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Johnson HK, Wahl SE, Sesay F, Litovchick L, Dickinson AJ. Dyrk1a is required for craniofacial development in Xenopus laevis. Dev Biol 2024; 511:63-75. [PMID: 38621649 DOI: 10.1016/j.ydbio.2024.04.004] [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: 12/16/2023] [Revised: 03/29/2024] [Accepted: 04/11/2024] [Indexed: 04/17/2024]
Abstract
Loss of function variations in the dual specificity tyrosine-phosphorylation-regulated kinase 1 A (DYRK1A) gene are associated with craniofacial malformations in humans. Here we characterized the effects of deficient DYRK1A in craniofacial development using a developmental model, Xenopus laevis. Dyrk1a mRNA and protein were expressed throughout the developing head and both were enriched in the branchial arches which contribute to the face and jaw. Consistently, reduced Dyrk1a function, using dyrk1a morpholinos and pharmacological inhibitors, resulted in orofacial malformations including hypotelorism, altered mouth shape, slanted eyes, and narrower face accompanied by smaller jaw cartilage and muscle. Inhibition of Dyrk1a function resulted in misexpression of key craniofacial regulators including transcription factors and members of the retinoic acid signaling pathway. Two such regulators, sox9 and pax3 are required for neural crest development and their decreased expression corresponds with smaller neural crest domains within the branchial arches. Finally, we determined that the smaller size of the faces, jaw elements and neural crest domains in embryos deficient in Dyrk1a could be explained by increased cell death and decreased proliferation. This study is the first to provide insight into why craniofacial birth defects might arise in humans with variants of DYRK1A.
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Affiliation(s)
| | - Stacey E Wahl
- Department of Biology, Virginia Commonwealth University, Richmond, VA, USA
| | - Fatmata Sesay
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University, Richmond, VA, USA
| | - Larisa Litovchick
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, Virginia Commonwealth University, Richmond, VA, USA; Massey Comprehensive Cancer Center, Richmond, VA, USA
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2
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Johnson HK, Wahl SE, Sesay F, Litovchick L, Dickinson AJ. Dyrk1a is required for craniofacial development in Xenopus laevis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.13.575394. [PMID: 38260562 PMCID: PMC10802584 DOI: 10.1101/2024.01.13.575394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Loss of function mutations in the dual specificity tyrosine-phosphorylation-regulated kinase 1A (DYRK1A) gene are associated with craniofacial malformations in humans. Here we characterized the effects of deficient DYRK1A in craniofacial development using a developmental model, Xenopus laevis . Dyrk1a mRNA and protein was expressed throughout the developing head and was enriched in the branchial arches which contribute to the face and jaw. Consistently, reduced Dyrk1a function, using dyrk1a morpholinos and pharmacological inhibitors, resulted in orofacial malformations including hypotelorism, altered mouth shape, slanted eyes, and narrower face accompanied by smaller jaw cartilage and muscle. Inhibition of Dyrk1a function resulted in misexpression of key craniofacial regulators including transcription factors and members of the retinoic acid signaling pathway. Two such regulators, sox9 and pax3 are required for neural crest development and their decreased expression corresponds with smaller neural crest domains within the branchial arches. Finally, we determined that the smaller size of the faces, jaw elements and neural crest domains in embryos deficient in Dyrk1a could be explained by increased cell death and decreased proliferation. This study is the first to provide insight into why craniofacial birth defects might arise in humans with DYRK1A mutations.
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Duperray M, Hardet F, Henriet E, Saint-Marc C, Boué-Grabot E, Daignan-Fornier B, Massé K, Pinson B. Purine Biosynthesis Pathways Are Required for Myogenesis in Xenopus laevis. Cells 2023; 12:2379. [PMID: 37830593 PMCID: PMC10571971 DOI: 10.3390/cells12192379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 09/20/2023] [Accepted: 09/25/2023] [Indexed: 10/14/2023] Open
Abstract
Purines are required for fundamental biological processes and alterations in their metabolism lead to severe genetic diseases associated with developmental defects whose etiology remains unclear. Here, we studied the developmental requirements for purine metabolism using the amphibian Xenopus laevis as a vertebrate model. We provide the first functional characterization of purine pathway genes and show that these genes are mainly expressed in nervous and muscular embryonic tissues. Morphants were generated to decipher the functions of these genes, with a focus on the adenylosuccinate lyase (ADSL), which is an enzyme required for both salvage and de novo purine pathways. adsl.L knockdown led to a severe reduction in the expression of the myogenic regulatory factors (MRFs: Myod1, Myf5 and Myogenin), thus resulting in defects in somite formation and, at later stages, the development and/or migration of both craniofacial and hypaxial muscle progenitors. The reduced expressions of hprt1.L and ppat, which are two genes specific to the salvage and de novo pathways, respectively, resulted in similar alterations. In conclusion, our data show for the first time that de novo and recycling purine pathways are essential for myogenesis and highlight new mechanisms in the regulation of MRF gene expression.
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Affiliation(s)
- Maëlle Duperray
- Institut de Biochimie et Génétique Cellulaires, CNRS, UMR 5095, Université de Bordeaux, F-33000 Bordeaux, France
| | - Fanny Hardet
- CNRS, IMN, UMR 5293, Université de Bordeaux, F-33000 Bordeaux, France
| | - Elodie Henriet
- CNRS, IMN, UMR 5293, Université de Bordeaux, F-33000 Bordeaux, France
| | - Christelle Saint-Marc
- Institut de Biochimie et Génétique Cellulaires, CNRS, UMR 5095, Université de Bordeaux, F-33000 Bordeaux, France
| | - Eric Boué-Grabot
- CNRS, IMN, UMR 5293, Université de Bordeaux, F-33000 Bordeaux, France
| | - Bertrand Daignan-Fornier
- Institut de Biochimie et Génétique Cellulaires, CNRS, UMR 5095, Université de Bordeaux, F-33000 Bordeaux, France
| | - Karine Massé
- CNRS, IMN, UMR 5293, Université de Bordeaux, F-33000 Bordeaux, France
| | - Benoît Pinson
- Institut de Biochimie et Génétique Cellulaires, CNRS, UMR 5095, Université de Bordeaux, F-33000 Bordeaux, France
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Parast SM, Yu D, Chen C, Dickinson AJ, Chang C, Wang H. Recognition of H2AK119ub plays an important role in RSF1-regulated early Xenopus development. Front Cell Dev Biol 2023; 11:1168643. [PMID: 37529237 PMCID: PMC10389277 DOI: 10.3389/fcell.2023.1168643] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 07/07/2023] [Indexed: 08/03/2023] Open
Abstract
Polycomb group (PcG) proteins are key regulators of gene expression and developmental programs via covalent modification of histones, but the factors that interpret histone modification marks to regulate embryogenesis are less studied. We previously identified Remodeling and Spacing Factor 1 (RSF1) as a reader of histone H2A lysine 119 ubiquitination (H2AK119ub), the histone mark deposited by Polycomb Repressive Complex 1 (PRC1). In the current study, we used Xenopus laevis as a model to investigate how RSF1 affects early embryonic development and whether recognition of H2AK119ub is important for the function of RSF1. We showed that knockdown of Xenopus RSF1, rsf1, not only induced gastrulation defects as reported previously, but specific targeted knockdown in prospective neural precursors induced neural and neural crest defects, with reductions of marker genes. In addition, similar to knockdown of PRC1 components in Xenopus, the anterior-posterior neural patterning was affected in rsf1 knockdown embryos. Binding of H2AK119ub appeared to be crucial for rsf1 function, as a construct with deletion of the UAB domain, which is required for RSF1 to recognize the H2AK119ub nucleosomes, failed to rescue rsf1 morphant embryos and was less effective in interfering with early Xenopus development when ectopically expressed. Furthermore, ectopic deposition of H2AK119ub on the Smad2 target gene gsc using a ring1a-smad2 fusion protein led to ectopic recruitment of RSF1. The fusion protein was inefficient in inducing mesodermal markers in the animal region or a secondary axis when expressed in the ventral tissues. Taken together, our results reveal that rsf1 modulates similar developmental processes in early Xenopus embryos as components of PRC1 do, and that RSF1 acts at least partially through binding to the H2AK119ub mark via the UAB domain during development.
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Affiliation(s)
- Saeid Mohammad Parast
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Deli Yu
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Chunxu Chen
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- Department of Biomedical Engineering, School of Engineering, Virginia Commonwealth University, Richmond, VA, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
| | - Amanda J. Dickinson
- Department of Biology, College of Humanities and Sciences, Virginia Commonwealth University, Richmond, VA, United States
| | - Chenbei Chang
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, Birmingham, AL, United States
| | - Hengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL, United States
- Massey Cancer Center, Virginia Commonwealth University, Richmond, VA, United States
- Department of Internal Medicine, Division of Hematology, Oncology and Palliative Care, School of Medicine, Virginia Commonwealth University, Richmond, VA, United States
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Brunner N, Stein L, Amasheh S. Cellular Distribution Pattern of tjp1 (ZO-1) in Xenopus laevis Oocytes Heterologously Expressing Claudins. J Membr Biol 2023; 256:51-61. [PMID: 35737002 PMCID: PMC9884258 DOI: 10.1007/s00232-022-00251-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/02/2022] [Indexed: 02/07/2023]
Abstract
Epithelial barriers constitute a fundamental requirement in every organism, as they allow the separation of different environments and set boundaries against noxious and other adverse effectors. In many inflammatory and degenerative diseases, epithelial barrier function is impaired because of a disturbance of the paracellular seal. Recently, the Xenopus laevis oocyte has been established as a heterologous expression model for the analysis of transmembrane tight junction protein interactions and is currently considered to be a suitable screening model for barrier effectors. A prerequisite for this application is a physiological anchoring of claudins to the cytoskeleton via the major scaffolding protein tjp1 (tight junction protein 1, ZO-1). We have analyzed the oocyte model with regard to the interaction of heterologously expressed claudins and tjp1. Our experiments have revealed endogenous tjp1 expression in protein and mRNA analyses of unfertilized Xenopus laevis oocytes expressing human claudin 1 (CLDN1) to claudin 5 (CLDN5). The amphibian cell model can therefore be used for the analysis of claudin interactions.
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Affiliation(s)
- Nora Brunner
- Institute of Veterinary Physiology, Freie Universität Berlin, Oertzenweg 19b, 14163 Berlin, Germany
| | - Laura Stein
- Institute of Veterinary Physiology, Freie Universität Berlin, Oertzenweg 19b, 14163 Berlin, Germany
| | - Salah Amasheh
- Institute of Veterinary Physiology, Freie Universität Berlin, Oertzenweg 19b, 14163 Berlin, Germany
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Hudson DT, Bromell JS, Day RC, McInnes T, Ward JM, Beck CW. Gene expression analysis of the Xenopus laevis early limb bud proximodistal axis. Dev Dyn 2022; 251:1880-1896. [PMID: 35809036 PMCID: PMC9796579 DOI: 10.1002/dvdy.517] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/30/2022] [Accepted: 07/06/2022] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Limb buds develop as bilateral outgrowths of the lateral plate mesoderm and are patterned along three axes. Current models of proximal to distal patterning of early amniote limb buds suggest that two signals, a distal organizing signal from the apical epithelial ridge (AER, Fgfs) and an opposing proximal (retinoic acid [RA]) act early on pattern this axis. RESULTS Transcriptional analysis of stage 51 Xenopus laevis hindlimb buds sectioned along the proximal-distal axis showed that the distal region is distinct from the rest of the limb. Expression of capn8.3, a novel calpain, was located in cells immediately flanking the AER. The Wnt antagonist Dkk1 was AER-specific in Xenopus limbs. Two transcription factors, sall1 and zic5, were expressed in distal mesenchyme. Zic5 has no described association with limb development. We also describe expression of two proximal genes, gata5 and tnn, not previously associated with limb development. Differentially expressed genes were associated with Fgf, Wnt, and RA signaling as well as differential cell adhesion and proliferation. CONCLUSIONS We identify new candidate genes for early proximodistal limb patterning. Our analysis of RA-regulated genes supports a role for transient RA gradients in early limb bud in proximal-to-distal patterning in this anamniote model organism.
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Affiliation(s)
- Daniel T. Hudson
- Department of ZoologyUniversity of OtagoDunedinNew Zealand,Oritain GlobalDunedinNew Zealand
| | - Jessica S. Bromell
- Department of ZoologyUniversity of OtagoDunedinNew Zealand,Dairy Goat Co‐operativeHamiltonNew Zealand
| | - Robert C. Day
- Department of BiochemistryUniversity of OtagoDunedinNew Zealand
| | - Tyler McInnes
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
| | - Joanna M. Ward
- Department of ZoologyUniversity of OtagoDunedinNew Zealand
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Abstract
The function of many biological systems, such as embryos, liver lobules, intestinal villi, and tumors, depends on the spatial organization of their cells. In the past decade, high-throughput technologies have been developed to quantify gene expression in space, and computational methods have been developed that leverage spatial gene expression data to identify genes with spatial patterns and to delineate neighborhoods within tissues. To comprehensively document spatial gene expression technologies and data-analysis methods, we present a curated review of literature on spatial transcriptomics dating back to 1987, along with a thorough analysis of trends in the field, such as usage of experimental techniques, species, tissues studied, and computational approaches used. Our Review places current methods in a historical context, and we derive insights about the field that can guide current research strategies. A companion supplement offers a more detailed look at the technologies and methods analyzed: https://pachterlab.github.io/LP_2021/ .
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Niziolek M, Bicka M, Osinka A, Samsel Z, Sekretarska J, Poprzeczko M, Bazan R, Fabczak H, Joachimiak E, Wloga D. PCD Genes-From Patients to Model Organisms and Back to Humans. Int J Mol Sci 2022; 23:ijms23031749. [PMID: 35163666 PMCID: PMC8836003 DOI: 10.3390/ijms23031749] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 01/27/2023] Open
Abstract
Primary ciliary dyskinesia (PCD) is a hereditary genetic disorder caused by the lack of motile cilia or the assembxly of dysfunctional ones. This rare human disease affects 1 out of 10,000-20,000 individuals and is caused by mutations in at least 50 genes. The past twenty years brought significant progress in the identification of PCD-causative genes and in our understanding of the connections between causative mutations and ciliary defects observed in affected individuals. These scientific advances have been achieved, among others, due to the extensive motile cilia-related research conducted using several model organisms, ranging from protists to mammals. These are unicellular organisms such as the green alga Chlamydomonas, the parasitic protist Trypanosoma, and free-living ciliates, Tetrahymena and Paramecium, the invertebrate Schmidtea, and vertebrates such as zebrafish, Xenopus, and mouse. Establishing such evolutionarily distant experimental models with different levels of cell or body complexity was possible because both basic motile cilia ultrastructure and protein composition are highly conserved throughout evolution. Here, we characterize model organisms commonly used to study PCD-related genes, highlight their pros and cons, and summarize experimental data collected using these models.
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Affiliation(s)
- Michal Niziolek
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Marta Bicka
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
- Faculty of Chemistry, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland
| | - Anna Osinka
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Zuzanna Samsel
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Justyna Sekretarska
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Martyna Poprzeczko
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
- Laboratory of Immunology, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawinskiego Street, 02-106 Warsaw, Poland
| | - Rafal Bazan
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Hanna Fabczak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
| | - Ewa Joachimiak
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
- Correspondence: (E.J.); (D.W.); Tel.: +48-22-58-92-338 (E.J. & D.W.)
| | - Dorota Wloga
- Laboratory of Cytoskeleton and Cilia Biology, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 3 Pasteur Street, 02-093 Warsaw, Poland; (M.N.); (M.B.); (A.O.); (Z.S.); (J.S.); (M.P.); (R.B.); (H.F.)
- Correspondence: (E.J.); (D.W.); Tel.: +48-22-58-92-338 (E.J. & D.W.)
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Reverdatto S, Prasad A, Belrose JL, Zhang X, Sammons MA, Gibbs KM, Szaro BG. Developmental and Injury-induced Changes in DNA Methylation in Regenerative versus Non-regenerative Regions of the Vertebrate Central Nervous System. BMC Genomics 2022; 23:2. [PMID: 34979916 PMCID: PMC8725369 DOI: 10.1186/s12864-021-08247-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 12/09/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Because some of its CNS neurons (e.g., retinal ganglion cells after optic nerve crush (ONC)) regenerate axons throughout life, whereas others (e.g., hindbrain neurons after spinal cord injury (SCI)) lose this capacity as tadpoles metamorphose into frogs, the South African claw-toed frog, Xenopus laevis, offers unique opportunities for exploring differences between regenerative and non-regenerative responses to CNS injury within the same organism. An earlier, three-way RNA-seq study (frog ONC eye, tadpole SCI hindbrain, frog SCI hindbrain) identified genes that regulate chromatin accessibility among those that were differentially expressed in regenerative vs non-regenerative CNS [11]. The current study used whole genome bisulfite sequencing (WGBS) of DNA collected from these same animals at the peak period of axon regeneration to study the extent to which DNA methylation could potentially underlie differences in chromatin accessibility between regenerative and non-regenerative CNS. RESULTS Consistent with the hypothesis that DNA of regenerative CNS is more accessible than that of non-regenerative CNS, DNA from both the regenerative tadpole hindbrain and frog eye was less methylated than that of the non-regenerative frog hindbrain. Also, consistent with observations of CNS injury in mammals, DNA methylation in non-regenerative frog hindbrain decreased after SCI. However, contrary to expectations that the level of DNA methylation would decrease even further with axotomy in regenerative CNS, DNA methylation in these regions instead increased with injury. Injury-induced differences in CpG methylation in regenerative CNS became especially enriched in gene promoter regions, whereas non-CpG methylation differences were more evenly distributed across promoter regions, intergenic, and intragenic regions. In non-regenerative CNS, tissue-related (i.e., regenerative vs. non-regenerative CNS) and injury-induced decreases in promoter region CpG methylation were significantly correlated with increased RNA expression, but the injury-induced, increased CpG methylation seen in regenerative CNS across promoter regions was not, suggesting it was associated with increased rather than decreased chromatin accessibility. This hypothesis received support from observations that in regenerative CNS, many genes exhibiting increased, injury-induced, promoter-associated CpG-methylation also exhibited increased RNA expression and association with histone markers for active promoters and enhancers. DNA immunoprecipitation for 5hmC in optic nerve regeneration found that the promoter-associated increases seen in CpG methylation were distinct from those exhibiting changes in 5hmC. CONCLUSIONS Although seemingly paradoxical, the increased injury-associated DNA methylation seen in regenerative CNS has many parallels in stem cells and cancer. Thus, these axotomy-induced changes in DNA methylation in regenerative CNS provide evidence for a novel epigenetic state favoring successful over unsuccessful CNS axon regeneration. The datasets described in this study should help lay the foundations for future studies of the molecular and cellular mechanisms involved. The insights gained should, in turn, help point the way to novel therapeutic approaches for treating CNS injury in mammals.
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Affiliation(s)
- Sergei Reverdatto
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY, 12222, USA
- RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Aparna Prasad
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY, 12222, USA
- RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Jamie L Belrose
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Xiang Zhang
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Morgan A Sammons
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA
- RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA
| | - Kurt M Gibbs
- Department of Biology & Chemistry, Morehead State University, Morehead, KY, 40351, USA
| | - Ben G Szaro
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, 12222, USA.
- Center for Neuroscience Research, University at Albany, State University of New York, Albany, NY, 12222, USA.
- RNA Institute, University at Albany, State University of New York, Albany, NY, 12222, USA.
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10
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Analysis of the early response to spinal cord injury identified a key role for mTORC1 signaling in the activation of neural stem progenitor cells. NPJ Regen Med 2021; 6:68. [PMID: 34686684 PMCID: PMC8536777 DOI: 10.1038/s41536-021-00179-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 09/30/2021] [Indexed: 02/07/2023] Open
Abstract
Xenopus laevis are able to regenerate the spinal cord during larvae stages through the activation of neural stem progenitor cells (NSPCs). Here we use high-resolution expression profiling to characterize the early transcriptome changes induced after spinal cord injury, aiming to identify the signals that trigger NSPC proliferation. The analysis delineates a pathway that starts with a rapid and transitory activation of immediate early genes, followed by migration processes and immune response genes, the pervasive increase of NSPC-specific ribosome biogenesis factors, and genes involved in stem cell proliferation. Western blot and immunofluorescence analysis showed that mTORC1 is rapidly and transiently activated after SCI, and its pharmacological inhibition impairs spinal cord regeneration and proliferation of NSPC through the downregulation of genes involved in the G1/S transition of cell cycle, with a strong effect on PCNA. We propose that the mTOR signaling pathway is a key player in the activation of NPSCs during the early steps of spinal cord regeneration.
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11
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Wyatt BH, Raymond TO, Lansdon LA, Darbro BW, Murray JC, Manak JR, Dickinson AJG. Using an aquatic model, Xenopus laevis, to uncover the role of chromodomain 1 in craniofacial disorders. Genesis 2021; 59:e23394. [PMID: 32918369 PMCID: PMC10701884 DOI: 10.1002/dvg.23394] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 08/04/2020] [Accepted: 08/08/2020] [Indexed: 12/14/2022]
Abstract
The chromodomain family member chromodomain 1 (CHD1) has been shown to have numerous critical molecular functions including transcriptional regulation, splicing, and DNA repair. Complete loss of function of this gene is not compatible with life. On the other hand, missense and copy number variants of CHD1 can result in intellectual disabilities and craniofacial malformations in human patients including cleft palate and Pilarowski-Bjornsson Syndrome. We have used the aquatic developmental model organism Xenopus laevis, to determine a specific role for Chd1 in such cranioafcial disorders. Protein and gene knockdown techniques in Xenopus, including antisense oligos and mosaic Crispr/Cas9-mediated mutagenesis, recapitulated the craniofacial defects observed in humans. Further analysis indicated that embryos deficient in Chd1 had defects in cranial neural crest development and jaw cartilage morphology. Additionally, flow cytometry and immunohistochemistry revealed that decreased Chd1 resulted in increased in apoptosis in the developing head. Together, these experiments demonstrate that Chd1 is critical for fundamental processes and cell survival in craniofacial development. We also presented evidence that Chd1 is regulated by retinoic acid signaling during craniofacial development. Expression levels of chd1 mRNA, specifically in the head, were increased by RAR agonist exposure and decreased upon antagonist treatment. Subphenotypic levels of an RAR antagonist and Chd1 morpholinos synergized to result in orofacial defects. Further, RAR DNA binding sequences (RAREs) were detected in chd1 regulatory regions by bioinformatic analysis. In summary, by combining human genetics and experiments in an aquatic model we now have a better understanding of the role of CHD1 in craniofacial disorders.
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Affiliation(s)
- Brent H. Wyatt
- Department of Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Thomas O. Raymond
- Department of Biology, Virginia Commonwealth University, Richmond, Virginia
| | - Lisa A. Lansdon
- Department of Biology, University of Iowa, Iowa City, Iowa
- Department of Pathology and Laboratory Medicine, Children’s Mercy Hospital, Kansas City, Missouri
| | | | | | - John Robert Manak
- Department of Biology, University of Iowa, Iowa City, Iowa
- Department of Pediatrics, University of Iowa, Iowa City, Iowa
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12
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Chowanadisai W, Hart MD, Strong MD, Graham DM, Rucker RB, Smith BJ, Keen CL, Messerli MA. Genetic and Genomic Advances in Developmental Models: Applications for Nutrition Research. Adv Nutr 2020; 11:971-978. [PMID: 32135011 PMCID: PMC7360451 DOI: 10.1093/advances/nmaa022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 10/22/2019] [Accepted: 02/13/2020] [Indexed: 12/11/2022] Open
Abstract
There is increasing appreciation that dietary components influence and interact with genes important to metabolism. How such influences impact developmental regulation and programming or risks of chronic diseases remains unclear. Nutrition is recognized to affect development and chronic diseases, but our understanding about how genes essential to nutrient metabolism regulate development and impact risks of these diseases remains unclear. Historically, mammalian models, especially rodents such as rats and mice, have been the primary models used for nutrition and developmental nutrition science, although their complexity and relatively slow rate of development often compromise rapid progress in resolving fundamental, genetic-related questions. Accordingly, the objective of this review is to highlight the opportunities for developmental models in the context of uncovering the function of gene products that are relevant to human nutrition and provide the scientific bases for these opportunities. We present recent studies in zebrafish related to obesity as applications of developmental models in nutritional science. Although the control of external factors and dependent variables, such as nutrition, can be a challenge, suggestions for standardizations related to diet are made to improve consistency in findings between laboratories. The review also highlights the need for standardized diets across different developmental models, which could improve consistency in findings across laboratories. Alternative and developmental animal models have advantages and largely untapped potential for the advancement of nutrigenomics and nutritionally relevant research areas.
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Affiliation(s)
- Winyoo Chowanadisai
- Department of Nutritional Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Matthew D Hart
- Department of Nutritional Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Morgan D Strong
- Department of Nutritional Sciences, Oklahoma State University, Stillwater, OK, USA
| | - David M Graham
- Department of Biology, University of North Carolina, Chapel Hill, Chapel Hill, NC, USA
| | - Robert B Rucker
- Department of Nutrition, University of California, Davis, Davis, CA, USA
| | - Brenda J Smith
- Department of Nutritional Sciences, Oklahoma State University, Stillwater, OK, USA
| | - Carl L Keen
- Department of Nutrition, University of California, Davis, Davis, CA, USA
| | - Mark A Messerli
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
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13
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Mackrill JJ, Shiels HA. Evolution of Excitation-Contraction Coupling. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1131:281-320. [DOI: 10.1007/978-3-030-12457-1_12] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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14
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Karimi K, Fortriede JD, Lotay VS, Burns KA, Wang DZ, Fisher ME, Pells TJ, James-Zorn C, Wang Y, Ponferrada VG, Chu S, Chaturvedi P, Zorn AM, Vize PD. Xenbase: a genomic, epigenomic and transcriptomic model organism database. Nucleic Acids Res 2019; 46:D861-D868. [PMID: 29059324 PMCID: PMC5753396 DOI: 10.1093/nar/gkx936] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 10/02/2017] [Indexed: 01/03/2023] Open
Abstract
Xenbase (www.xenbase.org) is an online resource for researchers utilizing Xenopus laevis and Xenopus tropicalis, and for biomedical scientists seeking access to data generated with these model systems. Content is aggregated from a variety of external resources and also generated by in-house curation of scientific literature and bioinformatic analyses. Over the past two years many new types of content have been added along with new tools and functionalities to reflect the impact of high-throughput sequencing. These include new genomes for both supported species (each with chromosome scale assemblies), new genome annotations, genome segmentation, dynamic and interactive visualization for RNA-Seq data, updated ChIP-Seq mapping, GO terms, protein interaction data, ORFeome support, and improved connectivity to other biomedical and bioinformatic resources.
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Affiliation(s)
- Kamran Karimi
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
| | - Joshua D Fortriede
- Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Vaneet S Lotay
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
| | - Kevin A Burns
- Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Dong Zhou Wang
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
| | - Malcom E Fisher
- Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Troy J Pells
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
| | - Christina James-Zorn
- Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Ying Wang
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
| | - V G Ponferrada
- Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Stanley Chu
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
| | - Praneet Chaturvedi
- Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Aaron M Zorn
- Cincinnati Children's Hospital, Division of Developmental Biology, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Peter D Vize
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alberta T2N1N4, Canada
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15
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Zhu S, Wu X, Fu H, Ye C, Chen M, Jiang Z, Ji G. Modeling of Genome-Wide Polyadenylation Signals in Xenopus tropicalis. Front Genet 2019; 10:647. [PMID: 31333724 PMCID: PMC6616101 DOI: 10.3389/fgene.2019.00647] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 06/18/2019] [Indexed: 12/22/2022] Open
Abstract
Alternative polyadenylation (APA) is an important post-transcriptional modification event to process messenger RNA (mRNA) for transcriptional termination, transport, and translation. In the present study, we characterized poly(A) signals in Xenopus tropicalis using 70,918 highly confident poly(A) sites derived from 16,511 protein-coding genes to understand their roles in the regulation of embryo development and gender difference. We examined potential factors, including the gene length, the number of introns in a gene, and the intron length, that may affect the prevalence of APA. We observed 12 prominent poly(A) signal patterns, which accounted for approximately 92% of total APA sites in Xenopus tropicalis. Among them, three patterns are specific to X. tropicalis, so they are absent in other animals such as humans or mice. We catalogued APA sites based on their genomic regions and developed a bioinformatics pipeline to identify over-represented signal patterns for each class. Then the schema of cis elements for APA sites in each genomic region was proposed. More importantly, APA usage is dramatically dynamic in embryos along five developmental stages and well-coordinated with the maternal-to-zygotic transition event. We used an entropy-based method to identify developmental stage-specific APA sites and identified significant signal patterns around specific sites and constitutive sites. We found that the APA frequency in different genomic regions varies with developmental stages and that those sites located in intron or coding sequence regions contribute most to the dynamics of gene expression during developmental stages. This study deciphers the characteristics and poly(A) signal patterns for both canonical APA sites and non-canonical APA sites across different developmental stages and gender dimorphisms in X. tropicalis, providing new insights into the dynamic regulation of distal and proximal APA.
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Affiliation(s)
- Sheng Zhu
- Department of Automation, Xiamen University, Xiamen, China.,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China
| | - Xiaohui Wu
- Department of Automation, Xiamen University, Xiamen, China.,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, China
| | - Hongjuan Fu
- Department of Automation, Xiamen University, Xiamen, China
| | - Congting Ye
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Moliang Chen
- Department of Automation, Xiamen University, Xiamen, China
| | - Zhihua Jiang
- Department of Animal Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States
| | - Guoli Ji
- Department of Automation, Xiamen University, Xiamen, China.,National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, China.,Innovation Center for Cell Signaling Network, Xiamen University, Xiamen, China
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16
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Abstract
Xenbase is the Xenopus model organism database ( www.xenbase.org ), a web-accessible resource that integrates the diverse genomic and biological data for Xenopus research. It hosts a variety of content including current and archived genomes for both X. laevis and X. tropicalis, bioinformatic tools for comparative genetic analyses including BLAST and GBrowse, annotated Xenopus literature, and catalogs of reagents including antibodies, ORFeome clones, morpholinos, and transgenic lines. Xenbase compiles gene-specific pages which include manually curated gene expression images, functional information including gene ontology (GO), disease associations, and links to other major data sources such as NCBI:Entrez, UniProtKB, and Ensembl. We also maintain the Xenopus Anatomy Ontology (XAO) which describes anatomy throughout embryonic development. This chapter provides a full description of the many features of Xenbase, and offers a guide on how to use various tools to perform a variety of common tasks such as identifying nucleic acid or protein sequences, finding gene expression patterns for specific genes, stages or tissues, identifying literature on a specific gene or tissue, locating useful reagents and downloading our extensive content, including Xenopus gene-Human gene disease mapping files.
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17
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Onjiko RM, Portero EP, Moody SA, Nemes P. Microprobe Capillary Electrophoresis Mass Spectrometry for Single-cell Metabolomics in Live Frog (Xenopus laevis) Embryos. J Vis Exp 2017. [PMID: 29286491 DOI: 10.3791/56956] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The quantification of small molecules in single cells raises new potentials for better understanding the basic processes that underlie embryonic development. To enable single-cell investigations directly in live embryos, new analytical approaches are needed, particularly those that are sensitive, selective, quantitative, robust, and scalable to different cell sizes. Here, we present a protocol that enables the in situ analysis of metabolism in single cells in freely developing embryos of the South African clawed frog (Xenopus laevis), a powerful model in cell and developmental biology. This approach uses a capillary microprobe to aspirate a defined portion from single identified cells in the embryo, leaving neighboring cells intact for subsequent analysis. The collected cell content is analyzed by a microscale capillary electrophoresis electrospray ionization (CE-ESI) interface coupled to a high-resolution tandem mass spectrometer. This approach is scalable to various cell sizes and compatible with the complex three-dimensional structure of the developing embryo. As an example, we demonstrate that microprobe single-cell CE-ESI-MS enables the elucidation of metabolic cell heterogeneity that unfolds as a progenitor cell gives rise to descendants during development of the embryo. Besides cell and developmental biology, the single-cell analysis protocols described here are amenable to other cell sizes, cell types, or animal models.
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Affiliation(s)
| | | | - Sally A Moody
- Department of Anatomy & Regenerative Biology, George Washington University
| | - Peter Nemes
- Department of Chemistry, George Washington University; Department of Chemistry & Biochemistry, University of Maryland, College Park;
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18
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Jullien J, Vodnala M, Pasque V, Oikawa M, Miyamoto K, Allen G, David SA, Brochard V, Wang S, Bradshaw C, Koseki H, Sartorelli V, Beaujean N, Gurdon J. Gene Resistance to Transcriptional Reprogramming following Nuclear Transfer Is Directly Mediated by Multiple Chromatin-Repressive Pathways. Mol Cell 2017; 65:873-884.e8. [PMID: 28257702 PMCID: PMC5344684 DOI: 10.1016/j.molcel.2017.01.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Revised: 01/05/2017] [Accepted: 01/24/2017] [Indexed: 12/22/2022]
Abstract
Understanding the mechanism of resistance of genes to reactivation will help improve the success of nuclear reprogramming. Using mouse embryonic fibroblast nuclei with normal or reduced DNA methylation in combination with chromatin modifiers able to erase H3K9me3, H3K27me3, and H2AK119ub1 from transplanted nuclei, we reveal the basis for resistance of genes to transcriptional reprogramming by oocyte factors. A majority of genes is affected by more than one type of treatment, suggesting that resistance can require repression through multiple epigenetic mechanisms. We classify resistant genes according to their sensitivity to 11 chromatin modifier combinations, revealing the existence of synergistic as well as adverse effects of chromatin modifiers on removal of resistance. We further demonstrate that the chromatin modifier USP21 reduces resistance through its H2AK119 deubiquitylation activity. Finally, we provide evidence that H2A ubiquitylation also contributes to resistance to transcriptional reprogramming in mouse nuclear transfer embryos. Identification of genes resistant to direct transcriptional reprogramming Determination of resistant gene sensitivity to 11 chromatin modifier combinations USP21 removes resistance through its H2AK119 deubiquitylation activity USP21 improves the reprogramming of gene expression in two-cell-stage mouse embryos
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Affiliation(s)
- Jerome Jullien
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK.
| | - Munender Vodnala
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Vincent Pasque
- Department of Development and Regeneration, KU Leuven, University of Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Mami Oikawa
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Kei Miyamoto
- Laboratory of Molecular Developmental Biology, Graduate School of Biology-Oriented Science and Technology, Kinki University, Wakayama 649-6493, Japan
| | - George Allen
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Sarah Anne David
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en Josas, France
| | - Vincent Brochard
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en Josas, France
| | - Stan Wang
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK; Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis, Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - Charles Bradshaw
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
| | - Haruhiko Koseki
- RIKEN Center for Integrative Medical Sciences, Laboratory for Developmental Genetics, North Research Building, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan
| | - Vittorio Sartorelli
- Laboratory of Muscle Stem Cells and Gene Regulation, National Institute of Arthritis, Musculoskeletal and Skin Diseases (NIAMS), NIH, Bethesda, MD 20892, USA
| | - Nathalie Beaujean
- UMR BDR, INRA, ENVA, Université Paris Saclay, 78350 Jouy en Josas, France
| | - John Gurdon
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, UK
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19
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Spirhanzlova P, Dhorne-Pollet S, Fellah J, Da Silva C, Tlapakova T, Labadie K, Weissenbach J, Poulain J, Jaffredo T, Wincker P, Krylov V, Pollet N. Construction and characterization of a BAC library for functional genomics in Xenopus tropicalis. Dev Biol 2017; 426:255-260. [DOI: 10.1016/j.ydbio.2016.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2016] [Revised: 03/18/2016] [Accepted: 05/10/2016] [Indexed: 12/20/2022]
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20
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Slater PG, Hayrapetian L, Lowery LA. Xenopus laevis as a model system to study cytoskeletal dynamics during axon pathfinding. Genesis 2017; 55. [PMID: 28095612 DOI: 10.1002/dvg.22994] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 01/17/2023]
Abstract
The model system, Xenopus laevis, has been used in innumerable research studies and has contributed to the understanding of multiple cytoskeletal components, including actin, microtubules, and neurofilaments, during axon pathfinding. Xenopus developmental stages have been widely characterized, and the Xenopus genome has been sequenced, allowing gene expression modifications through exogenous molecules. Xenopus cell cultures are ideal for long periods of live imaging because they are easily obtained and maintained, and they do not require special culture conditions. In addition, Xenopus have relatively large growth cones, compared to other vertebrates, thus providing a suitable system for imaging cytoskeletal components. Therefore, X. laevis is an ideal model organism in which to study cytoskeletal dynamics during axon pathfinding.
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Affiliation(s)
- Paula G Slater
- Department of Biology, Boston College, Chestnut Hill, Massachusetts
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21
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Abstract
Many publicly available data repositories and resources have been developed to support protein-related information management, data-driven hypothesis generation, and biological knowledge discovery. To help researchers quickly find the appropriate protein-related informatics resources, we present a comprehensive review (with categorization and description) of major protein bioinformatics databases in this chapter. We also discuss the challenges and opportunities for developing next-generation protein bioinformatics databases and resources to support data integration and data analytics in the Big Data era.
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Affiliation(s)
- Chuming Chen
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA.
| | - Hongzhan Huang
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, 19711, USA
| | - Cathy H Wu
- Center for Bioinformatics and Computational Biology, Department of Computer and Information Sciences, University of Delaware, Newark, DE, 19711, USA
- Protein Information Resource, Department of Biochemistry and Molecular and Cellular Biology, Georgetown University Medical Center, Washington, DC, 20007, USA
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22
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Cui H, Xu D, Chong SS, Ramirez M, Rodenhausen T, Macklin JA, Ludäscher B, Morris RA, Soto EM, Koch NM. Introducing Explorer of Taxon Concepts with a case study on spider measurement matrix building. BMC Bioinformatics 2016; 17:471. [PMID: 27855645 PMCID: PMC5114841 DOI: 10.1186/s12859-016-1352-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 11/11/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Taxonomic descriptions are traditionally composed in natural language and published in a format that cannot be directly used by computers. The Exploring Taxon Concepts (ETC) project has been developing a set of web-based software tools that convert morphological descriptions published in telegraphic style to character data that can be reused and repurposed. This paper introduces the first semi-automated pipeline, to our knowledge, that converts morphological descriptions into taxon-character matrices to support systematics and evolutionary biology research. We then demonstrate and evaluate the use of the ETC Input Creation - Text Capture - Matrix Generation pipeline to generate body part measurement matrices from a set of 188 spider morphological descriptions and report the findings. RESULTS From the given set of spider taxonomic publications, two versions of input (original and normalized) were generated and used by the ETC Text Capture and ETC Matrix Generation tools. The tools produced two corresponding spider body part measurement matrices, and the matrix from the normalized input was found to be much more similar to a gold standard matrix hand-curated by the scientist co-authors. Special conventions utilized in the original descriptions (e.g., the omission of measurement units) were attributed to the lower performance of using the original input. The results show that simple normalization of the description text greatly increased the quality of the machine-generated matrix and reduced edit effort. The machine-generated matrix also helped identify issues in the gold standard matrix. CONCLUSIONS ETC Text Capture and ETC Matrix Generation are low-barrier and effective tools for extracting measurement values from spider taxonomic descriptions and are more effective when the descriptions are self-contained. Special conventions that make the description text less self-contained challenge automated extraction of data from biodiversity descriptions and hinder the automated reuse of the published knowledge. The tools will be updated to support new requirements revealed in this case study.
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Affiliation(s)
- Hong Cui
- University of Arizona, Tucson, AZ USA
| | | | | | - Martin Ramirez
- Museo Argentino de Ciencias, Naturales, CONICET, Buenos Aires, Argentina
| | | | | | | | - Robert A. Morris
- University of Massachusetts at Boston and Harvard University Herbaria, Massachusetts, USA
| | - Eduardo M. Soto
- Department of Geology & Geophysics, Yale University, New Haven, Connecticut USA
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23
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Sequential Turnovers of Sex Chromosomes in African Clawed Frogs ( Xenopus) Suggest Some Genomic Regions Are Good at Sex Determination. G3-GENES GENOMES GENETICS 2016; 6:3625-3633. [PMID: 27605520 PMCID: PMC5100861 DOI: 10.1534/g3.116.033423] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Sexual differentiation is fundamentally important for reproduction, yet the genetic triggers of this developmental process can vary, even between closely related species. Recent studies have uncovered, for example, variation in the genetic triggers for sexual differentiation within and between species of African clawed frogs (genus Xenopus). Here, we extend these discoveries by demonstrating that yet another sex determination system exists in Xenopus, specifically in the species Xenopus borealis. This system evolved recently in an ancestor of X. borealis that had the same sex determination system as X. laevis, a system which itself is newly evolved. Strikingly, the genomic region carrying the sex determination factor in X. borealis is homologous to that of therian mammals, including humans. Our results offer insights into how the genetic underpinnings of conserved phenotypes evolve, and suggest an important role for cooption of genetic building blocks with conserved developmental roles.
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24
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Hatch VL, Marin-Barba M, Moxon S, Ford CT, Ward NJ, Tomlinson ML, Desanlis I, Hendry AE, Hontelez S, van Kruijsbergen I, Veenstra GJC, Münsterberg AE, Wheeler GN. The positive transcriptional elongation factor (P-TEFb) is required for neural crest specification. Dev Biol 2016; 416:361-72. [PMID: 27343897 DOI: 10.1016/j.ydbio.2016.06.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 05/06/2016] [Accepted: 06/08/2016] [Indexed: 12/31/2022]
Abstract
Regulation of gene expression at the level of transcriptional elongation has been shown to be important in stem cells and tumour cells, but its role in the whole animal is only now being fully explored. Neural crest cells (NCCs) are a multipotent population of cells that migrate during early development from the dorsal neural tube throughout the embryo where they differentiate into a variety of cell types including pigment cells, cranio-facial skeleton and sensory neurons. Specification of NCCs is both spatially and temporally regulated during embryonic development. Here we show that components of the transcriptional elongation regulatory machinery, CDK9 and CYCLINT1 of the P-TEFb complex, are required to regulate neural crest specification. In particular, we show that expression of the proto-oncogene c-Myc and c-Myc responsive genes are affected. Our data suggest that P-TEFb is crucial to drive expression of c-Myc, which acts as a 'gate-keeper' for the correct temporal and spatial development of the neural crest.
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Affiliation(s)
- Victoria L Hatch
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Marta Marin-Barba
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Christopher T Ford
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Nicole J Ward
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Matthew L Tomlinson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Ines Desanlis
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Adam E Hendry
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Saartje Hontelez
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Ila van Kruijsbergen
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Gert Jan C Veenstra
- Radboud University, Department of Molecular Developmental Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Nijmegen, The Netherlands
| | - Andrea E Münsterberg
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Grant N Wheeler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.
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25
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Clarkson MD. Representation of anatomy in online atlases and databases: a survey and collection of patterns for interface design. BMC DEVELOPMENTAL BIOLOGY 2016; 16:18. [PMID: 27206491 PMCID: PMC4875762 DOI: 10.1186/s12861-016-0116-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/09/2016] [Indexed: 12/17/2022]
Abstract
BACKGROUND A large number of online atlases and databases have been developed to mange the rapidly growing amount of data describing embryogenesis. As these community resources continue to evolve, it is important to understand how representations of anatomy can facilitate the sharing and integration of data. In addition, attention to the design of the interfaces is critical to make online resources useful and usable. RESULTS I first present a survey of online atlases and gene expression resources for model organisms, with a focus on methods of semantic and spatial representation of anatomy. A total of 14 anatomical atlases and 21 gene expression resources are included. This survey demonstrates how choices in semantic representation, in the form of ontologies, can enhance interface search functions and provide links between relevant information. This survey also reviews methods for spatially representing anatomy in online resources. I then provide a collection of patterns for interface design based on the atlases and databases surveyed. These patterns include methods for displaying graphics, integrating semantic and spatial representations, organizing information, and querying databases to find genes expressed in anatomical structures. CONCLUSIONS This collection of patterns for interface design will assist biologists and software developers in planning the interfaces of new atlases and databases or enhancing existing ones. They also show the benefits of standardizing semantic and spatial representations of anatomy by demonstrating how interfaces can use standardization to provide enhanced functionality.
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Affiliation(s)
- Melissa D Clarkson
- Department of Biological Structure, School of Medicine, University of Washington, Seattle, WA, USA.
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26
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Vize PD, Zorn AM. Xenopus genomic data and browser resources. Dev Biol 2016; 426:194-199. [PMID: 27039265 DOI: 10.1016/j.ydbio.2016.03.030] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 03/26/2016] [Accepted: 03/30/2016] [Indexed: 10/22/2022]
Abstract
The two species of Xenopus most commonly used in biomedical research are the diploid Xenopus (Silurana) tropicalis and the tetraploid Xenopus laevis. The X. tropicalis genome sequence has been available since 2010 and this year the X. laevis, genome from two distinct genetic backgrounds has been published. Multiple genome assemblies available for both species and transcriptomic and epigenetic data sets are growing rapidly, all of which are available from a variety of web resources. This review describes the contents of these resources, how to locate and download genomic data, and also how to view and manipulate these data on various public genome browsers, with an emphasis on Xenbase, the Xenopus model organism database.
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Affiliation(s)
- Peter D Vize
- Departments of Biological Science and Computer Science, University of Calgary, Alberta, Canada.
| | - Aaron M Zorn
- Division of Developmental Biology, Cincinnati Children's Research Foundation, Cincinnati, OH, USA
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Using Xenopus Embryos to Study Transcriptional and Posttranscriptional Gene Regulatory Mechanisms of Intermediate Filaments. Methods Enzymol 2016; 568:635-60. [DOI: 10.1016/bs.mie.2015.07.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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Koziol MJ, Bradshaw CR, Allen GE, Costa ASH, Frezza C, Gurdon JB. Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications. Nat Struct Mol Biol 2016; 23:24-30. [PMID: 26689968 PMCID: PMC4941928 DOI: 10.1038/nsmb.3145] [Citation(s) in RCA: 170] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/18/2015] [Indexed: 12/30/2022]
Abstract
Methylation of cytosine deoxynucleotides generates 5-methylcytosine (m(5)dC), a well-established epigenetic mark. However, in higher eukaryotes much less is known about modifications affecting other deoxynucleotides. Here, we report the detection of N(6)-methyldeoxyadenosine (m(6)dA) in vertebrate DNA, specifically in Xenopus laevis but also in other species including mouse and human. Our methylome analysis reveals that m(6)dA is widely distributed across the eukaryotic genome and is present in different cell types but is commonly depleted from gene exons. Thus, direct DNA modifications might be more widespread than previously thought.
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Affiliation(s)
- Magdalena J Koziol
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge
- Department of Zoology, University of Cambridge
| | - Charles R Bradshaw
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge
| | - George E Allen
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge
| | - Ana S H Costa
- Medical Research Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre
| | - Christian Frezza
- Medical Research Cancer Unit, University of Cambridge, Hutchison/MRC Research Centre
| | - John B Gurdon
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge
- Department of Zoology, University of Cambridge
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Evans BJ, Carter TF, Greenbaum E, Gvoždík V, Kelley DB, McLaughlin PJ, Pauwels OSG, Portik DM, Stanley EL, Tinsley RC, Tobias ML, Blackburn DC. Genetics, Morphology, Advertisement Calls, and Historical Records Distinguish Six New Polyploid Species of African Clawed Frog (Xenopus, Pipidae) from West and Central Africa. PLoS One 2015; 10:e0142823. [PMID: 26672747 PMCID: PMC4682732 DOI: 10.1371/journal.pone.0142823] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 10/27/2015] [Indexed: 01/08/2023] Open
Abstract
African clawed frogs, genus Xenopus, are extraordinary among vertebrates in the diversity of their polyploid species and the high number of independent polyploidization events that occurred during their diversification. Here we update current understanding of the evolutionary history of this group and describe six new species from west and central sub-Saharan Africa, including four tetraploids and two dodecaploids. We provide information on molecular variation, morphology, karyotypes, vocalizations, and estimated geographic ranges, which support the distinctiveness of these new species. We resurrect Xenopus calcaratus from synonymy of Xenopus tropicalis and refer populations from Bioko Island and coastal Cameroon (near Mt. Cameroon) to this species. To facilitate comparisons to the new species, we also provide comments on the type specimens, morphology, and distributions of X. epitropicalis, X. tropicalis, and X. fraseri. This includes significantly restricted application of the names X. fraseri and X. epitropicalis, the first of which we argue is known definitively only from type specimens and possibly one other specimen. Inferring the evolutionary histories of these new species allows refinement of species groups within Xenopus and leads to our recognition of two subgenera (Xenopus and Silurana) and three species groups within the subgenus Xenopus (amieti, laevis, and muelleri species groups).
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Affiliation(s)
- Ben J. Evans
- Department of Biology, Life Sciences Building Room 328 McMaster University, Hamilton, Ontario, Canada
- * E-mail:
| | - Timothy F. Carter
- Biomedical Sciences, Ontario Veterinary College, University of Guelph, Guelph, Ontario, Canada
| | - Eli Greenbaum
- Department of Biological Sciences, University of Texas at El Paso, El Paso, Texas, United States of America
| | - Václav Gvoždík
- Institute of Vertebrate Biology, Czech Academy of Sciences, Kvetna 8, Brno, Czech Republic
- Department of Zoology, National Museum, Prague, Czech Republic
| | - Darcy B. Kelley
- Department of Biological Sciences, Columbia University, New York, New York, United States of America
| | - Patrick J. McLaughlin
- Department of Biology, Papadakis Integrated Sciences Building, Drexel University, Philadelphia, Pennsylvania, United States of America
| | - Olivier S. G. Pauwels
- Département des Vertébrés Récents, Instítut Royal des Sciences Naturelles de Belgique, Brussels, Belgium
| | - Daniel M. Portik
- Museum of Vertebrate Zoology, University of California, Berkeley, California, United States of America
| | - Edward L. Stanley
- California Academy of Sciences, San Francisco, California, United States of America
| | - Richard C. Tinsley
- School of Biological Sciences, University of Bristol, Bristol, United Kingdom
| | | | - David C. Blackburn
- California Academy of Sciences, San Francisco, California, United States of America
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Liu W, Li F. Identification and Bioinformatics Analyses of the Basic Helix-loop-helix Transcription Factors in Xenopus laevis. Pak J Biol Sci 2015; 18:149-65. [PMID: 26506645 DOI: 10.3923/pjbs.2015.149.165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Xenopus laevis is a long established model organism for developmental, behavioral and neurological studies. Herein, an updated genome-wide survey was conducted using the ongoing genome project of Xenopus laevis and 106 non-redundant Basic Helix-Loop-Helix (bHLH) genes were identified in the Xenopus laevis genome databases. Gene Ontology (GO) enrichment statistics showed 51 significant GO annotations of biological processes and molecular functions and 5 significant KEGG pathways and a number of Xenopus laevis bHLH genes play significant role in specific development or special physiology processes like the development processes of muscle and eye and other organs. Furthermore, each sub-group of the bHLH family has its special gene functions except for the common GO term categories. Molecular phylogenetic analyses revealed that among these identified bHLH proteins, 105 sequences could classified into 39 families with 46, 25, 10, 5, 16 and 3 members in the corresponding high-order groups A, B, C, D, E and F, respectively with an addition bHLH member categorized as an orphan. The present study provides much useful information for further researches on Xenopus laevis.
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Ahmed A, Ward NJ, Moxon S, Lopez-Gomollon S, Viaut C, Tomlinson ML, Patrushev I, Gilchrist MJ, Dalmay T, Dotlic D, Münsterberg AE, Wheeler GN. A Database of microRNA Expression Patterns in Xenopus laevis. PLoS One 2015; 10:e0138313. [PMID: 26506012 PMCID: PMC4624429 DOI: 10.1371/journal.pone.0138313] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 08/28/2015] [Indexed: 12/31/2022] Open
Abstract
MicroRNAs (miRNAs) are short, non-coding RNAs around 22 nucleotides long. They inhibit gene expression either by translational repression or by causing the degradation of the mRNAs they bind to. Many are highly conserved amongst diverse organisms and have restricted spatio-temporal expression patterns during embryonic development where they are thought to be involved in generating accuracy of developmental timing and in supporting cell fate decisions and tissue identity. We determined the expression patterns of 180 miRNAs in Xenopus laevis embryos using LNA oligonucleotides. In addition we carried out small RNA-seq on different stages of early Xenopus development, identified 44 miRNAs belonging to 29 new families and characterized the expression of 5 of these. Our analyses identified miRNA expression in many organs of the developing embryo. In particular a large number were expressed in neural tissue and in the somites. Surprisingly none of the miRNAs we have looked at show expression in the heart. Our results have been made freely available as a resource in both XenMARK and Xenbase.
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Affiliation(s)
- Ayisha Ahmed
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Nicole J. Ward
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Simon Moxon
- The Genome Analysis Centre (TGAC), Norwich Research Park, Norwich, NR4 7UH, United Kingdom
| | - Sara Lopez-Gomollon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Camille Viaut
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Matthew L. Tomlinson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Ilya Patrushev
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, United Kingdom
| | - Michael J. Gilchrist
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London, NW7 1AA, United Kingdom
| | - Tamas Dalmay
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Dario Dotlic
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Andrea E. Münsterberg
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
| | - Grant N. Wheeler
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, United Kingdom
- * E-mail:
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Grant IM, Balcha D, Hao T, Shen Y, Trivedi P, Patrushev I, Fortriede JD, Karpinka JB, Liu L, Zorn AM, Stukenberg PT, Hill DE, Gilchrist MJ. The Xenopus ORFeome: A resource that enables functional genomics. Dev Biol 2015; 408:345-57. [PMID: 26391338 PMCID: PMC4684507 DOI: 10.1016/j.ydbio.2015.09.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Revised: 08/18/2015] [Accepted: 09/09/2015] [Indexed: 12/18/2022]
Abstract
Functional characterisation of proteins and large-scale, systems-level studies are enabled by extensive sets of cloned open reading frames (ORFs) in an easily-accessible format that enables many different applications. Here we report the release of the first stage of the Xenopus ORFeome, which contains 8673 ORFs from the Xenopus Gene Collection (XGC) for Xenopus laevis, cloned into a Gateway® donor vector enabling rapid in-frame transfer of the ORFs to expression vectors. This resource represents an estimated 7871 unique genes, approximately 40% of the non-redundant X. laevis gene complement, and includes 2724 genes where the human ortholog has an association with disease. Transfer into the Gateway system was validated by 5' and 3' end sequencing of the entire collection and protein expression of a set of test clones. In a parallel process, the underlying ORF predictions from the original XGC collection were re-analysed to verify quality and full-length status, identifying those proteins likely to exhibit truncations when translated. These data are integrated into Xenbase, the Xenopus community database, which associates genomic, expression, function and human disease model metadata to each ORF, enabling end-users to search for ORFeome clones with links to commercial distributors of the collection. When coupled with the experimental advantages of Xenopus eggs and embryos, the ORFeome collection represents a valuable resource for functional genomics and disease modelling.
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Affiliation(s)
- Ian M Grant
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Dawit Balcha
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Tong Hao
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yun Shen
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Prasad Trivedi
- University of Virginia, School of Medicine, Charlottesville, VA 22908, USA
| | - Ilya Patrushev
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Joshua D Fortriede
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - John B Karpinka
- Xenbase, Department of Biological Science, University of Calgary, Calgary, AB, Canada
| | - Limin Liu
- University of Virginia, School of Medicine, Charlottesville, VA 22908, USA
| | - Aaron M Zorn
- Xenbase, Division of Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - P Todd Stukenberg
- University of Virginia, School of Medicine, Charlottesville, VA 22908, USA
| | - David E Hill
- Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
| | - Michael J Gilchrist
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK.
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Richards AJ, Herrel A, Bonneaud C. htsint: a Python library for sequencing pipelines that combines data through gene set generation. BMC Bioinformatics 2015; 16:307. [PMID: 26399714 PMCID: PMC4581156 DOI: 10.1186/s12859-015-0729-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 09/08/2015] [Indexed: 11/10/2022] Open
Abstract
Background Sequencing technologies provide a wealth of details in terms of genes, expression, splice variants, polymorphisms, and other features. A standard for sequencing analysis pipelines is to put genomic or transcriptomic features into a context of known functional information, but the relationships between ontology terms are often ignored. For RNA-Seq, considering genes and their genetic variants at the group level enables a convenient way to both integrate annotation data and detect small coordinated changes between experimental conditions, a known caveat of gene level analyses. Results We introduce the high throughput data integration tool, htsint, as an extension to the commonly used gene set enrichment frameworks. The central aim of htsint is to compile annotation information from one or more taxa in order to calculate functional distances among all genes in a specified gene space. Spectral clustering is then used to partition the genes, thereby generating functional modules. The gene space can range from a targeted list of genes, like a specific pathway, all the way to an ensemble of genomes. Given a collection of gene sets and a count matrix of transcriptomic features (e.g. expression, polymorphisms), the gene sets produced by htsint can be tested for ‘enrichment’ or conditional differences using one of a number of commonly available packages. Conclusion The database and bundled tools to generate functional modules were designed with sequencing pipelines in mind, but the toolkit nature of htsint allows it to also be used in other areas of genomics. The software is freely available as a Python library through GitHub at https://github.com/ajrichards/htsint.
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Affiliation(s)
- Adam J Richards
- Station d'Ecologie Expérimentale du CNRS, USR 2936, Route du CNRS, Moulis, 09200, France.
| | - Anthony Herrel
- UMR 7179 CNRS/MNHN, Département d'Ecologie et de Gestion de la Biodiversité 57 rue Cuvier, Case postale 55, Paris, 75231, France. .,Ghent University, Evolutionary Morphology of Vertebrates, K.L. Ledeganckstraat 35, Ghent, B-9000, Belgium.
| | - Camille Bonneaud
- Station d'Ecologie Expérimentale du CNRS, USR 2936, Route du CNRS, Moulis, 09200, France. .,Centre for Ecology & Conservation, College of Life and Environmental Sciences, University of Exeter, Penryn TR10 9FE, Cornwall, UK.
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Gao Y, Cao Q, Lu L, Zhang X, Zhang Z, Dong X, Jia W, Cao Y. Kruppel-like factor family genes are expressed during Xenopus embryogenesis and involved in germ layer formation and body axis patterning. Dev Dyn 2015. [PMID: 26198170 DOI: 10.1002/dvdy.24310] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Kruppel-like factors (Klfs) are a family of transcription factors consisting of 17 members in mammals, Klf1-Klf17, which are involved in fundamental cellular physiological procedures, such as cell proliferation, differentiation, and apoptosis. However, their functions in embryonic development have been poorly understood. Our previous study has demonstrated that the pluripotency factor Klf4 participates in germ layer formation and axis patterning of Xenopus embryos by means of the regulation of key developmental signals. In the present study, we further investigated comprehensively the expression and functions of the klf family genes, klf2, klf5, klf6, klf7, klf8, klf11, klf15, and klf17, during the embryogenesis of Xenopus laevis. RESULTS Spatio-temporal expression analyses demonstrate that these genes are transcribed both maternally and zygotically in Xenopus embryos, and during organogenesis and tissue differentiation, they are localized to a variety of placodes and tissues. Gain and loss of function studies manifest that Klf factors play different roles in germ layer formation and body axis patterning. Moreover, each Klf factor exhibits distinct regulatory effects on the expression of genes that are essential for germ layer formation and body axis patterning. CONCLUSIONS These results suggest that Klf factors are involved in the fine-tuning of these genes during early embryogenesis.
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Affiliation(s)
- Yan Gao
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, Pukou High-Tech Zone, Nanjing, China
| | - Qing Cao
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, Pukou High-Tech Zone, Nanjing, China
| | - Lei Lu
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, Pukou High-Tech Zone, Nanjing, China
| | - Xuena Zhang
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, Pukou High-Tech Zone, Nanjing, China
| | - Zan Zhang
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, Pukou High-Tech Zone, Nanjing, China
| | - Xiaohua Dong
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, Pukou High-Tech Zone, Nanjing, China
| | - Wenshuang Jia
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, Pukou High-Tech Zone, Nanjing, China
| | - Ying Cao
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, Pukou High-Tech Zone, Nanjing, China
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Evans BJ, Schmid M. Preface. Cytogenet Genome Res 2015. [PMID: 26202694 DOI: 10.1159/000437176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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Evans BJ, Kwon T. Molecular Polymorphism and Divergence of Duplicated Genes in Tetraploid African Clawed Frogs (Xenopus). Cytogenet Genome Res 2015; 145:243-52. [PMID: 26066830 DOI: 10.1159/000431108] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Genome duplication creates redundancy in proteins and their interaction networks, and subsequent smaller-scale gene duplication can further amplify genetic redundancy. Mutations then lead to the loss, maintenance or functional divergence of duplicated genes. Genome duplication occurred many times in African clawed frogs (genus Xenopus), and almost all extant species in this group evolved from a polyploid ancestor. To better understand the nature of selective constraints in a polyploid genome, we examined molecular polymorphism and divergence of duplicates and single-copy genes in 2 tetraploid African clawed frog species, Xenopus laevis and X. victorianus. We found that molecular polymorphism in the coding regions of putative duplicated genes was higher than in singletons, but not significantly so. Our findings also suggest that transcriptome evolution in polyploids is influenced by variation in the genome-wide mutation rate, and do not reject the hypothesis that gene dosage balance is also important.
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Affiliation(s)
- Ben J Evans
- Department of Biology, McMaster University, Hamilton, Ont., Canada
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Chain FJJ. Sex-Biased Expression of Young Genes in Silurana (Xenopus) tropicalis. Cytogenet Genome Res 2015; 145:265-77. [PMID: 26065714 DOI: 10.1159/000430942] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Sex-biased gene expression can evolve from sex-specific selection and is often associated with sex-linked genes. Gene duplication is a particularly effective mechanism for the generation of sex-biased genes, in which a new copy can help resolve intralocus sexual conflicts. This study assesses sex-biased gene expression in an amphibian with homomorphic ZW sex chromosomes, the Western clawed frog Silurana (Xenopus)tropicalis. Previous work has shown that the sex chromosomes in this species are mainly undifferentiated and pseudoautosomal. Consistent with ongoing recombination between the sex chromosomes, this study detected little evidence for the general sexualization of sex-linked regions. A subset of genes closely linked to the sex determining locus displays a tendency for male-biased expression and elevated rates of evolution relative to genes in other genomic locations. This may be a symptom of an early stage of sex chromosome differentiation driven by, for example, chromosomal degeneration or natural selection on genes in this portion of the Z chromosome. Alternatively, it could reflect variation between the sexes in allelic copy number coupled with a lack of dosage compensation. Irrespective of the genomic location, lineage-specific genes and recently duplicated genes had significantly high levels of sex-biased expression, offering insights into the early transcriptional differentiation of young genes.
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Vize PD, Liu Y, Karimi K. Database and Informatic Challenges in Representing Both Diploid and Tetraploid Xenopus Species in Xenbase. Cytogenet Genome Res 2015; 145:278-82. [PMID: 26022975 DOI: 10.1159/000430427] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
At the heart of databases is a data model referred to as a schema. Relational databases store information in tables, and the schema defines the tables and provides a map of relationships that show how the different table/data types relate to one another. In Xenbase, we were tasked to represent genomic, molecular, and biological data of both a diploid and tetraploid Xenopus species. When the database model was built over a decade ago, we had very little information on the nature of the X.laevis tetraploidization, but a Chado-based data model was proposed that could deal with the various forms of data in both species. Once the X.laevis genome was sequenced and annotated, it became clear that the data schema is very like the evolutionary schema that resulted in the X.laevis genome.
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Affiliation(s)
- Peter D Vize
- Departments of Biological Sciences and Computer Science, University of Calgary, Calgary, Alta., Canada
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Lu L, Gao Y, Zhang Z, Cao Q, Zhang X, Zou J, Cao Y. Kdm2a/b Lysine Demethylases Regulate Canonical Wnt Signaling by Modulating the Stability of Nuclear β-Catenin. Dev Cell 2015; 33:660-74. [PMID: 26004508 DOI: 10.1016/j.devcel.2015.04.006] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2013] [Revised: 10/02/2014] [Accepted: 04/02/2015] [Indexed: 11/25/2022]
Abstract
In the absence of Wnt activation, cytosolic β-catenin is degraded through GSK3/CK1-mediated phosphorylation at the N terminus. Here, we show that, upon Wnt activation, the stability of nuclear β-catenin is regulated via methylation/demethylation. The protein lysine demethylases Kdm2a and Kdm2b regulate the turnover of non-phosphorylated β-catenin specifically within the nucleus via direct interaction with the fourth and fifth armadillo repeats. The lysine residues within this region are required for the methylation of non-phosphorylated β-catenin, which is demethylated by Kdm2a/b and subsequently ubiquitylated. During Xenopus embryogenesis, kdm2a/b genes are transcribed during early embryogenesis and are required for the specification of the body axis. Kdm2a/b knockdown in Xenopus embryos leads to increases in non-phosphorylated and methylated β-catenin, concurrent with the upregulation of β-catenin target genes. This mechanism is required for controlling the output of the Wnt/β-catenin signaling pathway to maintain normal cellular functions.
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Affiliation(s)
- Lei Lu
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, 12 Xuefu Road, Pukou High-Tech Zone, Nanjing 210061, China
| | - Yan Gao
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, 12 Xuefu Road, Pukou High-Tech Zone, Nanjing 210061, China
| | - Zan Zhang
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, 12 Xuefu Road, Pukou High-Tech Zone, Nanjing 210061, China
| | - Qing Cao
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, 12 Xuefu Road, Pukou High-Tech Zone, Nanjing 210061, China
| | - Xuena Zhang
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, 12 Xuefu Road, Pukou High-Tech Zone, Nanjing 210061, China
| | - Jianghuan Zou
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, 12 Xuefu Road, Pukou High-Tech Zone, Nanjing 210061, China
| | - Ying Cao
- Model Animal Research Center of Nanjing University and MOE Key Laboratory of Model Animals for Disease Study, 12 Xuefu Road, Pukou High-Tech Zone, Nanjing 210061, China.
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Colombo BM, Scalvenzi T, Benlamara S, Pollet N. Microbiota and mucosal immunity in amphibians. Front Immunol 2015; 6:111. [PMID: 25821449 PMCID: PMC4358222 DOI: 10.3389/fimmu.2015.00111] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2014] [Accepted: 02/26/2015] [Indexed: 12/11/2022] Open
Abstract
We know that animals live in a world dominated by bacteria. In the last 20 years, we have learned that microbes are essential regulators of mucosal immunity. Bacteria, archeas, and viruses influence different aspects of mucosal development and function. Yet, the literature mainly covers findings obtained in mammals. In this review, we focus on two major themes that emerge from the comparative analysis of mammals and amphibians. These themes concern: (i) the structure and functions of lymphoid organs and immune cells in amphibians, with a focus on the gut mucosal immune system; and (ii) the characteristics of the amphibian microbiota and its influence on mucosal immunity. Lastly, we propose to use Xenopus tadpoles as an alternative small-animal model to improve the fundamental knowledge on immunological functions of gut microbiota.
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Affiliation(s)
- Bruno M Colombo
- Institute of Systems and Synthetic Biology, Université d'Evry Val d'Essonne , Evry , France
| | - Thibault Scalvenzi
- Institute of Systems and Synthetic Biology, Université d'Evry Val d'Essonne , Evry , France
| | - Sarah Benlamara
- Institute of Systems and Synthetic Biology, Université d'Evry Val d'Essonne , Evry , France
| | - Nicolas Pollet
- Institute of Systems and Synthetic Biology, CNRS , Evry , France ; Evolution, Genome, Comportement et Ecologie, CNRS, Université Paris-Sud, IRD , Gif-sur-Yvette , France
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41
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Abstract
Cilia are key organelles in development and homeostasis. The ever-expanding complement of cilia associated proteins necessitates rapid and tractable models for in vivo functional investigation. Xenopus laevis provides an attractive model for such studies, having multiple ciliated populations, including primary and multiciliated tissues. The rapid external development of Xenopus and the large cells make it an especially excellent platform for imaging studies. Here we present embryological and cell biological methods for the investigation of cilia structure and function in X. laevis, with a focus on quantitative live and fixed imaging.
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Huang BK, Gamm UA, Jonas S, Khokha MK, Choma MA. Quantitative optical coherence tomography imaging of intermediate flow defect phenotypes in ciliary physiology and pathophysiology. JOURNAL OF BIOMEDICAL OPTICS 2015; 20:030502. [PMID: 25751026 PMCID: PMC4352652 DOI: 10.1117/1.jbo.20.3.030502] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/19/2015] [Indexed: 05/04/2023]
Abstract
Cilia-driven fluid flow is a critical yet poorly understood aspect of pulmonary physiology. Here, we demonstrate that optical coherence tomography-based particle tracking velocimetry can be used to quantify subtle variability in cilia-driven flow performance in Xenopus, an important animal model of ciliary biology. Changes in flow performance were quantified in the setting of normal development, as well as in response to three types of perturbations: mechanical (increased fluid viscosity), pharmacological (disrupted serotonin signaling), and genetic (diminished ciliary motor protein expression). Of note, we demonstrate decreased flow secondary to gene knockdown of kif3a, a protein involved in ciliogenesis, as well as a dose-response decrease in flow secondary to knockdown of dnah9, an important ciliary motor protein.
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Affiliation(s)
- Brendan K. Huang
- Yale University, Department of Biomedical Engineering, 55 Prospect Street, New Haven, Connecticut 06511, United States
- Address all correspondence to: Brendan K. Huang, E-mail:
| | - Ute A. Gamm
- Yale School of Medicine, Department of Diagnostic Radiology, P.O. Box 208043, New Haven, Connecticut 06520, United States
| | - Stephan Jonas
- Yale School of Medicine, Department of Diagnostic Radiology, P.O. Box 208043, New Haven, Connecticut 06520, United States
| | - Mustafa K. Khokha
- Yale School of Medicine, Department of Pediatrics, P.O. Box 208064, New Haven, Connecticut 06520, United States
- Yale School of Medicine, Department of Genetics, 333 Cedar Street, New Haven, Connecticut 06510, United States
| | - Michael A. Choma
- Yale University, Department of Biomedical Engineering, 55 Prospect Street, New Haven, Connecticut 06511, United States
- Yale School of Medicine, Department of Diagnostic Radiology, P.O. Box 208043, New Haven, Connecticut 06520, United States
- Yale School of Medicine, Department of Pediatrics, P.O. Box 208064, New Haven, Connecticut 06520, United States
- Yale University, Department of Applied Physics, P.O. Box 208267, New Haven, Connecticut 06520, United States
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43
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Liu Y, Wang C, Destin G, Szaro BG. Microtubule-associated protein tau promotes neuronal class II β-tubulin microtubule formation and axon elongation in embryonic Xenopus laevis. Eur J Neurosci 2015; 41:1263-75. [PMID: 25656701 DOI: 10.1111/ejn.12848] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 12/13/2014] [Accepted: 01/07/2015] [Indexed: 01/06/2023]
Abstract
Compared with its roles in neurodegeneration, much less is known about microtubule-associated protein tau's normal functions in vivo, especially during development. The external development and ease of manipulating gene expression of Xenopus laevis embryos make them especially useful for studying gene function during early development. To study tau's functions in axon outgrowth, we characterized the most prominent tau isoforms of Xenopus embryos and manipulated their expression. None of these four isoforms were strictly analogous to those commonly studied in mammals, as all constitutively contained exon 10, which is preferentially removed from mammalian fetal tau isoforms, as well as exon 8, which in mammals is rare. Nonetheless, like mammalian tau, Xenopus tau exhibited alternative splicing of exon 4a, which in mammals distinguishes 'big' tau of peripheral neurons, and exon 6. Strongly suppressing tau expression with antisense morpholino oligonucleotides only modestly compromised peripheral nerve outgrowth of intact tadpoles, but severely disrupted neuronal microtubules containing class II β-tubulins while leaving other microtubules largely unperturbed. Thus, the relatively mild dependence of axon development on tau likely resulted from having only a single class of microtubules disrupted by its loss. Also, consistent with its greater expression in long peripheral axons, boosting expression of 'big' tau increased neurite outgrowth significantly and enhanced tubulin acetylation more so than did the smaller isoform. These data demonstrate the utility of Xenopus as a tool to gain new insights into tau's functions in vivo.
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Affiliation(s)
- Yuanyuan Liu
- Department of Biological Sciences and the Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Chen Wang
- Department of Biological Sciences and the Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Giovanny Destin
- Department of Biological Sciences and the Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
| | - Ben G Szaro
- Department of Biological Sciences and the Center for Neuroscience Research, University at Albany, State University of New York, 1400 Washington Avenue, Albany, NY, 12222, USA
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44
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Nworu CU, Kraft R, Schnurr DC, Gregorio CC, Krieg PA. Leiomodin 3 and tropomodulin 4 have overlapping functions during skeletal myofibrillogenesis. J Cell Sci 2014; 128:239-50. [PMID: 25431137 DOI: 10.1242/jcs.152702] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Precise regulation of thin filament length is essential for optimal force generation during muscle contraction. The thin filament capping protein tropomodulin (Tmod) contributes to thin filament length uniformity by regulating elongation and depolymerization at thin filament ends. The leiomodins (Lmod1-3) are structurally related to Tmod1-4 and also localize to actin filament pointed ends, but in vitro biochemical studies indicate that Lmods act instead as robust nucleators. Here, we examined the roles of Tmod4 and Lmod3 during Xenopus skeletal myofibrillogenesis. Loss of Tmod4 or Lmod3 resulted in severe disruption of sarcomere assembly and impaired embryonic movement. Remarkably, when Tmod4-deficient embryos were supplemented with additional Lmod3, and Lmod3-deficient embryos were supplemented with additional Tmod4, sarcomere assembly was rescued and embryonic locomotion improved. These results demonstrate for the first time that appropriate levels of both Tmod4 and Lmod3 are required for embryonic myofibrillogenesis and, unexpectedly, both proteins can function redundantly during in vivo skeletal muscle thin filament assembly. Furthermore, these studies demonstrate the value of Xenopus for the analysis of contractile protein function during de novo myofibril assembly.
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Affiliation(s)
- Chinedu U Nworu
- Department of Cellular and Molecular Medicine, Sarver Molecular Cardiovascular Research Program, University of Arizona, 1656 E. Mabel St, Tucson, AZ 85724, USA
| | - Robert Kraft
- Department of Cellular and Molecular Medicine, Sarver Molecular Cardiovascular Research Program, University of Arizona, 1656 E. Mabel St, Tucson, AZ 85724, USA
| | - Daniel C Schnurr
- Department of Cellular and Molecular Medicine, Sarver Molecular Cardiovascular Research Program, University of Arizona, 1656 E. Mabel St, Tucson, AZ 85724, USA
| | - Carol C Gregorio
- Department of Cellular and Molecular Medicine, Sarver Molecular Cardiovascular Research Program, University of Arizona, 1656 E. Mabel St, Tucson, AZ 85724, USA
| | - Paul A Krieg
- Department of Cellular and Molecular Medicine, Sarver Molecular Cardiovascular Research Program, University of Arizona, 1656 E. Mabel St, Tucson, AZ 85724, USA
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45
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Karimi K, Vize PD. The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2014; 2014:bau108. [PMID: 25380782 PMCID: PMC4224262 DOI: 10.1093/database/bau108] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
As a model organism database, Xenbase has been providing informatics and genomic data on Xenopus (Silurana) tropicalis and Xenopus laevis frogs for more than a decade. The Xenbase database contains curated, as well as community-contributed and automatically harvested literature, gene and genomic data. A GBrowse genome browser, a BLAST+ server and stock center support are available on the site. When this resource was first built, all software services and components in Xenbase ran on a single physical server, with inherent reliability, scalability and inter-dependence issues. Recent advances in networking and virtualization techniques allowed us to move Xenbase to a virtual environment, and more specifically to a private cloud. To do so we decoupled the different software services and components, such that each would run on a different virtual machine. In the process, we also upgraded many of the components. The resulting system is faster and more reliable. System maintenance is easier, as individual virtual machines can now be updated, backed up and changed independently. We are also experiencing more effective resource allocation and utilization. Database URL:www.xenbase.org
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Affiliation(s)
- Kamran Karimi
- Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada, T2N 1N4
| | - Peter D Vize
- Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada, T2N 1N4
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46
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Chowanadisai W. Comparative genomic analysis of slc39a12/ZIP12: insight into a zinc transporter required for vertebrate nervous system development. PLoS One 2014; 9:e111535. [PMID: 25375179 PMCID: PMC4222902 DOI: 10.1371/journal.pone.0111535] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 10/04/2014] [Indexed: 01/23/2023] Open
Abstract
The zinc transporter ZIP12, which is encoded by the gene slc39a12, has previously been shown to be important for neuronal differentiation in mouse Neuro-2a neuroblastoma cells and primary mouse neurons and necessary for neurulation during Xenopus tropicalis embryogenesis. However, relatively little is known about the biochemical properties, cellular regulation, or the physiological role of this gene. The hypothesis that ZIP12 is a zinc transporter important for nervous system function and development guided a comparative genetics approach to uncover the presence of ZIP12 in various genomes and identify conserved sequences and expression patterns associated with ZIP12. Ortholog detection of slc39a12 was conducted with reciprocal BLAST hits with the amino acid sequence of human ZIP12 in comparison to the human paralog ZIP4 and conserved local synteny between genomes. ZIP12 is present in the genomes of almost all vertebrates examined, from humans and other mammals to most teleost fish. However, ZIP12 appears to be absent from the zebrafish genome. The discrimination of ZIP12 compared to ZIP4 was unsuccessful or inconclusive in other invertebrate chordates and deuterostomes. Splice variation, due to the inclusion or exclusion of a conserved exon, is present in humans, rats, and cows and likely has biological significance. ZIP12 also possesses many putative di-leucine and tyrosine motifs often associated with intracellular trafficking, which may control cellular zinc uptake activity through the localization of ZIP12 within the cell. These findings highlight multiple aspects of ZIP12 at the biochemical, cellular, and physiological levels with likely biological significance. ZIP12 appears to have conserved function as a zinc uptake transporter in vertebrate nervous system development. Consequently, the role of ZIP12 may be an important link to reported congenital malformations in numerous animal models and humans that are caused by zinc deficiency.
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Affiliation(s)
- Winyoo Chowanadisai
- Department of Nutrition, University of California Davis, Davis, California, United States of America
- * E-mail:
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47
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Square T, Jandzik D, Cattell M, Coe A, Doherty J, Medeiros DM. A gene expression map of the larval Xenopus laevis head reveals developmental changes underlying the evolution of new skeletal elements. Dev Biol 2014; 397:293-304. [PMID: 25446275 DOI: 10.1016/j.ydbio.2014.10.016] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 10/02/2014] [Accepted: 10/20/2014] [Indexed: 11/29/2022]
Abstract
The morphology of the vertebrate head skeleton is highly plastic, with the number, size, shape, and position of its components varying dramatically between groups. While this evolutionary flexibility has been key to vertebrate success, its developmental and genetic bases are poorly understood. The larval head skeleton of the frog Xenopus laevis possesses a unique combination of ancestral tetrapod features and anuran-specific novelties. We built a detailed gene expression map of the head mesenchyme in X. laevis during early larval development, focusing on transcription factor families with known functions in vertebrate head skeleton development. This map was then compared to homologous gene expression in zebrafish, mouse, and shark embryos to identify conserved and evolutionarily flexible aspects of vertebrate head skeleton development. While we observed broad conservation of gene expression between X. laevis and other gnathostomes, we also identified several divergent features that correlate to lineage-specific novelties. We noted a conspicuous change in dlx1/2 and emx2 expression in the second pharyngeal arch, presaging the differentiation of the reduced dorsal hyoid arch skeletal element typical of modern anamniote tetrapods. In the first pharyngeal arch we observed a shift in the expression of the joint inhibitor barx1, and new expression of the joint marker gdf5, shortly before skeletal differentiation. This suggests that the anuran-specific infrarostral cartilage evolved by partitioning of Meckel's cartilage with a new paired joint. Taken together, these comparisons support a model in which early patterning mechanisms divide the vertebrate head mesenchyme into a highly conserved set of skeletal precursor populations. While subtle changes in this early patterning system can affect skeletal element size, they do not appear to underlie the evolution of new joints or cartilages. In contrast, later expression of the genes that regulate skeletal element differentiation can be clearly linked to the evolution of novel skeletal elements. We posit that changes in the expression of downstream regulators of skeletal differentiation, like barx1 and gdf5, is one mechanism by which head skeletal element number and articulation are altered during evolution.
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Affiliation(s)
- Tyler Square
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA.
| | - David Jandzik
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA; Department of Zoology, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, 84215, Slovakia
| | - Maria Cattell
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - Alex Coe
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - Jacob Doherty
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
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Tocco A, Pinson B, Thiébaud P, Thézé N, Massé K. Comparative genomic and expression analysis of the adenosine signaling pathway members in Xenopus. Purinergic Signal 2014; 11:59-77. [PMID: 25319637 DOI: 10.1007/s11302-014-9431-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Accepted: 09/30/2014] [Indexed: 12/13/2022] Open
Abstract
Adenosine is an endogenous molecule that regulates many physiological processes via the activation of four specific G-protein-coupled ADORA receptors. Extracellular adenosine may originate either from the hydrolysis of released ATP by the ectonucleotidases or from cellular exit via the equilibrative nucleoside transporters (SLC29A). Adenosine extracellular concentration is also regulated by its successive hydrolysis into uric acid by membrane-bound enzymes or by cell influx via the concentrative nucleoside transporters (SLC28A). All of these members constitute the adenosine signaling pathway and regulate adenosine functions. Although the roles of this pathway are quite well understood in adults, little is known regarding its functions during vertebrate embryogenesis. We have used Xenopus laevis as a model system to provide a comparative expression map of the different members of this pathway during vertebrate development. We report the characterization of the different enzymes, receptors, and nucleoside transporters in both X. laevis and X. tropicalis, and we demonstrate by phylogenetic analyses the high level of conservation of these members between amphibians and mammals. A thorough expression analysis of these members during development and in the adult frog reveals that each member displays distinct specific expression patterns. These data suggest potentially different developmental roles for these proteins and therefore for extracellular adenosine. In addition, we show that adenosine levels during amphibian embryogenesis are very low, confirming that they must be tightly controlled for normal development.
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Affiliation(s)
- Alice Tocco
- Université de Bordeaux, CIRID UMR 5164, F-33000, Bordeaux, France
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Regnault C, Worms IAM, Oger-Desfeux C, MelodeLima C, Veyrenc S, Bayle ML, Combourieu B, Bonin A, Renaud J, Raveton M, Reynaud S. Impaired liver function in Xenopus tropicalis exposed to benzo[a]pyrene: transcriptomic and metabolic evidence. BMC Genomics 2014; 15:666. [PMID: 25103525 PMCID: PMC4141109 DOI: 10.1186/1471-2164-15-666] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 07/30/2014] [Indexed: 12/20/2022] Open
Abstract
Background Despite numerous studies suggesting that amphibians are highly sensitive to cumulative anthropogenic stresses, the role pollutants play in the decline of amphibian populations remains unclear. Amongst the most common aquatic contaminants, polycyclic aromatic hydrocarbons (PAHs) have been shown to induce several adverse effects on amphibian species in the larval stages. Conversely, adults exposed to high concentrations of the ubiquitous PAH, benzo[a]pyrene (BaP), tolerate the compound thanks to their highly efficient hepatic detoxification mechanisms. Due to this apparent lack of toxic effect on adults, no studies have examined in depth the potential toxicological impact of PAH on the physiology of adult amphibian livers. This study sheds light on the hepatic responses of Xenopus tropicalis when exposed to high environmentally relevant concentrations of BaP, by combining a high throughput transcriptomic approach (mRNA deep sequencing) and a characterization of cellular and physiological modifications to the amphibian liver. Results Transcriptomic changes observed in BaP-exposed Xenopus were further characterized using a time-dependent enrichment analysis, which revealed the pollutant-dependent gene regulation of important biochemical pathways, such as cholesterol biosynthesis, insulin signaling, adipocytokines signaling, glycolysis/gluconeogenesis and MAPK signaling. These results were substantiated at the physiological level with the detection of a pronounced metabolic disorder resulting in a possible insulin resistance-like syndrome phenotype. Hepatotoxicity induced by lipid and cholesterol metabolism impairments was clearly identified in BaP-exposed individuals. Conclusions Our data suggested that BaP may disrupt overall liver physiology, and carbohydrate and cholesterol metabolism in particular, even after short-term exposure. These results are further discussed in terms of how this deregulation of liver physiology can lead to general metabolic impairment in amphibians chronically exposed to contaminants, thereby illustrating the role xenobiotics might play in the global decline in amphibian populations. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-666) contains supplementary material, which is available to authorized users.
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50
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Grau JH, Poustka AJ, Meixner M, Plötner J. LTR retroelements are intrinsic components of transcriptional networks in frogs. BMC Genomics 2014; 15:626. [PMID: 25056159 PMCID: PMC4131045 DOI: 10.1186/1471-2164-15-626] [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: 03/18/2014] [Accepted: 07/15/2014] [Indexed: 12/16/2022] Open
Abstract
Background LTR retroelements (LTR REs) constitute a major group of transposable elements widely distributed in eukaryotic genomes. Through their own mechanism of retrotranscription LTR REs enrich the genomic landscape by providing genetic variability, thus contributing to genome structure and organization. Nonetheless, transcriptomic activity of LTR REs still remains an obscure domain within cell, developmental, and organism biology. Results Here we present a first comparative analysis of LTR REs for anuran amphibians based on a full depth coverage transcriptome of the European pool frog, Pelophylax lessonae, the genome of the African clawed frog, Silurana tropicalis (release v7.1), and additional transcriptomes of S. tropicalis and Cyclorana alboguttata. We identified over 1000 copies of LTR REs from all four families (Bel/Pao, Ty1/Copia, Ty3/Gypsy, Retroviridae) in the genome of S. tropicalis and discovered transcripts of several of these elements in all RNA-seq datasets analyzed. Elements of the Ty3/Gypsy family were most active, especially Amn-san elements, which accounted for approximately 0.27% of the genome in Silurana. Some elements exhibited tissue specific expression patterns, for example Hydra1.1 and MuERV-like elements in Pelophylax. In S. tropicalis considerable transcription of LTR REs was observed during embryogenesis as soon as the embryonic genome became activated, i.e. at midblastula transition. In the course of embryonic development the spectrum of transcribed LTR REs changed; during gastrulation and neurulation MuERV-like and SnRV like retroviruses were abundantly transcribed while during organogenesis transcripts of the XEN1 retroviruses became much more active. Conclusions The differential expression of LTR REs during embryogenesis in concert with their tissue-specificity and the protein domains they encode are evidence for the functional roles these elements play as integrative parts of complex regulatory networks. Our results support the meanwhile widely accepted concept that retroelements are not simple “junk DNA” or “harmful genomic parasites” but essential components of the transcriptomic machinery in vertebrates. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-626) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- José Horacio Grau
- Dahlem Center for Genome Research and Medical Systems Biology, Fabeckstraße 60-62, 14195 Berlin, Germany.
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