stockton, CA 98211, USA; (I.L.); (G.V.); (D.C.Z.); (J.Y.); (M.J.N.); (R.A.); (M.F.); (A.A.); (K.S.C.)
| | - Dale C. Zheng
- Department of Biological Sciences, University of the Pacific, Stockton, CA 98211, USA; (I.L.); (G.V.); (D.C.Z.); (J.Y.); (M.J.N.); (R.A.); (M.F.); (A.A.); (K.S.C.)
| | - Jason Young
- Department of Biological Sciences, University of the Pacific, Stockton, CA 98211, USA; (I.L.); (G.V.); (D.C.Z.); (J.Y.); (M.J.N.); (R.A.); (M.F.); (A.A.); (K.S.C.)
| | - Michael J. Nguyen
- Department of Biological Sciences, University of the Pacific, Stockton, CA 98211, USA; (I.L.); (G.V.); (D.C.Z.); (J.Y.); (M.J.N.); (R.A.); (M.F.); (A.A.); (K.S.C.)
| | - Rojin Amiri
- Department of Biological Sciences, University of the Pacific, Stockton, CA 98211, USA; (I.L.); (G.V.); (D.C.Z.); (J.Y.); (M.J.N.); (R.A.); (M.F.); (A.A.); (K.S.C.)
| | - Michelle Fong
- Department of Biological Sciences, University of the Pacific, Stockton, CA 98211, USA; (I.L.); (G.V.); (D.C.Z.); (J.Y.); (M.J.N.); (R.A.); (M.F.); (A.A.); (K.S.C.)
| | - Alisa Arata
- Department of Biological Sciences, University of the Pacific, Stockton, CA 98211, USA; (I.L.); (G.V.); (D.C.Z.); (J.Y.); (M.J.N.); (R.A.); (M.F.); (A.A.); (K.S.C.)
| | - Katia S. Chadaideh
- Department of Biological Sciences, University of the Pacific, Stockton, CA 98211, USA; (I.L.); (G.V.); (D.C.Z.); (J.Y.); (M.J.N.); (R.A.); (M.F.); (A.A.); (K.S.C.)
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Susan Walsh
- Life Sciences, Soka University of America, Aliso Viejo, CA 92656, USA;
| | - Douglas C. Weiser
- Department of Biological Sciences, University of the Pacific, Stockton, CA 98211, USA; (I.L.); (G.V.); (D.C.Z.); (J.Y.); (M.J.N.); (R.A.); (M.F.); (A.A.); (K.S.C.)
- Correspondence: ; Tel.: +1-209-946-2955
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Maguire M, Larsen MC, Vezina CM, Quadro L, Kim YK, Tanumihardjo SA, Jefcoate CR. Cyp1b1 directs Srebp-mediated cholesterol and retinoid synthesis in perinatal liver; Association with retinoic acid activity during fetal development. PLoS One 2020; 15:e0228436. [PMID: 32027669 PMCID: PMC7004353 DOI: 10.1371/journal.pone.0228436] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 01/16/2020] [Indexed: 12/13/2022] Open
Abstract
Background Cytochrome P450 1b1 (Cyp1b1) deletion and dietary retinol deficiency during pregnancy (GVAD) affect perinatal liver functions regulated by Srebp. Cyp1b1 is not expressed in perinatal liver but appears in the E9.5 embryo, close to sites of retinoic acid (RA) signaling. Hypothesis Parallel effects of Cyp1b1 and retinol on postnatal Srebp derive from effects in the developing liver or systemic signaling. Approach Cluster postnatal increases in hepatic genes in relation to effects of GVAD or Cyp1b1 deletion. Sort expression changes in relation to genes regulated by Srebp1 and Srebp2.Test these treatments on embryos at E9.5, examining changes at the site of liver initiation. Use in situ hybridization to resolve effects on mRNA distributions of Aldh1a2 and Cyp26a1 (RA homeostasis); Hoxb1 and Pax6 (RA targets). Assess mice lacking Lrat and Rbp4 (DKO mice) that severely limits retinol supply to embryos. Results At birth, GVAD and Cyp1b1 deletion stimulate gene markers of hepatic stellate cell (HSC) activation but also suppress Hamp. These treatments then selectively prevent the postnatal onset of genes that synthesize cholesterol (Hmgcr, Sqle) and fatty acids (Fasn, Scd1), but also direct cholesterol transport (Ldlr, Pcsk9, Stard4) and retinoid synthesis (Aldh1a1, Rdh11). Extensive support by Cyp1b1 is implicated, but with distinct GVAD interventions for Srebp1 and Srebp2. At E9.5, Cyp1b1 is expressed in the septum transversum mesenchyme (STM) with β-carotene oxygenase (Bco1) that generates retinaldehyde. STM provides progenitors for the HSC and supports liver expansion. GVAD and Cyp1b1-/- do not affect RA-dependent Hoxb1 and Pax6. In DKO embryos, RA-dependent Cyp26a1 is lost but Hoxb1 is sustained with Cyp1b1 at multiple sites. Conclusion Cyp1b1-/- suppresses genes supported by Srebp. GVAD effects distinguish Srebp1 and Srebp2 mediation. Srebp regulation overlaps appreciably in cholesterol and retinoid homeostasis. Bco1/Cyp1b1 partnership in the STM may contribute to this later liver regulation.
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Affiliation(s)
- Meghan Maguire
- Endocrinology and Reproductive Physiology Program, University of Wisconsin-Madison, Madison, WI
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI
| | | | - Chad M. Vezina
- Department of Comparative Biosciences, University of Wisconsin-Madison, Madison, WI
| | - Loredana Quadro
- Department of Food Science and Rutgers Center for Lipid Research, Rutgers University, New Brunswick, New Jersey
| | - Youn-Kyung Kim
- Department of Food Science and Rutgers Center for Lipid Research, Rutgers University, New Brunswick, New Jersey
| | | | - Colin R. Jefcoate
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI
- * E-mail:
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Parker HJ, Krumlauf R. A Hox gene regulatory network for hindbrain segmentation. Curr Top Dev Biol 2020; 139:169-203. [DOI: 10.1016/bs.ctdb.2020.03.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Frank D, Sela-Donenfeld D. Hindbrain induction and patterning during early vertebrate development. Cell Mol Life Sci 2019; 76:941-960. [PMID: 30519881 PMCID: PMC11105337 DOI: 10.1007/s00018-018-2974-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 11/19/2018] [Accepted: 11/21/2018] [Indexed: 12/28/2022]
Abstract
The hindbrain is a key relay hub of the central nervous system (CNS), linking the bilaterally symmetric half-sides of lower and upper CNS centers via an extensive network of neural pathways. Dedicated neural assemblies within the hindbrain control many physiological processes, including respiration, blood pressure, motor coordination and different sensations. During early development, the hindbrain forms metameric segmented units known as rhombomeres along the antero-posterior (AP) axis of the nervous system. These compartmentalized units are highly conserved during vertebrate evolution and act as the template for adult brainstem structure and function. TALE and HOX homeodomain family transcription factors play a key role in the initial induction of the hindbrain and its specification into rhombomeric cell fate identities along the AP axis. Signaling pathways, such as canonical-Wnt, FGF and retinoic acid, play multiple roles to initially induce the hindbrain and regulate Hox gene-family expression to control rhombomeric identity. Additional transcription factors including Krox20, Kreisler and others act both upstream and downstream to Hox genes, modulating their expression and protein activity. In this review, we will examine the earliest embryonic signaling pathways that induce the hindbrain and subsequent rhombomeric segmentation via Hox and other gene expression. We will examine how these signaling pathways and transcription factors interact to activate downstream targets that organize the segmented AP pattern of the embryonic vertebrate hindbrain.
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Affiliation(s)
- Dale Frank
- Department of Biochemistry, Faculty of Medicine, The Rappaport Family Institute for Research in the Medical Sciences, Technion-Israel Institute of Technology, 31096, Haifa, Israel.
| | - Dalit Sela-Donenfeld
- Koret School of Veterinary Medicine, The Robert H Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel.
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Abstract
Studies of the vertebrate hindbrain have revealed parallel mechanisms that establish sharp segments with a distinct and homogeneous regional identity. Recent work has revealed roles of cell identity regulation and its relationships with cell segregation. At early stages, there is overlapping expression at segment borders of the Egr2 and Hoxb1 transcription factors that specify distinct identities, which is resolved by reciprocal repression. Computer simulations show that this dynamic regulation of cell identity synergises with cell segregation to generate sharp borders. Some intermingling between segments occurs at early stages, and ectopic egr2-expressing cells switch identity to match their new neighbours. This switching is mediated by coupling between egr2 expression and the level of retinoic acid signalling, which acts in a community effect to maintain homogeneous segmental identity. These findings reveal an interplay between cell segregation and the dynamic regulation of cell identity in the formation of sharp patterns in the hindbrain and raise the question of whether similar mechanisms occur in other tissues.
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11
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Ghosh P, Maurer JM, Sagerström CG. Analysis of novel caudal hindbrain genes reveals different regulatory logic for gene expression in rhombomere 4 versus 5/6 in embryonic zebrafish. Neural Dev 2018; 13:13. [PMID: 29945667 PMCID: PMC6020313 DOI: 10.1186/s13064-018-0112-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 06/19/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Previous work aimed at understanding the gene regulatory networks (GRNs) governing caudal hindbrain formation identified morphogens such as Retinoic Acid (RA) and Fibroblast growth factors (FGFs), as well as transcription factors like hoxb1b, hoxb1a, hnf1ba, and valentino as being required for rhombomere (r) r4-r6 formation in zebrafish. Considering that the caudal hindbrain is relatively complex - for instance, unique sets of neurons are formed in each rhombomere segment - it is likely that additional essential genes remain to be identified and integrated into the caudal hindbrain GRN. METHODS By taking advantage of gene expression data available in the Zebrafish Information Network (ZFIN), we identified 84 uncharacterized genes that are expressed in r4-r6. We selected a representative set of 22 genes and assayed their expression patterns in hoxb1b, hoxb1a, hnf1b, and valentino mutants with the goal of positioning them in the caudal hindbrain GRN. We also investigated the effects of RA and FGF on the expression of this gene set. To examine whether these genes are necessary for r4-r6 development, we analyzed germline mutants for six of the genes (gas6, gbx1, sall4, eglf6, celf2, and greb1l) for defects in hindbrain development. RESULTS Our results reveal that r4 gene expression is unaffected by the individual loss of hoxb1b, hoxb1a or RA, but is under the combinatorial regulation of RA together with hoxb1b. In contrast, r5/r6 gene expression is dependent on RA, FGF, hnf1ba and valentino - as individual loss of these factors abolishes r5/r6 gene expression. Our analysis of six mutant lines did not reveal rhombomere or neuronal defects, but transcriptome analysis of one line (gas6 mutant) identified expression changes for genes involved in several developmental processes - suggesting that these genes may have subtle roles in hindbrain development. CONCLUSION We conclude that r4-r6 formation is relatively robust, such that very few genes are absolutely required for this process. However, there are mechanistic differences in r4 versus r5/r6, such that no single factor is required for r4 development while several genes are individually required for r5/r6 formation.
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Affiliation(s)
- Priyanjali Ghosh
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St/LRB815, Worcester, MA, USA
| | - Jennifer M Maurer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St/LRB815, Worcester, MA, USA
| | - Charles G Sagerström
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St/LRB815, Worcester, MA, USA.
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12
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Coupling the roles of Hox genes to regulatory networks patterning cranial neural crest. Dev Biol 2018; 444 Suppl 1:S67-S78. [PMID: 29571614 DOI: 10.1016/j.ydbio.2018.03.016] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 03/17/2018] [Accepted: 03/17/2018] [Indexed: 11/20/2022]
Abstract
The neural crest is a transient population of cells that forms within the developing central nervous system and migrates away to generate a wide range of derivatives throughout the body during vertebrate embryogenesis. These cells are of evolutionary and clinical interest, constituting a key defining trait in the evolution of vertebrates and alterations in their development are implicated in a high proportion of birth defects and craniofacial abnormalities. In the hindbrain and the adjacent cranial neural crest cells (cNCCs), nested domains of Hox gene expression provide a combinatorial'Hox-code' for specifying regional properties in the developing head. Hox genes have been shown to play important roles at multiple stages in cNCC development, including specification, migration, and differentiation. However, relatively little is known about the underlying gene-regulatory mechanisms involved, both upstream and downstream of Hox genes. Furthermore, it is still an open question as to how the genes of the neural crest GRN are linked to Hox-dependent pathways. In this review, we describe Hox gene expression, function and regulation in cNCCs with a view to integrating these genes within the emerging gene regulatory network for cNCC development. We highlight early roles for Hox1 genes in cNCC specification, proposing that this may be achieved, in part, by regulation of the balance between pluripotency and differentiation in precursor cells within the neuro-epithelium. We then describe what is known about the regulation of Hox gene expression in cNCCs and discuss this from the perspective of early vertebrate evolution.
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13
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Maurer JM, Sagerström CG. A parental requirement for dual-specificity phosphatase 6 in zebrafish. BMC DEVELOPMENTAL BIOLOGY 2018; 18:6. [PMID: 29544468 PMCID: PMC5856328 DOI: 10.1186/s12861-018-0164-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 02/13/2018] [Indexed: 02/06/2023]
Abstract
Background Signaling cascades, such as the extracellular signal-regulated kinase (ERK) pathway, play vital roles in early vertebrate development. Signals through these pathways are initiated by a growth factor or hormone, are transduced through a kinase cascade, and result in the expression of specific downstream genes that promote cellular proliferation, growth, or differentiation. Tight regulation of these signals is provided by positive or negative modulators at varying levels in the pathway, and is required for proper development and function. Two members of the dual-specificity phosphatase (Dusp) family, dusp6 and dusp2, are believed to be negative regulators of the ERK pathway and are expressed in both embryonic and adult zebrafish, but their specific roles in embryogenesis remain to be fully understood. Results Using CRISPR/Cas9 genome editing technology, we generated zebrafish lines harboring germ line deletions in dusp6 and dusp2. We do not detect any overt defects in dusp2 mutants, but we find that approximately 50% of offspring from homozygous dusp6 mutants do not proceed through embryonic development. These embryos are fertilized, but are unable to proceed past the first zygotic mitosis and stall at the 1-cell stage for several hours before dying by 10 h post fertilization. We demonstrate that dusp6 is expressed in gonads of both male and female zebrafish, suggesting that loss of dusp6 causes defects in germ cell production. Notably, the 50% of homozygous dusp6 mutants that complete the first cell division appear to progress through embryogenesis normally and give rise to fertile adults. Conclusions The fact that offspring of homozygous dusp6 mutants stall prior to activation of the zygotic genome, suggests that loss of dusp6 affects gametogenesis and/or parentally-directed early development. Further, since only approximately 50% of homozygous dusp6 mutants are affected, we postulate that ERK signaling is tightly regulated and that dusp6 is required to keep ERK signaling within a range that is permissive for proper embryogenesis. Lastly, since dusp6 is expressed throughout zebrafish embryogenesis, but dusp6 mutants do not exhibit defects after the first cell division, it is possible that other regulators of the ERK pathway compensate for loss of dusp6 at later stages. Electronic supplementary material The online version of this article (10.1186/s12861-018-0164-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jennifer M Maurer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Charles G Sagerström
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
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14
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Selland LG, Koch S, Laraque M, Waskiewicz AJ. Coordinate regulation of retinoic acid synthesis by pbx genes and fibroblast growth factor signaling by hoxb1b is required for hindbrain patterning and development. Mech Dev 2018; 150:28-41. [PMID: 29496480 DOI: 10.1016/j.mod.2018.02.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 02/23/2018] [Accepted: 02/23/2018] [Indexed: 10/17/2022]
Abstract
The vertebrate hindbrain is composed of a series of lineage-restricted segments termed rhombomeres. Segment-specific gene expression drives unique programs of neuronal differentiation. Two critical embryonic signaling pathways, Fibroblast Growth Factor (FGF) and Retinoic Acid (RA), regulate early embryonic rhombomere patterning. The earliest expressed hox genes, hoxb1b and hoxb1a in zebrafish, are logical candidates for establishing signaling networks that specify segmental identity. We sought to determine the mechanism by which hox genes regulate hindbrain patterning in zebrafish. We demonstrate that hoxb1a regulates r4-specific patterning, while hoxb1b regulates rhombomere segmentation and size. Hoxb1a and hoxb1b redundantly regulate vhnf1 expression. Loss of hoxb1b together with pbx4 reverts the hindbrain to a groundstate identity, demonstrating the importance of hox genes in patterning nearly the entire hindbrain, and a key requirement for Pbx in this process. Additionally, we provide evidence that while pbx genes regulate RA signaling, hoxb1b regulates hindbrain identity through complex regulation of FGF signaling.
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Affiliation(s)
- Lyndsay G Selland
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Sophie Koch
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Malcolm Laraque
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Andrew J Waskiewicz
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
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15
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Sanna-Cherchi S, Khan K, Westland R, Krithivasan P, Fievet L, Rasouly HM, Ionita-Laza I, Capone VP, Fasel DA, Kiryluk K, Kamalakaran S, Bodria M, Otto EA, Sampson MG, Gillies CE, Vega-Warner V, Vukojevic K, Pediaditakis I, Makar GS, Mitrotti A, Verbitsky M, Martino J, Liu Q, Na YJ, Goj V, Ardissino G, Gigante M, Gesualdo L, Janezcko M, Zaniew M, Mendelsohn CL, Shril S, Hildebrandt F, van Wijk JAE, Arapovic A, Saraga M, Allegri L, Izzi C, Scolari F, Tasic V, Ghiggeri GM, Latos-Bielenska A, Materna-Kiryluk A, Mane S, Goldstein DB, Lifton RP, Katsanis N, Davis EE, Gharavi AG. Exome-wide Association Study Identifies GREB1L Mutations in Congenital Kidney Malformations. Am J Hum Genet 2017; 101:789-802. [PMID: 29100090 DOI: 10.1016/j.ajhg.2017.09.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/22/2017] [Indexed: 01/02/2023] Open
Abstract
Renal agenesis and hypodysplasia (RHD) are major causes of pediatric chronic kidney disease and are highly genetically heterogeneous. We conducted whole-exome sequencing in 202 case subjects with RHD and identified diagnostic mutations in genes known to be associated with RHD in 7/202 case subjects. In an additional affected individual with RHD and a congenital heart defect, we found a homozygous loss-of-function (LOF) variant in SLIT3, recapitulating phenotypes reported with Slit3 inactivation in the mouse. To identify genes associated with RHD, we performed an exome-wide association study with 195 unresolved case subjects and 6,905 control subjects. The top signal resided in GREB1L, a gene implicated previously in Hoxb1 and Shha signaling in zebrafish. The significance of the association, which was p = 2.0 × 10-5 for novel LOF, increased to p = 4.1 × 10-6 for LOF and deleterious missense variants combined, and augmented further after accounting for segregation and de novo inheritance of rare variants (joint p = 2.3 × 10-7). Finally, CRISPR/Cas9 disruption or knockdown of greb1l in zebrafish caused specific pronephric defects, which were rescued by wild-type human GREB1L mRNA, but not mRNA containing alleles identified in case subjects. Together, our study provides insight into the genetic landscape of kidney malformations in humans, presents multiple candidates, and identifies SLIT3 and GREB1L as genes implicated in the pathogenesis of RHD.
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Affiliation(s)
| | - Kamal Khan
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Rik Westland
- Division of Nephrology, Columbia University, New York, NY 10032, USA; Department of Pediatric Nephrology, VU University Medical Center, Amsterdam 1007 MB, the Netherlands
| | - Priya Krithivasan
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Lorraine Fievet
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Hila Milo Rasouly
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | | | | | - David A Fasel
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Sitharthan Kamalakaran
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Monica Bodria
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa 16147, Italy
| | - Edgar A Otto
- University of Michigan School of Medicine, Department of Internal Medicine-Nephrology, Ann Arbor, MI 48109, USA
| | - Matthew G Sampson
- University of Michigan School of Medicine, Department of Pediatrics-Nephrology, Ann Arbor, MI 48109, USA
| | - Christopher E Gillies
- University of Michigan School of Medicine, Department of Pediatrics-Nephrology, Ann Arbor, MI 48109, USA
| | - Virginia Vega-Warner
- University of Michigan School of Medicine, Department of Pediatrics-Nephrology, Ann Arbor, MI 48109, USA
| | - Katarina Vukojevic
- Department of Anatomy, Histology, and Embryology, School of Medicine, University of Split, Split 21000, Croatia
| | - Igor Pediaditakis
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Gabriel S Makar
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Adele Mitrotti
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Miguel Verbitsky
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Jeremiah Martino
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Qingxue Liu
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Young-Ji Na
- Division of Nephrology, Columbia University, New York, NY 10032, USA
| | - Vinicio Goj
- Pediatric Unit, Fatebenefratelli Hospital, Milan 20121, Italy
| | - Gianluigi Ardissino
- Pediatric Nephrology and Dialysis Unit, Fondazione Ca' Granda IRCCS Ospedale Maggiore Policlinico Milano, 20122 Milan, Italy
| | - Maddalena Gigante
- Department of Medical and Surgical Sciences, University of Foggia, Foggia 71121, Italy
| | - Loreto Gesualdo
- Section of Nephrology, Department of Emergency and Organ Transplantation, University of Bari, Bari 70121, Italy
| | - Magdalena Janezcko
- Department of Medical Genetics, Chair of Pediatrics, Jagiellonian University, Collegium Medicum, Krakow 31-008, Poland
| | | | - Cathy Lee Mendelsohn
- Department of Urology, Pathology and Cell Biology, Genetics and Development, Columbia University, New York, NY 10032, USA
| | - Shirlee Shril
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Friedhelm Hildebrandt
- Department of Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Joanna A E van Wijk
- Department of Pediatric Nephrology, VU University Medical Center, Amsterdam 1007 MB, the Netherlands
| | - Adela Arapovic
- Department of Pediatrics, University Hospital of Split, Split 21000, Croatia
| | - Marijan Saraga
- Department of Pediatrics, University Hospital of Split, Split 21000, Croatia; School of Medicine, University of Split, Split 21000, Croatia
| | - Landino Allegri
- Department of Medicine and Surgery, University of Parma, Parma 43100, Italy
| | - Claudia Izzi
- Cattedra di Nefrologia, Università di Brescia, Seconda Divisione di Nefrologia Azienda Ospedaliera Spedali Civili di Brescia Presidio di Montichiari, Brescia 25018, Italy; Dipartimento Ostetrico Ginecologico, Azienda Ospedaliera Spedali Civili di Brescia, Brescia 25018, Italy
| | - Francesco Scolari
- Cattedra di Nefrologia, Università di Brescia, Seconda Divisione di Nefrologia Azienda Ospedaliera Spedali Civili di Brescia Presidio di Montichiari, Brescia 25018, Italy
| | - Velibor Tasic
- Department of Pediatric Nephrology, University Children's Hospital, Medical Faculty of Skopje, Skopje 1000, Macedonia
| | - Gian Marco Ghiggeri
- Division of Nephrology, Dialysis, Transplantation, and Laboratory on Pathophysiology of Uremia, Istituto G. Gaslini, Genoa 16147, Italy
| | - Anna Latos-Bielenska
- Department of Medical Genetics, Poznan University of Medical Sciences, and Center for Medical Genetics GENESIS, Poznan 61-701, Poland
| | - Anna Materna-Kiryluk
- Department of Medical Genetics, Poznan University of Medical Sciences, and Center for Medical Genetics GENESIS, Poznan 61-701, Poland
| | - Shrikant Mane
- Department of Human Genetics, Yale University School of Medicine, New Haven, CT 06510, USA
| | - David B Goldstein
- Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Richard P Lifton
- Department of Human Genetics, Yale University School of Medicine, New Haven, CT 06510, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA
| | - Erica E Davis
- Center for Human Disease Modeling, Duke University, Durham, NC 27701, USA.
| | - Ali G Gharavi
- Division of Nephrology, Columbia University, New York, NY 10032, USA
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16
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Parker HJ, Krumlauf R. Segmental arithmetic: summing up the Hox gene regulatory network for hindbrain development in chordates. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2017; 6. [PMID: 28771970 DOI: 10.1002/wdev.286] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 06/13/2017] [Accepted: 06/15/2017] [Indexed: 11/10/2022]
Abstract
Organization and development of the early vertebrate hindbrain are controlled by a cascade of regulatory interactions that govern the process of segmentation and patterning along the anterior-posterior axis via Hox genes. These interactions can be assembled into a gene regulatory network that provides a framework to interpret experimental data, generate hypotheses, and identify gaps in our understanding of the progressive process of hindbrain segmentation. The network can be broadly separated into a series of interconnected programs that govern early signaling, segmental subdivision, secondary signaling, segmentation, and ultimately specification of segmental identity. Hox genes play crucial roles in multiple programs within this network. Furthermore, the network reveals properties and principles that are likely to be general to other complex developmental systems. Data from vertebrate and invertebrate chordate models are shedding light on the origin and diversification of the network. Comprehensive cis-regulatory analyses of vertebrate Hox gene regulation have enabled powerful cross-species gene regulatory comparisons. Such an approach in the sea lamprey has revealed that the network mediating segmental Hox expression was present in ancestral vertebrates and has been maintained across diverse vertebrate lineages. Invertebrate chordates lack hindbrain segmentation but exhibit conservation of some aspects of the network, such as a role for retinoic acid in establishing nested Hox expression domains. These comparisons lead to a model in which early vertebrates underwent an elaboration of the network between anterior-posterior patterning and Hox gene expression, leading to the gene-regulatory programs for segmental subdivision and rhombomeric segmentation. WIREs Dev Biol 2017, 6:e286. doi: 10.1002/wdev.286 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Hugo J Parker
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Robb Krumlauf
- Stowers Institute for Medical Research, Kansas City, MO, USA.,Department of Anatomy and Cell Biology, Kansas University Medical Center, Kansas City, Kansas 66160, USA
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17
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A Hox complex activates and potentiates the Epidermal Growth Factor signaling pathway to specify Drosophila oenocytes. PLoS Genet 2017; 13:e1006910. [PMID: 28715417 PMCID: PMC5536354 DOI: 10.1371/journal.pgen.1006910] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 07/31/2017] [Accepted: 07/06/2017] [Indexed: 11/19/2022] Open
Abstract
Hox transcription factors specify distinct cell types along the anterior-posterior axis of metazoans by regulating target genes that modulate signaling pathways. A well-established example is the induction of Epidermal Growth Factor (EGF) signaling by an Abdominal-A (Abd-A) Hox complex during the specification of Drosophila hepatocyte-like cells (oenocytes). Previous studies revealed that Abd-A is non-cell autonomously required to promote oenocyte fate by directly activating a gene (rhomboid) that triggers EGF secretion from sensory organ precursor (SOP) cells. Neighboring cells that receive the EGF signal initiate a largely unknown pathway to promote oenocyte fate. Here, we show that Abd-A also plays a cell autonomous role in inducing oenocyte fate by activating the expression of the Pointed-P1 (PntP1) ETS transcription factor downstream of EGF signaling. Genetic studies demonstrate that both PntP1 and PntP2 are required for oenocyte specification. Moreover, we found that PntP1 contains a conserved enhancer (PntP1OE) that is activated in oenocyte precursor cells by EGF signaling via direct regulation by the Pnt transcription factors as well as a transcription factor complex consisting of Abd-A, Extradenticle, and Homothorax. Our findings demonstrate that the same Abd-A Hox complex required for sending the EGF signal from SOP cells, enhances the competency of receiving cells to select oenocyte cell fate by up-regulating PntP1. Since PntP1 is a downstream effector of EGF signaling, these findings provide insight into how a Hox factor can both trigger and potentiate the EGF signal to promote an essential cell fate along the body plan.
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18
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Rouhiainen A, Zhao X, Vanttola P, Qian K, Kulesskiy E, Kuja-Panula J, Gransalke K, Grönholm M, Unni E, Meistrich M, Tian L, Auvinen P, Rauvala H. HMGB4 is expressed by neuronal cells and affects the expression of genes involved in neural differentiation. Sci Rep 2016; 6:32960. [PMID: 27608812 PMCID: PMC5036535 DOI: 10.1038/srep32960] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Accepted: 08/18/2016] [Indexed: 12/21/2022] Open
Abstract
HMGB4 is a new member in the family of HMGB proteins that has been characterized in sperm cells, but little is known about its functions in somatic cells. Here we show that HMGB4 and the highly similar rat Transition Protein 4 (HMGB4L1) are expressed in neuronal cells. Both proteins had slow mobility in nucleus of living NIH-3T3 cells. They interacted with histones and their differential expression in transformed cells of the nervous system altered the post-translational modification statuses of histones in vitro. Overexpression of HMGB4 in HEK 293T cells made cells more susceptible to cell death induced by topoisomerase inhibitors in an oncology drug screening array and altered variant composition of histone H3. HMGB4 regulated over 800 genes in HEK 293T cells with a p-value ≤0.013 (n = 3) in a microarray analysis and displayed strongest association with adhesion and histone H2A –processes. In neuronal and transformed cells HMGB4 regulated the expression of an oligodendrocyte marker gene PPP1R14a and other neuronal differentiation marker genes. In conclusion, our data suggests that HMGB4 is a factor that regulates chromatin and expression of neuronal differentiation markers.
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Affiliation(s)
- Ari Rouhiainen
- Neuroscience center, University of Helsinki, Finland.,Department of Biosciences, University of Helsinki, Finland
| | - Xiang Zhao
- Neuroscience center, University of Helsinki, Finland.,Schools of Pharmacy and Medicine, Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, California, USA
| | | | - Kui Qian
- Institute of Biotechnology, University of Helsinki, Finland
| | - Evgeny Kulesskiy
- Neuroscience center, University of Helsinki, Finland.,Institute for Molecular Medicine Finland, FIMM, University of Helsinki, Finland
| | | | | | | | - Emmanual Unni
- Department of Biochemistry, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Marvin Meistrich
- Department of Experimental Radiation Oncology, Division of Radiation Oncology, MD Anderson Cancer Center, Houston, Texas, USA
| | - Li Tian
- Neuroscience center, University of Helsinki, Finland.,Psychiatry Research Center, Beijing Hui Long Guan Hospital, Peking University, Beijing, China
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Finland
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19
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Kctd12 and Ulk2 partner to regulate dendritogenesis and behavior in the habenular nuclei. PLoS One 2014; 9:e110280. [PMID: 25329151 PMCID: PMC4203773 DOI: 10.1371/journal.pone.0110280] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 09/15/2014] [Indexed: 11/30/2022] Open
Abstract
The habenular nuclei of the limbic system regulate responses, such as anxiety, to aversive stimuli in the environment. The habenulae receive inputs from the telencephalon via elaborate dendrites that form in the center of the nuclei. The kinase Ulk2 positively regulates dendritogenesis on habenular neurons, and in turn is negatively regulated by the cytoplasmic protein Kctd12. Given that the habenulae are a nexus in the aversive response circuit, we suspected that incomplete habenular dendritogenesis would have profound implications for behavior. We find that Ulk2, which interacts with Kctd12 proteins via a small proline-serine rich domain, promotes branching and elaboration of dendrites. Loss of Kctd12 results in increased branching/elaboration and decreased anxiety. We conclude that fine-tuning of habenular dendritogenesis during development is essential for appropriate behavioral responses to negative stimuli.
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20
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Zannino DA, Downes GB, Sagerström CG. prdm12b specifies the p1 progenitor domain and reveals a role for V1 interneurons in swim movements. Dev Biol 2014. [PMID: 24631215 DOI: 10.1016/j.vdbio.2014.02.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Proper functioning of the vertebrate central nervous system requires the precise positioning of many neuronal cell types. This positioning is established during early embryogenesis when gene regulatory networks pattern the neural tube along its anteroposterior and dorsoventral axes. Dorsoventral patterning of the embryonic neural tube gives rise to multiple progenitor cell domains that go on to differentiate unique classes of neurons and glia. While the genetic program is reasonably well understood for some lineages, such as ventrally derived motor neurons and glia, other lineages are much less characterized. Here we show that prdm12b, a member of the PR domain containing-family of transcriptional regulators, is expressed in the p1 progenitor domain of the zebrafish neural tube in response to Sonic Hedgehog signaling. We find that disruption of prdm12b function leads to dorsal expansion of nkx6.1 expression and loss of p1-derived eng1b-expressing V1 interneurons, while the adjacent p0 and p2 domains are unaffected. We also demonstrate that prdm12b-deficient fish exhibit an abnormal touch-evoked escape response with excessive body contractions and a prolonged response time, as well as an inability to coordinate swimming movements, thereby revealing a functional role for V1 interneurons in locomotor circuits. We conclude that prdm12b is required for V1 interneuron specification and that these neurons control swimming movements in zebrafish.
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Affiliation(s)
- Denise A Zannino
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St./LRB815, Worcester, MA 01605-2324, USA
| | - Gerald B Downes
- Department of Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Charles G Sagerström
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St./LRB815, Worcester, MA 01605-2324, USA.
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21
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Zigman M, Laumann-Lipp N, Titus T, Postlethwait J, Moens CB. Hoxb1b controls oriented cell division, cell shape and microtubule dynamics in neural tube morphogenesis. Development 2014; 141:639-49. [PMID: 24449840 PMCID: PMC3899817 DOI: 10.1242/dev.098731] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Hox genes are classically ascribed to function in patterning the anterior-posterior axis of bilaterian animals; however, their role in directing molecular mechanisms underlying morphogenesis at the cellular level remains largely unstudied. We unveil a non-classical role for the zebrafish hoxb1b gene, which shares ancestral functions with mammalian Hoxa1, in controlling progenitor cell shape and oriented cell division during zebrafish anterior hindbrain neural tube morphogenesis. This is likely distinct from its role in cell fate acquisition and segment boundary formation. We show that, without affecting major components of apico-basal or planar cell polarity, Hoxb1b regulates mitotic spindle rotation during the oriented neural keel symmetric mitoses that are required for normal neural tube lumen formation in the zebrafish. This function correlates with a non-cell-autonomous requirement for Hoxb1b in regulating microtubule plus-end dynamics in progenitor cells in interphase. We propose that Hox genes can influence global tissue morphogenesis by control of microtubule dynamics in individual cells in vivo.
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Affiliation(s)
- Mihaela Zigman
- Centre for Organismal Studies (COS), University of Heidelberg, Im Neuenheimer Feld 329, 69120 Heidelberg, Germany
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22
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Zannino DA, Downes GB, Sagerström CG. prdm12b specifies the p1 progenitor domain and reveals a role for V1 interneurons in swim movements. Dev Biol 2014; 390:247-60. [PMID: 24631215 DOI: 10.1016/j.ydbio.2014.02.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 02/12/2014] [Accepted: 02/28/2014] [Indexed: 01/23/2023]
Abstract
Proper functioning of the vertebrate central nervous system requires the precise positioning of many neuronal cell types. This positioning is established during early embryogenesis when gene regulatory networks pattern the neural tube along its anteroposterior and dorsoventral axes. Dorsoventral patterning of the embryonic neural tube gives rise to multiple progenitor cell domains that go on to differentiate unique classes of neurons and glia. While the genetic program is reasonably well understood for some lineages, such as ventrally derived motor neurons and glia, other lineages are much less characterized. Here we show that prdm12b, a member of the PR domain containing-family of transcriptional regulators, is expressed in the p1 progenitor domain of the zebrafish neural tube in response to Sonic Hedgehog signaling. We find that disruption of prdm12b function leads to dorsal expansion of nkx6.1 expression and loss of p1-derived eng1b-expressing V1 interneurons, while the adjacent p0 and p2 domains are unaffected. We also demonstrate that prdm12b-deficient fish exhibit an abnormal touch-evoked escape response with excessive body contractions and a prolonged response time, as well as an inability to coordinate swimming movements, thereby revealing a functional role for V1 interneurons in locomotor circuits. We conclude that prdm12b is required for V1 interneuron specification and that these neurons control swimming movements in zebrafish.
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Affiliation(s)
- Denise A Zannino
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St./LRB815, Worcester, MA 01605-2324, USA
| | - Gerald B Downes
- Department of Biology, University of Massachusetts, Amherst, MA 01003, USA
| | - Charles G Sagerström
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St./LRB815, Worcester, MA 01605-2324, USA.
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23
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Kim YI, Bhandari S, Lee JN, Yoo KW, Kim SJ, Oh GS, Kim HJ, Cho M, Kwak JY, So HS, Park R, Choe SK. Developmental roles of D-bifunctional protein-A zebrafish model of peroxisome dysfunction. Mol Cells 2014; 37:74-80. [PMID: 24552713 PMCID: PMC3907007 DOI: 10.14348/molcells.2014.2300] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 11/08/2013] [Accepted: 11/08/2013] [Indexed: 12/17/2022] Open
Abstract
The peroxisome is an intracellular organelle that responds dynamically to environmental changes. Various model organisms have been used to study the roles of peroxisomal proteins in maintaining cellular homeostasis. By taking advantage of the zebrafish model whose early stage of embryogenesis is dependent on yolk components, we examined the developmental roles of the D-bifunctional protein (Dbp), an essential enzyme in the peroxisomal β-oxidation. The knockdown of dbp in zebrafish phenocopied clinical manifestations of its deficiency in human, including defective craniofacial morphogenesis, growth retardation, and abnormal neuronal development. Overexpression of murine Dbp rescued the morphological phenotypes induced by dbp knockdown, indicative of conserved roles of Dbp during zebrafish and mammalian development. Knockdown of dbp impaired normal development of blood, blood vessels, and most strikingly, endoderm-derived organs including the liver and pancreas - a phenotype not reported elsewhere in connection with peroxisome dysfunction. Taken together, our results demonstrate for the first time that zebrafish might be a useful model animal to study the role of peroxisomes during vertebrate development.
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Affiliation(s)
- Yong-Il Kim
- Center for Metabolic Function Regulation, and Department of Microbiology, School of Medicine, Wonkwang University, Iksan 570-749,
Korea
| | - Sushil Bhandari
- Center for Metabolic Function Regulation, and Department of Microbiology, School of Medicine, Wonkwang University, Iksan 570-749,
Korea
| | - Joon No Lee
- Center for Metabolic Function Regulation, and Department of Microbiology, School of Medicine, Wonkwang University, Iksan 570-749,
Korea
| | - Kyeong-Won Yoo
- Center for Metabolic Function Regulation, and Department of Microbiology, School of Medicine, Wonkwang University, Iksan 570-749,
Korea
- Immune-network Pioneer Research Center, Department of Biochemistry, College of Medicine, Dong-A University, Busan 602-714,
Korea
| | - Se-Jin Kim
- Center for Metabolic Function Regulation, and Department of Microbiology, School of Medicine, Wonkwang University, Iksan 570-749,
Korea
| | - Gi-Su Oh
- Center for Metabolic Function Regulation, and Department of Microbiology, School of Medicine, Wonkwang University, Iksan 570-749,
Korea
| | - Hyung-Jin Kim
- Center for Metabolic Function Regulation, and Department of Microbiology, School of Medicine, Wonkwang University, Iksan 570-749,
Korea
| | - Meyoung Cho
- Department of Internal Medicine, Gunsan Medical Center, Gunsan 573-713
Korea
| | - Jong-Young Kwak
- Immune-network Pioneer Research Center, Department of Biochemistry, College of Medicine, Dong-A University, Busan 602-714,
Korea
| | - Hong-Seob So
- Center for Metabolic Function Regulation, and Department of Microbiology, School of Medicine, Wonkwang University, Iksan 570-749,
Korea
| | - Raekil Park
- Center for Metabolic Function Regulation, and Department of Microbiology, School of Medicine, Wonkwang University, Iksan 570-749,
Korea
| | - Seong-Kyu Choe
- Center for Metabolic Function Regulation, and Department of Microbiology, School of Medicine, Wonkwang University, Iksan 570-749,
Korea
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24
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Abstract
The zebrafish model organism is well suited to study the role of specific genes, such as hox genes, in embryogenesis and organ function. The ability to modulate the activity of hox genes in living zebrafish embryos represents a cornerstone of such functional analyses. In this chapter we outline the basic methodology for nucleic acid injections into 1-2-cell-stage zebrafish embryos. We also report variations in this method to allow injection of mRNA, DNA, and antisense oligonucleotides to either overexpress, knock down, or knock out specific genes in zebrafish embryos.
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Affiliation(s)
- Franck Ladam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01605, USA
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25
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Schulte D, Frank D. TALE transcription factors during early development of the vertebrate brain and eye. Dev Dyn 2013; 243:99-116. [DOI: 10.1002/dvdy.24030] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 07/11/2013] [Accepted: 07/13/2013] [Indexed: 12/25/2022] Open
Affiliation(s)
- Dorothea Schulte
- Institute of Neurology (Edinger Institute); University Hospital Frankfurt, J.W. Goethe University; Frankfurt Germany
| | - Dale Frank
- Department of Biochemistry; The Rappaport Family Institute for Research in the Medical Sciences, Faculty of Medicine, Technion-Israel Institute of Technology; Haifa Israel
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