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Castillo H, Hanna P, Sachs LM, Buisine N, Godoy F, Gilbert C, Aguilera F, Muñoz D, Boisvert C, Debiais-Thibaud M, Wan J, Spicuglia S, Marcellini S. Xenopus tropicalis osteoblast-specific open chromatin regions reveal promoters and enhancers involved in human skeletal phenotypes and shed light on early vertebrate evolution. Cells Dev 2024:203924. [PMID: 38692409 DOI: 10.1016/j.cdev.2024.203924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 04/18/2024] [Accepted: 04/26/2024] [Indexed: 05/03/2024]
Abstract
While understanding the genetic underpinnings of osteogenesis has far-reaching implications for skeletal diseases and evolution, a comprehensive characterization of the osteoblastic regulatory landscape in non-mammalian vertebrates is still lacking. Here, we compared the ATAC-Seq profile of Xenopus tropicalis (Xt) osteoblasts to a variety of non mineralizing control tissues, and identified osteoblast-specific nucleosome free regions (NFRs) at 527 promoters and 6747 distal regions. Sequence analyses, Gene Ontology, RNA-Seq and ChIP-Seq against four key histone marks confirmed that the distal regions correspond to bona fide osteogenic transcriptional enhancers exhibiting a shared regulatory logic with mammals. We report 425 regulatory regions conserved with human and globally associated to skeletogenic genes. Of these, 35 regions have been shown to impact human skeletal phenotypes by GWAS, including one trps1 enhancer and the runx2 promoter, two genes which are respectively involved in trichorhinophalangeal syndrome type I and cleidocranial dysplasia. Intriguingly, 60 osteoblastic NFRs also align to the genome of the elephant shark, a species lacking osteoblasts and bone tissue. To tackle this paradox, we chose to focus on dlx5 because its conserved promoter, known to integrate regulatory inputs during mammalian osteogenesis, harbours an osteoblast-specific NFR in both frog and human. Hence, we show that dlx5 is expressed in Xt and elephant shark odontoblasts, supporting a common cellular and genetic origin of bone and dentine. Taken together, our work (i) unravels the Xt osteogenic regulatory landscape, (ii) illustrates how cross-species comparisons harvest data relevant to human biology and (iii) reveals that a set of genes including bnc2, dlx5, ebf3, mir199a, nfia, runx2 and zfhx4 drove the development of a primitive form of mineralized skeletal tissue deep in the vertebrate lineage.
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Affiliation(s)
- Héctor Castillo
- Group for the Study of Developmental Processes (GDeP), School of Biological Sciences, University of Concepción, Chile.
| | - Patricia Hanna
- Group for the Study of Developmental Processes (GDeP), School of Biological Sciences, University of Concepción, Chile
| | - Laurent M Sachs
- UMR7221, Physiologie Moléculaire et Adaptation, CNRS, MNHN, Paris Cedex 05, France
| | - Nicolas Buisine
- UMR7221, Physiologie Moléculaire et Adaptation, CNRS, MNHN, Paris Cedex 05, France
| | - Francisco Godoy
- Group for the Study of Developmental Processes (GDeP), School of Biological Sciences, University of Concepción, Chile
| | - Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 12 route 128, 91190 Gif-sur-Yvette, France
| | - Felipe Aguilera
- Group for the Study of Developmental Processes (GDeP), School of Biological Sciences, University of Concepción, Chile
| | - David Muñoz
- Group for the Study of Developmental Processes (GDeP), School of Biological Sciences, University of Concepción, Chile
| | - Catherine Boisvert
- School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Mélanie Debiais-Thibaud
- Institut des Sciences de l'Evolution de Montpellier, ISEM, Univ Montpellier, CNRS, IRD, Montpellier, France
| | - Jing Wan
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France; Equipe Labelisée LIGUE contre le Cancer, Marseille, France
| | - Salvatore Spicuglia
- Aix-Marseille University, INSERM, TAGC, UMR 1090, Marseille, France; Equipe Labelisée LIGUE contre le Cancer, Marseille, France
| | - Sylvain Marcellini
- Group for the Study of Developmental Processes (GDeP), School of Biological Sciences, University of Concepción, Chile.
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Malik MQ, Bertke MM, Huber PW. Small ubiquitin-like modifier (SUMO)-mediated repression of the Xenopus Oocyte 5 S rRNA genes. J Biol Chem 2014; 289:35468-81. [PMID: 25368327 DOI: 10.1074/jbc.m114.609123] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The 5 S rRNA gene-specific transcription factor IIIA (TFIIIA) interacts with the small ubiquitin-like modifier (SUMO) E3 ligase PIAS2b and with one of its targets, the transcriptional corepressor, XCtBP. PIAS2b is restricted to the cytoplasm of Xenopus oocytes but relocates to the nucleus immediately after fertilization. Following the midblastula transition, PIAS2b and XCtBP are present on oocyte-type, but not somatic-type, 5 S rRNA genes up through the neurula stage, as is a limiting amount of TFIIIA. Histone H3 methylation, coincident with the binding of XCtBP, also occurs exclusively on the oocyte-type genes. Immunohistochemical staining of embryos confirms the occupancy of a subset of the oocyte-type genes by TFIIIA that become positioned at the nuclear periphery shortly after the midblastula transition. Inhibition of SUMOylation activity relieves repression of oocyte-type 5 S rRNA genes and is correlated with a decrease in methylation of H3K9 and H3K27 and disruption of subnuclear localization. These results reveal a novel function for TFIIIA as a negative regulator that recruits histone modification activity through the CtBP repressor complex exclusively to the oocyte-type 5 S rRNA genes, leading to their terminal repression.
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Affiliation(s)
- Mariam Q Malik
- From the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Michelle M Bertke
- From the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
| | - Paul W Huber
- From the Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556
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Bellavia D, Dimarco E, Naselli F, Caradonna F. DNA-methylation dependent regulation of embryo-specific 5S ribosomal DNA cluster transcription in adult tissues of sea urchin Paracentrotus lividus. Genomics 2013; 102:397-402. [PMID: 23933480 DOI: 10.1016/j.ygeno.2013.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Revised: 07/25/2013] [Accepted: 08/01/2013] [Indexed: 11/26/2022]
Abstract
We have previously reported a molecular and cytogenetic characterization of three different 5S rDNA clusters in the sea urchin Paracentrotus lividus and recently, demonstrated the presence of high heterogeneity in functional 5S rRNA. In this paper, we show some important distinctive data on 5S rRNA transcription for this organism. Using single strand conformation polymorphism (SSCP) analysis, we demonstrate the existence of two classes of 5S rRNA, one which is embryo-specific and encoded by the smallest (700 bp) cluster and the other which is expressed at every stage and encoded by longer clusters (900 and 950 bp). We also demonstrate that the embryo-specific class of 5S rRNA is expressed in oocytes and embryonic stages and is silenced in adult tissue and that this phenomenon appears to be due exclusively to DNA methylation, as indicated by sensitivity to 5-azacytidine, unlike Xenopus where this mechanism is necessary but not sufficient to maintain the silenced status.
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Affiliation(s)
- Daniele Bellavia
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Sezione di Biologia Cellulare, Ed. 16, Università degli Studi di Palermo, V.le delle Scienze, 90128 Palermo, Italy; Istituto Ortopedico Rizzoli, c/o Dipartimento di Biopatologia e Biotecnologie Mediche e Forensi (DIBIMEF), Università degli Studi di Palermo, Via Divisi 81, 90133 Palermo, Italy.
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Dimarco E, Cascone E, Bellavia D, Caradonna F. Functional variants of 5S rRNA in the ribosomes of common sea urchin Paracentrotus lividus. Gene 2012; 508:21-5. [PMID: 22967708 DOI: 10.1016/j.gene.2012.07.067] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 07/30/2012] [Indexed: 11/28/2022]
Abstract
We have previously reported a molecular and cytogenetic characterization of three different 5S rDNA clusters in the sea urchin Paracentrotus lividus; this study, performed at DNA level only, lends itself as starting point to verify that these clusters could contain transcribed genes, then, to demonstrate the presence of heterogeneity at functional RNA level, also. In the present work we report in P. lividus ribosomes the existence of several transcribed variants of the 5S rRNA and we associate all transcribed variants to the cluster to which belong. Our finding is the first demonstration of the presence of high heterogeneity in functional 5S rRNA molecules in animal ribosomes, a feature that had been considered a peculiarity of some plants.
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Affiliation(s)
- Eufrosina Dimarco
- Dipartimento di Scienze e Tecnologie Molecolari e Biomolecolari (STEMBIO), Sezione di Biologia Cellulare, Università degli Studi di Palermo, V.le delle Scienze—90128 Palermo, Italy
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Taghli-Lamallem O, Hsia C, Ronshaugen M, McGinnis W. Context-dependent regulation of Hox protein functions by CK2 phosphorylation sites. Dev Genes Evol 2008; 218:321-32. [PMID: 18504607 PMCID: PMC2443945 DOI: 10.1007/s00427-008-0224-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Accepted: 04/21/2008] [Indexed: 10/22/2022]
Abstract
Variations in Hox protein sequences and functions have been proposed to contribute to evolutionary changes in appendage shape and number in crustaceans and insects. One model is that insect Hox proteins of the Ultrabithorax (UBX) ortholog class evolved increased abilities to repress Distal-less (Dll) transcription and appendage development in part through the loss of serine and threonine residues in casein kinase 2 (CK2) phosphorylation sites. To explore this possibility, we constructed and tested the appendage repression function of chimeric proteins with insertions of different CK2 consensus sites or phosphomimetics of CK2 sites in C-terminal regions of Drosophila melanogaster UBX. Our results indicate that CK2 sites C-terminal to the homeodomain can inhibit the appendage repression functions of UBX proteins, but only in the context of specific amino acid sequences. Our results, combined with previous findings on evolutionary changes in Hox protein, suggest how intra-protein regulatory changes can diversify Hox protein function, and thus animal morphology.
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Affiliation(s)
- Ouarda Taghli-Lamallem
- Neuroscience & Aging Research Center, The Burnham Institute for Medical Research, 10901 North Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Cheryl Hsia
- Section in Cell and Developmental Biology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA, e-mail:
| | - Matthew Ronshaugen
- The Healing Foundation Centre, Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - William McGinnis
- Section in Cell and Developmental Biology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA, e-mail:
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