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Neil CR, Jeschonek SP, Cabral SE, O'Connell LC, Powrie EA, Otis JP, Wood TR, Mowry KL. L-bodies are RNA-protein condensates driving RNA localization in Xenopus oocytes. Mol Biol Cell 2021; 32:ar37. [PMID: 34613784 PMCID: PMC8694076 DOI: 10.1091/mbc.e21-03-0146-t] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Ribonucleoprotein (RNP) granules are membraneless compartments within cells, formed by phase separation, that function as regulatory hubs for diverse biological processes. However, the mechanisms by which RNAs and proteins interact to promote RNP granule structure and function in vivo remain unclear. In Xenopus laevis oocytes, maternal mRNAs are localized as large RNPs to the vegetal hemisphere of the developing oocyte, where local translation is critical for proper embryonic patterning. Here we demonstrate that RNPs containing vegetally localized RNAs represent a new class of cytoplasmic RNP granule, termed localization-bodies (L-bodies). We show that L-bodies contain a dynamic protein-containing phase surrounding a nondynamic RNA-containing phase. Our results support a role for RNA as a critical component within these RNP granules and suggest that cis-elements within localized mRNAs may drive subcellular RNA localization through control over phase behavior.
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Affiliation(s)
- Christopher R Neil
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Samantha P Jeschonek
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Sarah E Cabral
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Liam C O'Connell
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Erin A Powrie
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Jessica P Otis
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Timothy R Wood
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Kimberly L Mowry
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
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Lewis V, Laberge F, Heyland A. Temporal Profile of Brain Gene Expression After Prey Catching Conditioning in an Anuran Amphibian. Front Neurosci 2020; 13:1407. [PMID: 31992968 PMCID: PMC6971186 DOI: 10.3389/fnins.2019.01407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 12/12/2019] [Indexed: 12/19/2022] Open
Abstract
A key goal in modern neurobiology is to understand the mechanisms underlying learning and memory. To that end, it is essential to identify the patterns of gene expression and the temporal sequence of molecular events associated with learning and memory processes. It is also important to ascertain if and how these molecular events vary between organisms. In vertebrates, learning and memory processes are characterized by distinct phases of molecular activity involving gene transcription, structural change, and long-term maintenance of such structural change in the nervous system. Utilizing next generation sequencing techniques, we profiled the temporal expression patterns of genes in the brain of the fire-bellied toad Bombina orientalis after prey catching conditioning. The fire-bellied toad is a basal tetrapod whose neural architecture and molecular pathways may help us understand the ancestral state of learning and memory mechanisms in tetrapods. Differential gene expression following conditioning revealed activity in molecular pathways related to immediate early genes (IEG), cytoskeletal modification, axon guidance activity, and apoptotic processes. Conditioning induced early IEG activity coinciding with transcriptional activity and neuron structural modification, followed by axon guidance and cell adhesion activity, and late neuronal pruning. While some of these gene expression patterns are similar to those found in mammals submitted to conditioning, some interesting divergent expression profiles were seen, and differential expression of some well-known learning-related mammalian genes is missing altogether. These results highlight the importance of using a comparative approach in the study of the mechanisms of leaning and memory and provide molecular resources for a novel vertebrate model in the relatively poorly studied Amphibia.
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Affiliation(s)
- Vern Lewis
- Integrative Biology, University of Guelph, Guelph, ON, Canada
| | | | - Andreas Heyland
- Integrative Biology, University of Guelph, Guelph, ON, Canada
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Kwon T. AmphiBase: A new genomic resource for non-model amphibian species. Genesis 2017; 55. [PMID: 28095648 DOI: 10.1002/dvg.23010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 11/29/2016] [Accepted: 12/02/2016] [Indexed: 11/11/2022]
Abstract
More than five thousand genes annotated in the recently published Xenopus laevis and Xenopus tropicalis genomes do not have a candidate orthologous counterpart in other vertebrate species. To determine whether these sequences represent genuine amphibian-specific genes or annotation errors, it is necessary to analyze them alongside sequences from other amphibian species. However, due to large genome sizes and an abundance of repeat sequences, there are limited numbers of gene sequences available from amphibian species other than Xenopus. AmphiBase is a new genomic resource covering non-model amphibian species, based on public domain transcriptome data and computational methods developed during the X. laevis genome project. Here, I review the current status of AmphiBase, including amphibian species with available transcriptome data or biological samples, and describe the challenges of building a comprehensive amphibian genomic resource in the absence of genomes. This mini-review will be informative for researchers interested in functional genomic experiments using amphibian model organisms, such as Xenopus and axolotl, and will assist in interpretation of results implicating "orphan genes." Additionally, this study highlights an opportunity for researchers working on non-model amphibian species to collaborate in their future efforts and develop amphibian genomic resources as a community.
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Affiliation(s)
- Taejoon Kwon
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, 44919, Republic of Korea
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Noiret M, Méreau A, Angrand G, Bervas M, Gautier-Courteille C, Legagneux V, Deschamps S, Lerivray H, Viet J, Hardy S, Paillard L, Audic Y. Robust identification of Ptbp1-dependent splicing events by a junction-centric approach in Xenopus laevis. Dev Biol 2016; 426:449-459. [PMID: 27546377 DOI: 10.1016/j.ydbio.2016.08.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Revised: 08/02/2016] [Accepted: 08/17/2016] [Indexed: 10/25/2022]
Abstract
Regulation of alternative splicing is an important process for cell differentiation and development. Down-regulation of Ptbp1, a regulatory RNA-binding protein, leads to developmental skin defects in Xenopus laevis. To identify Ptbp1-dependent splicing events potentially related to the phenotype, we conducted RNAseq experiments following Ptbp1 depletion. We systematically compared exon-centric and junction-centric approaches to detect differential splicing events. We showed that the junction-centric approach performs far better than the exon-centric approach in Xenopus laevis. We carried out the same comparisons using simulated data in human, which led us to propose that the better performances of the junction-centric approach in Xenopus laevis essentially relies on an incomplete exonic annotation associated with a correct transcription unit annotation. We assessed the capacity of the exon-centric and junction-centric approaches to retrieve known and to discover new Ptbp1-dependent splicing events. Notably, the junction-centric approach identified Ptbp1-controlled exons in agfg1, itga6, actn4, and tpm4 mRNAs, which were independently confirmed. We conclude that the junction-centric approach allows for a more complete and informative description of splicing events, and we propose that this finding might hold true for other species with incomplete annotations.
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Affiliation(s)
- Maud Noiret
- Université de Rennes 1, Université Européenne de Bretagne, Biosit, Rennes 35000, France; Centre National de la Recherche Scientifique UMR 6290, Institut de Génétique et Développement de Rennes, Rennes 35000, France
| | - Agnès Méreau
- Université de Rennes 1, Université Européenne de Bretagne, Biosit, Rennes 35000, France; Centre National de la Recherche Scientifique UMR 6290, Institut de Génétique et Développement de Rennes, Rennes 35000, France
| | - Gaëlle Angrand
- Université de Rennes 1, Université Européenne de Bretagne, Biosit, Rennes 35000, France; Centre National de la Recherche Scientifique UMR 6290, Institut de Génétique et Développement de Rennes, Rennes 35000, France
| | - Marion Bervas
- Université de Rennes 1, Université Européenne de Bretagne, Biosit, Rennes 35000, France; Centre National de la Recherche Scientifique UMR 6290, Institut de Génétique et Développement de Rennes, Rennes 35000, France
| | - Carole Gautier-Courteille
- Université de Rennes 1, Université Européenne de Bretagne, Biosit, Rennes 35000, France; Centre National de la Recherche Scientifique UMR 6290, Institut de Génétique et Développement de Rennes, Rennes 35000, France
| | - Vincent Legagneux
- Université de Rennes 1, Université Européenne de Bretagne, Biosit, Rennes 35000, France; Centre National de la Recherche Scientifique UMR 6290, Institut de Génétique et Développement de Rennes, Rennes 35000, France
| | - Stéphane Deschamps
- Université de Rennes 1, Université Européenne de Bretagne, Biosit, Rennes 35000, France; Centre National de la Recherche Scientifique UMR 6290, Institut de Génétique et Développement de Rennes, Rennes 35000, France
| | - Hubert Lerivray
- Université de Rennes 1, Université Européenne de Bretagne, Biosit, Rennes 35000, France; Centre National de la Recherche Scientifique UMR 6290, Institut de Génétique et Développement de Rennes, Rennes 35000, France
| | - Justine Viet
- Université de Rennes 1, Université Européenne de Bretagne, Biosit, Rennes 35000, France; Centre National de la Recherche Scientifique UMR 6290, Institut de Génétique et Développement de Rennes, Rennes 35000, France
| | - Serge Hardy
- Université de Rennes 1, Université Européenne de Bretagne, Biosit, Rennes 35000, France; Centre National de la Recherche Scientifique UMR 6290, Institut de Génétique et Développement de Rennes, Rennes 35000, France
| | - Luc Paillard
- Université de Rennes 1, Université Européenne de Bretagne, Biosit, Rennes 35000, France; Centre National de la Recherche Scientifique UMR 6290, Institut de Génétique et Développement de Rennes, Rennes 35000, France
| | - Yann Audic
- Université de Rennes 1, Université Européenne de Bretagne, Biosit, Rennes 35000, France; Centre National de la Recherche Scientifique UMR 6290, Institut de Génétique et Développement de Rennes, Rennes 35000, France.
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Riadi G, Ossandón F, Larraín J, Melo F. Towards the bridging of molecular genetics data across Xenopus species. BMC Genomics 2016; 17:161. [PMID: 26925848 PMCID: PMC4772642 DOI: 10.1186/s12864-016-2440-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Accepted: 02/05/2016] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The clawed African frog Xenopus laevis has been one of the main vertebrate models for studies in developmental biology. However, for genetic studies, Xenopus tropicalis has been the experimental model of choice because it shorter life cycle and due to a more tractable genome that does not result from genome duplication as in the case of X. laevis. Today, although still organized in a large number of scaffolds, nearly 85% of X. tropicalis and 89% of X. laevis genomes have been sequenced. There is expectation for a comparative physical map that can be used as a Rosetta Stone between X. laevis genetic studies and X. tropicalis genomic research. RESULTS In this work, we have mapped using coarse-grained alignment the 18 chromosomes of X. laevis, release 9.1, on the 10 reference scaffolds representing the haploid genome of X. tropicalis, release 9.0. After validating the mapping with theoretical data, and estimating reference averages of genome sequence identity, 37 to 44% between the two species, we have carried out a synteny analysis for 2,112 orthologous genes. We found that 99.6% of genes are in the same organization. CONCLUSIONS Taken together, our results make possible to establish the correspondence between 62 and 65.5% of both genomes, percentage of identity, synteny and automatic annotation of transcripts of both species, providing a new and more comprehensive tool for comparative analysis of these two species, by allowing to bridge molecular genetics data among them.
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Affiliation(s)
- Gonzalo Riadi
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile. .,Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca, Talca, Chile.
| | | | - Juan Larraín
- Center for Aging and Regeneration and Millennium Nucleus in Regenerative Biology, Santiago, Chile.
| | - Francisco Melo
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile.
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