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Talross GJS, Deryusheva S, Gall JG. Stable lariats bearing a snoRNA (slb-snoRNA) in eukaryotic cells: A level of regulation for guide RNAs. Proc Natl Acad Sci U S A 2021; 118:e2114156118. [PMID: 34725166 PMCID: PMC8609340 DOI: 10.1073/pnas.2114156118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2021] [Indexed: 12/31/2022] Open
Abstract
Small nucleolar (sno)RNAs guide posttranscriptional modifications essential for the biogenesis and function of their target. The majority of snoRNAs in higher eukaryotes are encoded within introns. They are first released from nascent transcripts in the form of a lariat and rapidly targeted by the debranching enzyme and nuclear exonucleases for linearization and further trimming. In this study, we report that some snoRNAs are encoded within unusually stable intronic RNAs. These intronic sequences can escape the debranching enzyme and accumulate as lariats. Stable lariats bearing a snoRNA, or slb-snoRNA, are associated with snoRNA binding proteins but do not guide posttranscriptional modification. While most slb-snoRNAs accumulate in the nucleus, some can be exported to the cytoplasm. We find that this export competes with snoRNA maturation. Slb-snoRNAs provide a previously unknown layer of regulation to snoRNA and snoRNA binding proteins.
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Affiliation(s)
- Gaëlle J S Talross
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218
| | - Svetlana Deryusheva
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218
| | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218
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2
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Abstract
In eukaryotes, rRNAs and spliceosomal snRNAs are heavily modified post-transcriptionally. Pseudouridylation and 2'-O-methylation are the most abundant types of RNA modifications. They are mediated by modification guide RNAs, also known as small nucleolar (sno)RNAs and small Cajal body-specific (sca)RNAs. We used yeast and vertebrate cells to test guide activities predicted for a number of snoRNAs, based on their regions of complementarity with rRNAs. We showed that human SNORA24 is a genuine guide RNA for 18S-Ψ609, despite some noncanonical base-pairing with its target. At the same time, we found quite a few snoRNAs that have the ability to base-pair with rRNAs and can induce predicted modifications in artificial substrate RNAs, but do not modify the same target sequence within endogenous rRNA molecules. Furthermore, certain fragments of rRNAs can be modified by the endogenous yeast modification machinery when inserted into an artificial backbone RNA, even though the same sequences are not modified in endogenous yeast rRNAs. In Xenopus cells, a guide RNA generated from scaRNA, but not from snoRNA, could induce an additional pseudouridylation of U2 snRNA at position 60; both guide RNAs were equally active on a U2 snRNA-specific substrate in yeast cells. Thus, post-transcriptional modification of functionally important RNAs, such as rRNAs and snRNAs, is highly regulated and more complex than simply strong base-pairing between a guide RNA and substrate RNA. We discuss possible regulatory roles for these unexpected modifications.
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Affiliation(s)
- Svetlana Deryusheva
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
| | - Gaëlle J S Talross
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
| | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
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3
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Bizarro J, Deryusheva S, Wacheul L, Gupta V, Ernst FGM, Lafontaine DLJ, Gall JG, Meier UT. Nopp140-chaperoned 2'-O-methylation of small nuclear RNAs in Cajal bodies ensures splicing fidelity. Genes Dev 2021; 35:1123-1141. [PMID: 34301768 PMCID: PMC8336889 DOI: 10.1101/gad.348660.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/29/2021] [Indexed: 12/27/2022]
Abstract
In this study, Bizarro et al. sought to understand the function and subcellular site of snRNA modification, and found that Cajal body (CB) localization of the protein Nopp140 is essential for concentration of small Cajal body-specific ribonucleoproteins (scaRNPs) in nuclear condensate and that phosphorylation by casein kinase 2 (CK2) at ∼80 serines targets Nopp140 to CBs. Nopp140 knockdown-mediated release of scaRNPs from CBs severely compromises 2′-O-methylation of spliceosomal snRNAs, identifying CBs as the site of scaRNP catalysis. Spliceosomal small nuclear RNAs (snRNAs) are modified by small Cajal body (CB)-specific ribonucleoproteins (scaRNPs) to ensure snRNP biogenesis and pre-mRNA splicing. However, the function and subcellular site of snRNA modification are largely unknown. We show that CB localization of the protein Nopp140 is essential for concentration of scaRNPs in that nuclear condensate; and that phosphorylation by casein kinase 2 (CK2) at ∼80 serines targets Nopp140 to CBs. Transiting through CBs, snRNAs are apparently modified by scaRNPs. Indeed, Nopp140 knockdown-mediated release of scaRNPs from CBs severely compromises 2′-O-methylation of spliceosomal snRNAs, identifying CBs as the site of scaRNP catalysis. Additionally, alternative splicing patterns change indicating that these modifications in U1, U2, U5, and U12 snRNAs safeguard splicing fidelity. Given the importance of CK2 in this pathway, compromised splicing could underlie the mode of action of small molecule CK2 inhibitors currently considered for therapy in cholangiocarcinoma, hematological malignancies, and COVID-19.
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Affiliation(s)
| | | | - Ludivine Wacheul
- RNA Molecular Biology, Fonds National de la Recherche Scientifique (FRS/FNRS), Université Libre de Bruxelles (ULB), B-6041 Gosselies, Belgium
| | - Varun Gupta
- Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Felix G M Ernst
- RNA Molecular Biology, Fonds National de la Recherche Scientifique (FRS/FNRS), Université Libre de Bruxelles (ULB), B-6041 Gosselies, Belgium
| | - Denis L J Lafontaine
- RNA Molecular Biology, Fonds National de la Recherche Scientifique (FRS/FNRS), Université Libre de Bruxelles (ULB), B-6041 Gosselies, Belgium
| | - Joseph G Gall
- Carnegie Institution for Science, Baltimore, Maryland 21218, USA
| | - U Thomas Meier
- Albert Einstein College of Medicine, Bronx, New York 10461, USA
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4
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Bizarro J, Deryusheva S, Wacheul L, Gupta V, Ernst FGM, Lafontaine DLJ, Gall JG, Meier UT. Nopp140-chaperoned 2'-O-methylation of small nuclear RNAs in Cajal bodies ensures splicing fidelity. bioRxiv 2021:2021.04.29.441821. [PMID: 33948588 PMCID: PMC8095195 DOI: 10.1101/2021.04.29.441821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Spliceosomal small nuclear RNAs (snRNAs) are modified by small Cajal body (CB) specific ribonucleoproteins (scaRNPs) to ensure snRNP biogenesis and pre-mRNA splicing. However, the function and subcellular site of snRNA modification are largely unknown. We show that CB localization of the protein Nopp140 is essential for concentration of scaRNPs in that nuclear condensate; and that phosphorylation by casein kinase 2 (CK2) at some 80 serines targets Nopp140 to CBs. Transiting through CBs, snRNAs are apparently modified by scaRNPs. Indeed, Nopp140 knockdown-mediated release of scaRNPs from CBs severely compromises 2'-O-methylation of spliceosomal snRNAs, identifying CBs as the site of scaRNP catalysis. Additionally, alternative splicing patterns change indicating that these modifications in U1, U2, U5, and U12 snRNAs safeguard splicing fidelity. Given the importance of CK2 in this pathway, compromised splicing could underlie the mode of action of small molecule CK2 inhibitors currently considered for therapy in cholangiocarcinoma, hematological malignancies, and COVID-19.
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5
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Keinath MC, Davidian A, Timoshevskiy V, Timoshevskaya N, Gall JG. Characterization of axolotl lampbrush chromosomes by fluorescence in situ hybridization and immunostaining. Exp Cell Res 2021; 401:112523. [PMID: 33675804 PMCID: PMC8123938 DOI: 10.1016/j.yexcr.2021.112523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 02/08/2021] [Accepted: 02/15/2021] [Indexed: 10/25/2022]
Abstract
The lampbrush chromosomes (LBCs) in oocytes of the Mexican axolotl (Ambystoma mexicanum) were identified some time ago by their relative lengths and predicted centromeres, but they have never been associated completely with the mitotic karyotype, linkage maps or genome assembly. We identified 9 of the axolotl LBCs using RNAseq to identify actively transcribed genes and 13 BAC (bacterial artificial clone) probes containing pieces of active genes. Using read coverage analysis to find candidate centromere sequences, we developed a centromere probe that localizes to all 14 centromeres. Measurements of relative LBC arm lengths and polymerase III localization patterns enabled us to identify all LBCs. This study presents a relatively simple and reliable way to identify each axolotl LBC cytologically and to anchor chromosome-length sequences (from the axolotl genome assembly) to the physical LBCs by immunostaining and fluorescence in situ hybridization. Our data will facilitate a more detailed transcription analysis of individual LBC loops.
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Affiliation(s)
| | - Asya Davidian
- Carnegie Institution for Science, Baltimore, MD, USA; Saint Petersburg State University, Saint Petersburg, Russia
| | | | | | - Joseph G Gall
- Carnegie Institution for Science, Baltimore, MD, USA.
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6
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Liu JL, Gall JG. Cold shock induces novel nuclear bodies in Xenopus oocytes. Exp Cell Res 2021; 398:112386. [PMID: 33220259 PMCID: PMC7771896 DOI: 10.1016/j.yexcr.2020.112386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 11/22/2022]
Abstract
Here we describe novel spherical structures that are induced by cold shock on the lampbrush chromosomes (LBCs) of Xenopus laevis oocytes. We call these structures cold bodies or C-bodies. C-bodies are distributed symmetrically on homologous LBCs, with a pattern similar to that of 5S rDNA. Neither active transcription nor translation is necessary for their formation. Similar protrusions occur on the edges of some nucleoli. Endogenous LBCs as well as those derived from injected sperm form C-bodies under cold shock conditions. The function of C-bodies is unknown.
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Affiliation(s)
- Ji-Long Liu
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA; Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK; School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA.
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Hurlock ME, Čavka I, Kursel LE, Haversat J, Wooten M, Nizami Z, Turniansky R, Hoess P, Ries J, Gall JG, Rog O, Köhler S, Kim Y. Identification of novel synaptonemal complex components in C. elegans. J Cell Biol 2020; 219:e201910043. [PMID: 32211899 PMCID: PMC7199856 DOI: 10.1083/jcb.201910043] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 02/04/2020] [Accepted: 02/26/2020] [Indexed: 11/22/2022] Open
Abstract
The synaptonemal complex (SC) is a tripartite protein scaffold that forms between homologous chromosomes during meiosis. Although the SC is essential for stable homologue pairing and crossover recombination in diverse eukaryotes, it is unknown how individual components assemble into the highly conserved SC structure. Here we report the biochemical identification of two new SC components, SYP-5 and SYP-6, in Caenorhabditis elegans. SYP-5 and SYP-6 are paralogous to each other and play redundant roles in synapsis, providing an explanation for why these genes have evaded previous genetic screens. Superresolution microscopy reveals that they localize between the chromosome axes and span the width of the SC in a head-to-head manner, similar to the orientation of other known transverse filament proteins. Using genetic redundancy and structure-function analyses to truncate C-terminal tails of SYP-5/6, we provide evidence supporting the role of SC in both limiting and promoting crossover formation.
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Affiliation(s)
| | - Ivana Čavka
- The European Molecular Biology Laboratory, Heidelberg, Germany
| | - Lisa E. Kursel
- School of Biological Sciences, University of Utah, Salt Lake City, UT
| | | | - Matthew Wooten
- Department of Biology, Johns Hopkins University, Baltimore, MD
| | - Zehra Nizami
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD
| | | | - Philipp Hoess
- The European Molecular Biology Laboratory, Heidelberg, Germany
- Collaboration for joint PhD degree between European Molecular Biology Laboratory and Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Jonas Ries
- The European Molecular Biology Laboratory, Heidelberg, Germany
| | - Joseph G. Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD
| | - Ofer Rog
- School of Biological Sciences, University of Utah, Salt Lake City, UT
| | - Simone Köhler
- The European Molecular Biology Laboratory, Heidelberg, Germany
| | - Yumi Kim
- Department of Biology, Johns Hopkins University, Baltimore, MD
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8
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Gall JG. The Third Lens: Metaphor and the creation of modern cell biologyAndrew S.ReynoldsChicago, IL: University of Chicago Press, 2018. FASEB J 2020. [DOI: 10.1096/fj.202000721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Joseph G. Gall
- Department of Embryology Carnegie Institution for Science Baltimore MD USA
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9
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Abstract
Small nucleolar RNAs (snoRNAs) function primarily as guide RNAs for posttranscriptional modification of rRNAs and spliceosomal snRNAs, both of which are functionally important and evolutionarily conserved molecules. It is commonly believed that snoRNAs and the modifications they mediate are highly conserved across species. However, most relevant data on snoRNA annotation and RNA modification are limited to studies on human and yeast. Here, we used RNA-sequencing data from the giant oocyte nucleus of the frog Xenopus tropicalis to annotate a nearly complete set of snoRNAs. We compared the frog data with snoRNA sets from human and other vertebrate genomes, including mammals, birds, reptiles, and fish. We identified many Xenopus-specific (or nonhuman) snoRNAs and Xenopus-specific domains in snoRNAs from conserved RNA families. We predicted that some of these nonhuman snoRNAs and domains mediate modifications at unexpected positions in rRNAs and snRNAs. These modifications were mapped as predicted when RNA modification assays were applied to RNA from nine vertebrate species: frogs X. tropicalis and X. laevis, newt Notophthalmus viridescens, axolotl Ambystoma mexicanum, whiptail lizard Aspidoscelis neomexicana, zebrafish Danio rerio, chicken, mouse, and human. This analysis revealed that only a subset of RNA modifications is evolutionarily conserved and that modification patterns may vary even between closely related species. We speculate that each functional domain in snoRNAs (half of an snoRNA) may evolve independently and shuffle between different snoRNAs.
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Affiliation(s)
| | | | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD
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10
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Abstract
Although the nucleolus was first described in the early 19th century from both animal and plant cells, human nucleoli and particularly the five human nucleolus organizers have not been well characterized. In this issue of Genes & Development, van Sluis and colleagues (pp. 1688-1701) present a detailed molecular analysis of these organizers, which occur on the short arms of five human chromosomes. The near identity of these arms suggests extensive interchromosomal exchange during evolutionary history.
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Affiliation(s)
- Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
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11
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Deryusheva S, Gall JG. Small, Smaller, Smallest: Minimal Structural Requirements for a Fully Functional Box C/D Modification Guide RNA. Biomolecules 2019; 9:E457. [PMID: 31500270 PMCID: PMC6770171 DOI: 10.3390/biom9090457] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 08/29/2019] [Accepted: 09/06/2019] [Indexed: 01/08/2023] Open
Abstract
Site-specific 2'-O-ribose methylation is an abundant post-transcriptional modification mediated by small non-coding nuclear RNAs known as box C/D modification guide RNAs. The minimal structural requirements for these guide RNAs to function in higher eukaryotes are still unclear. To address this question, we generated a series of mutant variants of Drosophila box C/D scaRNA:MeU2-C28 and tested their modification guide activities in the Xenopus oocyte system. Our data suggest that box C/D guide RNA function requires either a terminal or an internal consensus kink-turn structure. We identified the minimal functional box C/D guide RNA. It consists of a single-domain molecule with (i) a terminal stem with a consensus kink-turn domain, (ii) one box C and box D connected by a 14-nucleotide antisense element and (iii) a one-nucleotide spacer between the box C and the antisense element. In this single domain RNA, the sequence of the spacer is more important than its length. We suggest that the secondary structure of box C/D RNAs, essential for guide RNA function, is more complex than generally supposed. At the same time, the expression of functional extremely short single-domain box C/D RNAs is possible in higher eukaryotes.
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Affiliation(s)
- Svetlana Deryusheva
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA.
| | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA.
- Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA.
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12
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Abstract
Posttranscriptional modifications of rRNA occur in the nucleolus where rRNA modification guide RNAs, or snoRNAs, concentrate. On the other hand, scaRNAs, the modification guide RNAs for spliceosomal snRNAs, concentrate in the Cajal body (CB). It is generally assumed, therefore, that snRNAs must accumulate in CBs to be modified by scaRNAs. Here we demonstrate that the evidence for the latter postulate is not consistent. In the nucleus, scaRNA localization is not limited to CBs. Furthermore, canonical scaRNAs can modify rRNAs. We suggest that the conventional view that scaRNAs function only in the CB needs revision.
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MESH Headings
- Animals
- Base Sequence
- Coiled Bodies/metabolism
- HeLa Cells
- Humans
- Nucleic Acid Conformation
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Small Nuclear/chemistry
- RNA, Small Nuclear/genetics
- RNA, Small Nuclear/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Spliceosomes/genetics
- Spliceosomes/metabolism
- Xenopus/genetics
- Xenopus/metabolism
- RNA, Guide, CRISPR-Cas Systems
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Affiliation(s)
- Svetlana Deryusheva
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
| | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
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13
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Affiliation(s)
- Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA.
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14
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Abstract
We report that 7SL, the RNA component of the signal recognition particle (SRP), is an abundant noncoding RNA (ncRNA) in mature red blood cells (RBCs) of human, mouse, and the frog Xenopus. 7SL RNA in RBCs is not associated with the canonical proteins of the SRP. Instead, it coimmunoprecipitates from a lysate of RBCs with a number of membrane-binding proteins. Human and mouse RBCs also contain a previously undescribed 68 nt RNA, sRN7SL, derived from the "S domain" of 7SL RNA. We discuss the possibility that 7SL RNA is selectively protected from nucleases by association with the RBC membrane. Because 7SL is not associated with the canonical proteins of the SRP, it could represent a nonfunctional remnant of the protein synthetic machinery. Alternatively, it could play a new, as yet undefined role in RBC metabolism.
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Affiliation(s)
- Gaëlle J S Talhouarne
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
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Deryusheva S, Gall JG. Orchestrated positioning of post-transcriptional modifications at the branch point recognition region of U2 snRNA. RNA 2018; 24:30-42. [PMID: 28974555 PMCID: PMC5733568 DOI: 10.1261/rna.063842.117] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 09/25/2017] [Indexed: 05/21/2023]
Abstract
The branch point recognition region of spliceosomal snRNA U2 is heavily modified post-transcriptionally in most eukaryotic species. We focused on this region to learn how nearby positions may interfere with each other when targeted for modification. Using an in vivo yeast Saccharomyces cerevisiae cell system, we tested the modification activity of several guide RNAs from human, mouse, the frog Xenopus tropicalis, the fruit fly Drosophila melanogaster, and the worm Caenorhabditis elegans We experimentally verified predictions for vertebrate U2 modification guide RNAs SCARNA4 and SCARNA15, and identified a C. elegans ortholog of SCARNA15. We observed crosstalk between sites in the heavily modified regions, such that modification at one site may inhibit modification at nearby sites. This is true for the branch point recognition region of U2 snRNA, the 5' loop of U5 snRNA, and certain regions of rRNAs, when tested either in yeast or in HeLa cells. The position preceding a uridine targeted for isomerization by a box H/ACA guide RNA is the most sensitive for noncanonical base-pairing and modification (either pseudouridylation or 2'-O-methylation). Based on these findings, we propose that modification must occur stepwise starting with the most vulnerable positions and ending with the most inhibiting modifications. We discuss possible strategies that cells use to reach complete modification in heavily modified regions.
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Affiliation(s)
- Svetlana Deryusheva
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
| | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
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16
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Deryusheva S, Gall JG. Dual nature of pseudouridylation in U2 snRNA: Pus1p-dependent and Pus1p-independent activities in yeasts and higher eukaryotes. RNA 2017; 23:1060-1067. [PMID: 28432181 PMCID: PMC5473140 DOI: 10.1261/rna.061226.117] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 04/18/2017] [Indexed: 05/05/2023]
Abstract
The pseudouridine at position 43 in vertebrate U2 snRNA is one of the most conserved post-transcriptional modifications of spliceosomal snRNAs; the equivalent position is pseudouridylated in U2 snRNAs in different phyla including fungi, insects, and worms. Pseudouridine synthase Pus1p acts alone on U2 snRNA to form this pseudouridine in yeast Saccharomyces cerevisiae and mouse. Furthermore, in S. cerevisiae, Pus1p is the only pseudouridine synthase for this position. Using an in vivo yeast cell system, we tested enzymatic activity of Pus1p from the fission yeast Schizosaccharomyces pombe, the worm Caenorhabditis elegans, the fruit fly Drosophila melanogaster, and the frog Xenopus tropicalis We demonstrated that Pus1p from C. elegans has no enzymatic activity on U2 snRNA when expressed in yeast cells, whereas in similar experiments, position 44 in yeast U2 snRNA (equivalent to position 43 in vertebrates) is a genuine substrate for Pus1p from S. cerevisiae, S. pombe, Drosophila, Xenopus, and mouse. However, when we analyzed U2 snRNAs from Pus1 knockout mice and the pus1Δ S. pombe strain, we could not detect any changes in their modification patterns when compared to wild-type U2 snRNAs. In S. pombe, we found a novel box H/ACA RNA encoded downstream from the RPC10 gene and experimentally verified its guide RNA activity for positioning Ψ43 and Ψ44 in U2 snRNA. In vertebrates, we showed that SCARNA8 (also known as U92 scaRNA) is a guide for U2-Ψ43 in addition to its previously established targets U2-Ψ34/Ψ44.
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Affiliation(s)
- Svetlana Deryusheva
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
| | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
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17
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Abstract
We describe methods for studying the giant transcriptionally active lampbrush chromosomes (LBCs) found in the oocyte, or unlaid egg, of frogs and salamanders. Individual LBCs can be up to 1 mm in length and they reside in a gigantic nucleus, itself up to 0.5 mm in diameter. The large size of the chromosomes permits unparalleled observations of active genes by light optical microscopy, but at the same time special techniques are required for isolating the nucleus, removing the nuclear envelope, and spreading the chromosomes on a microscope slide. The oocyte nucleus, also called the germinal vesicle (GV), is isolated in a medium that allows partial gelling of the nuclear actin and preserves the delicate structure of the LBCs. This step is carried out manually under a dissecting microscope using jeweler's forceps. Next, the nuclear envelope is removed, again manually with jeweler's forceps. The nuclear contents are quickly transferred to a medium that disperses the actin gel and allows the undamaged LBCs to settle onto a microscope slide. At this point the LBCs and other nuclear organelles can be viewed by phase contrast or differential interference contrast microscopy, although finer details are obscured by Brownian motion. For high resolution microscopical observation or molecular analysis, the whole preparation is centrifuged to attach the delicate LBCs firmly to the slide. A brief fixation in paraformaldehyde is then followed by immunofluorescent staining or in situ hybridization. LBCs are in a transcriptionally active state and their enormous size permits molecular analysis at the individual gene level using confocal or super-resolution microscopy.
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Affiliation(s)
- Joseph G Gall
- Department of Embryology, Carnegie Institution for Science;
| | - Zehra F Nizami
- Department of Embryology, Carnegie Institution for Science
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18
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Craddock EM, Gall JG, Jonas M. Hawaiian Drosophila genomes: size variation and evolutionary expansions. Genetica 2016; 144:107-24. [PMID: 26790663 DOI: 10.1007/s10709-016-9882-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 01/09/2016] [Indexed: 01/24/2023]
Abstract
This paper reports genome sizes of one Hawaiian Scaptomyza and 16 endemic Hawaiian Drosophila species that include five members of the antopocerus species group, one member of the modified mouthpart group, and ten members of the picture wing clade. Genome size expansions have occurred independently multiple times among Hawaiian Drosophila lineages, and have resulted in an over 2.3-fold range of genome sizes among species, with the largest observed in Drosophila cyrtoloma (1C = 0.41 pg). We find evidence that these repeated genome size expansions were likely driven by the addition of significant amounts of heterochromatin and satellite DNA. For example, our data reveal that the addition of seven heterochromatic chromosome arms to the ancestral haploid karyotype, and a remarkable proportion of ~70 % satellite DNA, account for the greatly expanded size of the D. cyrtoloma genome. Moreover, the genomes of 13/17 Hawaiian picture wing species are composed of substantial proportions (22-70 %) of detectable satellites (all but one of which are AT-rich). Our results suggest that in this tightly knit group of recently evolved species, genomes have expanded, in large part, via evolutionary amplifications of satellite DNA sequences in centric and pericentric domains (especially of the X and dot chromosomes), which have resulted in longer acrocentric chromosomes or metacentrics with an added heterochromatic chromosome arm. We discuss possible evolutionary mechanisms that may have shaped these patterns, including rapid fixation of novel expanded genomes during founder-effect speciation.
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Affiliation(s)
- Elysse M Craddock
- Natural Sciences Building, Purchase College, State University of New York, 735 Anderson Hill Road, Purchase, NY, 10577, USA.
| | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, USA
| | - Mark Jonas
- Natural Sciences Building, Purchase College, State University of New York, 735 Anderson Hill Road, Purchase, NY, 10577, USA
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19
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Abstract
In situ hybridization is the technique by which specific RNA or DNA molecules are detected in cytological preparations. Basically it involves formation of a hybrid molecule between an endogenous single-stranded RNA or DNA in the cell and a complementary single-stranded RNA or DNA probe. In its original form the probe was labeled with (3)H and the hybrid was detected by autoradiography. The first successful experiments in 1968 involved detection of the highly amplified ribosomal DNA in oocytes of the frog Xenopus, followed soon after by the reiterated "satellite DNA" in mouse and Drosophila chromosomes. Fluorescent probes were developed about ten years later.
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Affiliation(s)
- Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, United States.
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20
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Abstract
Fluorescent in situ hybridization (FISH) is a technique for determining the cytological localization of RNA or DNA molecules. There are many approaches available for generating in situ hybridization probes and conducting the subsequent hybridization steps. Here, we describe a simple and reliable FISH method to label small RNAs (200-500 nucleotides in length) that are enriched in nuclear bodies in Drosophila melanogaster ovaries, such as Cajal bodies (CBs) and histone locus bodies (HLBs). This technique can also be applied to other Drosophila tissues, and to abundant mRNAs such as histone transcripts.
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Affiliation(s)
- Zehra F Nizami
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
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21
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Abstract
We previously demonstrated that the oocyte nucleus (germinal vesicle or GV) of Xenopus tropicalis contains a population of stable RNA molecules derived from the introns of most expressed genes. Here we show that similar stable intronic sequence (sis) RNAs occur in the oocyte cytoplasm. About 9000 cytoplasmic sisRNAs have been identified, all of which are resistant to the exonuclease RNase R. About half have been confirmed as lariat molecules and the rest are presumed to be lariats, whereas nuclear sisRNAs are a mixture of lariat and linear molecules. Cytoplasmic sisRNAs are more abundant on a molar basis than nuclear sisRNAs and are derived from short introns, mostly under 1 kb in length. Both nuclear and cytoplasmic sisRNAs are transmitted intact to the egg at GV breakdown and persist until at least the blastula stage of embryogenesis, when zygotic transcription begins. We compared cytoplasmic sisRNAs derived from orthologous genes of X. tropicalis and X. laevis, and found that the specific introns from which sisRNAs are derived are not conserved. The existence of sisRNAs in the cytoplasm of the oocyte, their transmission to the fertilized egg, and their persistence during early embryogenesis suggest that they might play a regulatory role in mRNA translation.
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Affiliation(s)
- Gaëlle J S Talhouarne
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA Department of Biology, Mudd Hall, Johns Hopkins University, Baltimore, Maryland 21218, USA
| | - Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA Department of Biology, Mudd Hall, Johns Hopkins University, Baltimore, Maryland 21218, USA
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22
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Deryusheva S, Gall JG. Novel small Cajal-body-specific RNAs identified in Drosophila: probing guide RNA function. RNA 2013; 19:1802-14. [PMID: 24149844 PMCID: PMC3884663 DOI: 10.1261/rna.042028.113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Accepted: 09/23/2013] [Indexed: 05/05/2023]
Abstract
The spliceosomal small nuclear RNAs (snRNAs) are modified post-transcriptionally by introduction of pseudouridines and 2'-O-methyl modifications, which are mediated by box H/ACA and box C/D guide RNAs, respectively. Because of their concentration in the nuclear Cajal body (CB), these guide RNAs are known as small CB-specific (sca) RNAs. In the cell, scaRNAs are associated with the WD-repeat protein WDR79. We used coimmunoprecipitation with WDR79 to recover seven new scaRNAs from Drosophila cell lysates. We demonstrated concentration of these new scaRNAs in the CB by in situ hybridization, and we verified experimentally that they can modify their putative target RNAs. Surprisingly, one of the new scaRNAs targets U6 snRNA, whose modification is generally assumed to occur in the nucleolus, not in the CB. Two other scaRNAs have dual guide functions, one for an snRNA and one for 28S rRNA. Again, the modification of 28S rRNA is assumed to take place in the nucleolus. These findings suggest that canonical scaRNAs may have functions in addition to their established role in modifying U1, U2, U4, and U5 snRNAs. We discuss the likelihood that processing by scaRNAs is not limited to the CB.
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Affiliation(s)
- Svetlana Deryusheva
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
| | - Joseph G. Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
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23
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Nizami ZF, Gall JG. Pearls are novel Cajal body-like structures in the Xenopus germinal vesicle that are dependent on RNA pol III transcription. Chromosome Res 2013; 20:953-69. [PMID: 23135638 DOI: 10.1007/s10577-012-9320-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We have identified novel nuclear bodies, which we call pearls, in the giant oocyte nuclei of Xenopus laevis and Xenopus tropicalis. Pearls are attached to the lampbrush chromosomes at specific loci that are transcribed by RNA polymerase III, and they disappear after inhibition of polymerase III activity. Pearls are enriched for small Cajal body-specific RNAs (scaRNAs), which are guide RNAs that modify specific nucleotides on splicing snRNAs. Surprisingly, snRNAs themselves are not present in pearls, suggesting that pearls are not functionally equivalent to Cajal bodies in other systems, which contain both snRNAs and scaRNAs. We suggest that pearls may function in the processing of RNA polymerase III transcripts, such as tRNA, 5S rRNA, and other short non-coding RNAs.
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Affiliation(s)
- Zehra F Nizami
- Department of Embryology, Carnegie Institution for Science, 3520 San Martin Drive, Baltimore, MD 21218, USA
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24
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Gardner EJ, Nizami ZF, Talbot CC, Gall JG. Stable intronic sequence RNA (sisRNA), a new class of noncoding RNA from the oocyte nucleus of Xenopus tropicalis. Genes Dev 2013; 26:2550-9. [PMID: 23154985 DOI: 10.1101/gad.202184.112] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
To compare nuclear and cytoplasmic RNA from a single cell type, free of cross-contamination, we studied the oocyte of the frog Xenopus tropicalis, a giant cell with an equally giant nucleus. We isolated RNA from manually dissected nuclei and cytoplasm of mature oocytes and subjected it to deep sequencing. Cytoplasmic mRNA consisted primarily of spliced exons derived from ∼6700 annotated genes. Nearly all of these genes were represented in the nucleus by intronic sequences. However, unspliced nascent transcripts were not detected. Inhibition of transcription or splicing for 1-2 d had little or no effect on the abundance of nuclear intronic sequences, demonstrating that they are unusually stable. RT-PCR analysis showed that these stable intronic sequences are transcribed from the coding strand and that a given intron can be processed into more than one molecule. Stable intronic sequence RNA (sisRNA) from the oocyte nucleus constitutes a new class of noncoding RNA. sisRNA is detectable by RT-PCR in samples of total RNA from embryos up to the mid-blastula stage, when zygotic transcription begins. Storage of sisRNA in the oocyte nucleus and its transmission to the developing embryo suggest that it may play important regulatory roles during oogenesis and/or early embryogenesis.
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Affiliation(s)
- Eugene J Gardner
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
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25
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Abstract
The survival of motor neuron (SMN) protein plays an important role in the biogenesis of spliceosomal snRNPs and is one factor required for the integrity of nuclear Cajal bodies (CBs). CBs are enriched in small CB-specific (sca) RNAs, which guide the formation of pseudouridylated and 2'-O-methylated residues in the snRNAs. Because SMN-deficient cells lack typical CBs, we asked whether the modification of internal residues of major and minor snRNAs is defective in these cells. We mapped modified nucleotides in the major U2 and the minor U4atac and U12 snRNAs. Using both radioactive and fluorescent primer extension approaches, we found that modification of major and minor spliceosomal snRNAs is normal in SMN-deficient cells. Our experiments also revealed a previously undetected pseudouridine at position 60 in human U2 and 2'-O-methylation of A1, A2, and G19 in human U4atac. These results confirm, and extend to minor snRNAs, previous experiments showing that scaRNPs can function in the absence of typical CBs. Furthermore, they show that the differential splicing defects in SMN-deficient cells are not due to failure of post-transcriptional modification of either major or minor snRNAs.
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Affiliation(s)
| | - Maria Choleza
- Institut de Génétique Moléculaire de Montpellier (IGMM), CNRS UMR 5535/IFR122, Université Montpellier, 34293 Montpellier Cedex 5, France
| | - Adrien Barbarossa
- Institut de Génétique Moléculaire de Montpellier (IGMM), CNRS UMR 5535/IFR122, Université Montpellier, 34293 Montpellier Cedex 5, France
| | | | - Rémy Bordonné
- Institut de Génétique Moléculaire de Montpellier (IGMM), CNRS UMR 5535/IFR122, Université Montpellier, 34293 Montpellier Cedex 5, France
- Corresponding author.E-mail .
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26
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Abstract
When living egg chambers of Drosophila are isolated in a saline solution and gently squashed between a microscope slide and coverslip, prominent nuclear bodies (1 - 20 mm diameter) can be seen inside the oocyte nucleus or germinal vesicle (GV). These bodies do not pre-exist within the GV and are not seen in material that is fixed in paraformaldehyde before squashing. Instead, they form spontaneously within minutes after an egg chamber is damaged and the cytoplasm is exposed to the isolation medium. Electron microscopy shows that the bodies lack an investing membrane and consist of closely packed, irregular particles 30-50 nm in diameter. We used GFP-tagged proteins from the Carnegie Protein Trap Library to identify 22 proteins that are either enriched in the bodies or excluded from them. We were unable to discern common features of proteins that are concentrated in the bodies, such as isoelectric point, molecular weight, or biological process. Induced bodies are formed in GVs of flies that are null for coilin or WDR79, proteins that are required for formation of Cajal bodies (CBs). We performed fluorescence recovery after photobleaching (FRAP) experiments on five GFP-tagged proteins that are enriched in the bodies. Four of the proteins regained the full pre-bleach fluorescence intensity, indicating that the contents of the bodies are in dynamic equilibrium with the surrounding nucleoplasm. Induced nuclear bodies presumably form as a result of unusual physico-chemical changes in the Drosophila GV. We suggest that their behavior serves as a useful model for self-assembly of nuclear bodies in general, and we discuss the possibility that similar bodies may occur normally in cells of other organisms.
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Affiliation(s)
- Alison B Singer
- Department of Embryology, Carnegie Institution for Science, Baltimore MD, USA
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27
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Abstract
Endopolyploidy arises during normal development in many species when cells undergo endocycles-variant cell cycles in which DNA replicates but daughter cells do not form. Normally, polyploid cells do not divide mitotically after initiating endocycles; hence, little is known about their mitotic competence. However, polyploid cells are found in many tumors, and the enhanced chromosomal instability of polyploid cells in culture suggests that such cells contribute to tumor aneuploidy. Here, we describe a novel polyploid Drosophila cell type that undergoes normal mitotic cycles as part of a remodeling process that forms the adult rectal papillae. Similar polyploid mitotic divisions, but not depolyploidizing divisions, were observed during adult ileum development in the mosquito Culex pipiens. Extended anaphases, chromosome bridges, and lagging chromosomes were frequent during these polyploid divisions, despite normal expression of cell cycle regulators. Our results show that the switch to endocycles during development is not irreversible, but argue that the polyploid mitotic cycle is inherently error-prone, and that polyploid mitoses may help destabilize the cancer genome.
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Affiliation(s)
- Donald T Fox
- Howard Hughes Medical Institute Research Laboratories, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
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28
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Abstract
The organization of the cell nucleus into specialized compartments is important for nuclear function. We address the significance of compartmentalization by studying the Cajal body, an evolutionarily conserved nuclear organelle proposed to be involved in such diverse functions as assembly of the spliceosome, assembly of the transcription machinery, and modification of spliceosomal small nuclear RNAs. The Cajal body is typically identified by the presence of coilin, a protein of poorly defined function. Here, we demonstrate that coilin is not a unique Cajal body marker but also occurs in a related yet distinct nuclear organelle known as the histone locus body in both Drosophila and Xenopus. We stress the importance of multiple markers not only for identification of nuclear bodies but also for assessing their functional significance.
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Affiliation(s)
- Z F Nizami
- Carnegie Institution for Science, Baltimore, Maryland 21218, USA
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29
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Chen M, Chang JS, Nason M, Rangel D, Gall JG, Graham BS, Ledgerwood JE. A flow cytometry-based assay to assess RSV-specific neutralizing antibody is reproducible, efficient and accurate. J Immunol Methods 2010; 362:180-4. [PMID: 20727896 DOI: 10.1016/j.jim.2010.08.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2010] [Revised: 07/20/2010] [Accepted: 08/11/2010] [Indexed: 11/20/2022]
Abstract
Respiratory syncytial virus (RSV) is an important cause of respiratory infection in people of all ages, and is the leading cause of hospitalization in infants. Although commercially available monoclonal antibody is available for passive prophylaxis of neonates at risk of severe disease, there is no available vaccine to prevent RSV. Measurement of neutralizing activity will be a key endpoint for vaccine evaluation. Assessment of neutralizing antibody against RSV has been limited to traditional plaque reduction, which is time-consuming and inherently operator dependent and highly variable. Here, we describe a flow cytometry-based RSV-specific neutralization assay which is more rapid than traditional methods, highly sensitive and highly reproducible.
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Affiliation(s)
- M Chen
- Viral Pathogenesis Laboratory and Clinical Trials Core, Vaccine Research Center, National Institutes of Allergy and Infectious Diseases, National Institutes of Health, US Department of Health and Human Services, 40 Convent Drive, Bethesda, MD 20892, United States
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30
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Abstract
The Cajal body (CB) is a nuclear organelle present in all eukaryotes that have been carefully studied. It is identified by the signature protein coilin and by CB-specific RNAs (scaRNAs). CBs contain high concentrations of splicing small nuclear ribonucleoproteins (snRNPs) and other RNA processing factors, suggesting that they are sites for assembly and/or posttranscriptional modification of the splicing machinery of the nucleus. The histone locus body (HLB) contains factors required for processing histone pre-mRNAs. As its name implies, the HLB is associated with the genes that code for histones, suggesting that it may function to concentrate processing factors at their site of action. CBs and HLBs are present throughout the interphase of the cell cycle, but disappear during mitosis. The biogenesis of CBs shows the features of a self-organizing structure.
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Affiliation(s)
- Zehra Nizami
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA
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31
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Gall JG, Wu Z. Examining the contents of isolated Xenopus germinal vesicles. Methods 2010; 51:45-51. [PMID: 20060047 DOI: 10.1016/j.ymeth.2009.12.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Revised: 12/22/2009] [Accepted: 12/23/2009] [Indexed: 11/29/2022] Open
Abstract
One can manually isolate the giant oocyte nucleus or germinal vesicle (GV) of Xenopus from a living oocyte with nothing more complicated than jewelers' forceps and a dissecting microscope. Similarly, one can remove the nuclear envelope by hand and allow the lampbrush chromosomes and other nuclear organelles to spread on a microscope slide. After centrifugation, the nuclear contents adhere tightly to the slide, where they can be subjected to immunostaining or fluorescent in situ hybridization for visualization by conventional or confocal microscopy. Preparations of isolated GV contents reveal details of nuclear structure that are almost impossible to attain by more conventional techniques.
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Affiliation(s)
- Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218, USA.
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32
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Deryusheva S, Gall JG. Small Cajal body-specific RNAs of Drosophila function in the absence of Cajal bodies. Mol Biol Cell 2009; 20:5250-9. [PMID: 19846657 PMCID: PMC2793299 DOI: 10.1091/mbc.e09-09-0777] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Revised: 09/29/2009] [Accepted: 10/09/2009] [Indexed: 12/17/2022] Open
Abstract
During their biogenesis small nuclear RNAs (snRNAs) undergo multiple covalent modifications that require guide RNAs to direct methylase and pseudouridylase enzymes to the appropriate nucleotides. Because of their localization in the nuclear Cajal body (CB), these guide RNAs are known as small CB-specific RNAs (scaRNAs). Using a fluorescent primer extension technique, we mapped the modified nucleotides in Drosophila U1, U2, U4, and U5 snRNAs. By fluorescent in situ hybridization (FISH) we showed that seven Drosophila scaRNAs are concentrated in easily detectable CBs. We used two assays based on Xenopus oocyte nuclei to demonstrate that three of these Drosophila scaRNAs do, in fact, function as guide RNAs. In flies null for the CB marker protein coilin, CBs are absent and there are no localized FISH signals for the scaRNAs. Nevertheless, biochemical experiments show that scaRNAs are present at normal levels and snRNAs are properly modified. Our experiments demonstrate that several scaRNAs are concentrated as expected in the CBs of wild-type Drosophila, but they function equally well in the nucleoplasm of mutant flies that lack CBs. We propose that the snRNA modification machinery is not limited to CBs, but is dispersed throughout the nucleoplasm of cells in general.
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Affiliation(s)
- Svetlana Deryusheva
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218
| | - Joseph G. Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD 21218
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33
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Khokha MK, Krylov V, Reilly MJ, Gall JG, Bhattacharya D, Cheung CYJ, Kaufman S, Lam DK, Macha J, Ngo C, Prakash N, Schmidt P, Tlapakova T, Trivedi T, Tumova L, Abu-Daya A, Geach T, Vendrell E, Ironfield H, Sinzelle L, Sater AK, Wells DE, Harland RM, Zimmerman LB. Rapid gynogenetic mapping of Xenopus tropicalis mutations to chromosomes. Dev Dyn 2009; 238:1398-46. [PMID: 19441086 DOI: 10.1002/dvdy.21965] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Pilot forward genetic screens in Xenopus tropicalis have isolated over 60 recessive mutations. Here we present a simple method for mapping mutations to chromosomes using gynogenesis and centromeric markers. When coupled with available genomic resources, gross mapping facilitates evaluation of candidate genes as well as higher resolution linkage studies. Using gynogenesis, we have mapped the genetic locations of the 10 X. tropicalis centromeres, and performed fluorescence in situ hybridization to validate these locations cytologically. We demonstrate the use of this very small set of centromeric markers to map mutations efficiently to specific chromosomes. Developmental Dynamics 238:1398-1406, 2009. (c) 2009 Wiley-Liss, Inc.
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Affiliation(s)
- Mustafa K Khokha
- Department of Pediatrics and Genetics, Yale University School of Medicine, New Haven, Connecticut, USA
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34
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Liu JL, Wu Z, Nizami Z, Deryusheva S, Rajendra TK, Beumer KJ, Gao H, Matera AG, Carroll D, Gall JG. Coilin is essential for Cajal body organization in Drosophila melanogaster. Mol Biol Cell 2009; 20:1661-70. [PMID: 19158395 DOI: 10.1091/mbc.e08-05-0525] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Cajal bodies (CBs) are nuclear organelles that occur in a variety of organisms, including vertebrates, insects, and plants. They are most often identified with antibodies against the marker protein coilin. Because the amino acid sequence of coilin is not strongly conserved evolutionarily, coilin orthologues have been difficult to recognize by homology search. Here, we report the identification of Drosophila melanogaster coilin and describe its distribution in tissues of the fly. Surprisingly, we found coilin not only in CBs but also in histone locus bodies (HLBs), calling into question the use of coilin as an exclusive marker for CBs. We analyzed two null mutants in the coilin gene and a piggyBac insertion mutant, which leads to specific loss of coilin from the germline. All three mutants are homozygous viable and fertile. Cells that lack coilin also lack distinct foci of other CB markers, including fibrillarin, the survival motor neuron (SMN) protein, U2 small nuclear RNA (snRNA), U5 snRNA, and the small CB-specific (sca) RNA U85. However, HLBs are not obviously affected in coilin-null flies. Thus, coilin is required for normal CB organization in Drosophila but is not essential for viability or production of functional gametes.
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Affiliation(s)
- Ji-Long Liu
- Carnegie Institution, Department of Embryology, Baltimore, MD 21218, USA
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35
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Abstract
Here I give a brief history of my scientific career, beginning with my early interest in natural history and my introduction to the microscope and the wonderful world of the cell. My studies have focused on chromosomes, nucleoli, and other nuclear structures, with a few forays into the cytoplasm. In each case, I have tried to understand how proteins and nucleic acids are physically organized to give rise to the structures seen under the microscope. I describe how studies in my laboratory on amplified ribosomal RNA genes led to the development of in situ hybridization, a technique that permitted us to localize specific nucleic acid sequences with high precision. My early exposure to the diversity of animals and plants made it seem natural to choose organisms best suited to a particular problem, hence the use of salamanders, frogs, and mice, as well as protozoa, fruit flies, and other invertebrates.
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Affiliation(s)
- Joseph G Gall
- Department of Embryology, Carnegie Institution for Science, Baltimore, Maryland 21218, USA.
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36
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Liu JL, Gall JG. U bodies are cytoplasmic structures that contain uridine-rich small nuclear ribonucleoproteins and associate with P bodies. Proc Natl Acad Sci U S A 2007; 104:11655-9. [PMID: 17595295 PMCID: PMC1899408 DOI: 10.1073/pnas.0704977104] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Uridine-rich small nuclear ribonucleoproteins (U snRNPs) are involved in key steps of pre-mRNA processing in the nucleus of eukaryotic cells. U snRNPs are enriched in the nucleus in discrete organelles that include speckles, Cajal bodies, and histone locus bodies. However, most U snRNPs are assembled in the cytoplasm, not in the nucleus. Despite extensive biochemical information, little is known about the spatial organization of U snRNPs in the cytoplasm. Here we show that U snRNPs in Drosophila are concentrated in discrete cytoplasmic structures, which we call U bodies, because they contain the major U snRNPs. In addition to snRNPs, U bodies contain essential snRNP assembly factors, suggesting that U bodies are sites for assembly or storage of snRNPs before their import into the nucleus. U bodies invariably associate with P bodies, which are involved in RNA surveillance and decay. Genetic disruption of P body components affects the organization of U bodies, suggesting that the two cytoplasmic bodies may cooperate in regulating aspects of snRNP metabolism. The identification of U bodies provides an opportunity to correlate specific biochemical steps of snRNP biogenesis with structural features of the cytoplasm.
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Affiliation(s)
- Ji-Long Liu
- Department of Embryology, Carnegie Institution of Washington, 3520 San Martin Drive, Baltimore, MD 21218
| | - Joseph G. Gall
- Department of Embryology, Carnegie Institution of Washington, 3520 San Martin Drive, Baltimore, MD 21218
- *To whom correspondence should be addressed. E-mail:
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37
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Affiliation(s)
- Joseph G Gall
- Department of Embryology, Carnegie Institution, 3520 San Martin Drive, Baltimore, Maryland 21218, USA.
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38
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Abstract
The germinal vesicle of the Drosophila oocyte is transcriptionally quiescent during the latter part of the first meiotic prophase. Concomitant with silencing of the genome, the nucleolus disappears at an early stage and the chromatin condenses into a compact mass called the karyosome. A prominent Cajal body (endobody) is present during most of prophase, attached to the karyosome. Components of the U7 small nuclear (sn) RNP reside in a separate body, the histone locus body, which is also attached to the karyosome. The histone locus body is no longer detectable with probes for the U7 snRNP after about stage 5 of oogenesis. Several other nuclear bodies of unknown nature can be detected by phase contrast, differential interference contrast, and electron microscopy.
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Affiliation(s)
- Ji-Long Liu
- Department of Embryology, Carnegie Institution, 3520 San Martin Drive, Baltimore, MD 21218, USA.
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39
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Abstract
Cajal bodies (CBs) are nuclear organelles that are usually identified by the marker protein p80-coilin. Because no orthologue of coilin is known in Drosophila melanogaster, we identified D. melanogaster CBs using probes for other components that are relatively diagnostic for CBs in vertebrate cells. U85 small CB–specific RNA, U2 small nuclear RNA, the survival of motor neurons protein, and fibrillarin occur together in a nuclear body that is closely associated with the nucleolus. Based on its similarity to CBs in other organisms, we refer to this structure as the D. melanogaster CB. Surprisingly, the D. melanogaster U7 small nuclear RNP resides in a separate nuclear body, which we call the histone locus body (HLB). The HLB is invariably colocalized with the histone gene locus. Thus, canonical CB components are distributed into at least two nuclear bodies in D. melanogaster. The identification of these nuclear bodies now permits a broad range of questions to be asked about CB structure and function in a genetically tractable organism.
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MESH Headings
- Animals
- Animals, Genetically Modified
- Cell Nucleus/genetics
- Cell Nucleus/metabolism
- Cell Nucleus/ultrastructure
- Coiled Bodies/genetics
- Coiled Bodies/metabolism
- Coiled Bodies/ultrastructure
- Drosophila melanogaster/cytology
- Drosophila melanogaster/embryology
- Drosophila melanogaster/genetics
- Embryo, Nonmammalian/cytology
- Embryo, Nonmammalian/embryology
- Embryo, Nonmammalian/metabolism
- Evolution, Molecular
- Gene Expression Regulation, Developmental/physiology
- Histones/genetics
- Histones/metabolism
- Histones/ultrastructure
- Larva/cytology
- Larva/growth & development
- Larva/metabolism
- Multigene Family/physiology
- Protein Biosynthesis/physiology
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Ribonucleoprotein, U7 Small Nuclear/genetics
- Ribonucleoprotein, U7 Small Nuclear/metabolism
- Ribonucleoprotein, U7 Small Nuclear/ultrastructure
- Ribonucleoproteins, Small Nuclear/genetics
- Ribonucleoproteins, Small Nuclear/metabolism
- Species Specificity
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Affiliation(s)
- Ji-Long Liu
- Department of Embryology, Carnegie Institution of Washington, Baltimore, MD 21218, USA
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Handwerger KE, Gall JG. Subnuclear organelles: new insights into form and function. Trends Cell Biol 2006; 16:19-26. [PMID: 16325406 DOI: 10.1016/j.tcb.2005.11.005] [Citation(s) in RCA: 187] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Revised: 09/15/2005] [Accepted: 11/21/2005] [Indexed: 11/30/2022]
Abstract
The cell nucleus is a complex and highly dynamic environment with many functionally specialized regions of substructure that form and maintain themselves in the absence of membranes. Relatively little is known about the basic physical properties of the nuclear interior or how domains within the nucleus are structurally and functionally organized and interrelated. Here, we summarize recent data that shed light on the structural and functional properties of three prominent subnuclear organelles--nucleoli, Cajal bodies (CBs) and speckles. We discuss how these findings impact our understanding of the guiding principles of nuclear organization and various types of human disease.
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Affiliation(s)
- Korie E Handwerger
- Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA.
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Handwerger KE, Cordero JA, Gall JG. Cajal bodies, nucleoli, and speckles in the Xenopus oocyte nucleus have a low-density, sponge-like structure. Mol Biol Cell 2004; 16:202-11. [PMID: 15509651 PMCID: PMC539164 DOI: 10.1091/mbc.e04-08-0742] [Citation(s) in RCA: 178] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Nuclear organelles, unlike many cytoplasmic organelles, lack investing membranes and are thus in direct contact with the surrounding nucleoplasm. Because the properties of the nucleoplasm and nuclear organelles influence the exchange of molecules from one compartment to another, it is important to understand their physical structure. We studied the density of the nucleoplasm and the density and permeability of nucleoli, Cajal bodies (CBs), and speckles in the Xenopus oocyte nucleus or germinal vesicle (GV). Refractive indices were measured by interferometry within intact GVs isolated in oil. The refractive indices were used to estimate protein concentrations for nucleoplasm (0.106 g/cm3), CBs (0.136 g/cm3), speckles (0.162 g/cm3), and the dense fibrillar region of nucleoli (0.215 g/cm3). We determined similar protein concentrations for nuclear organelles isolated in aqueous media, where they are no longer surrounded by nucleoplasm. To examine the permeability of nuclear organelles, we injected fluorescent dextrans of various molecular masses (3-2000 kDa) into the cytoplasm or directly into the GV and measured the extent to which they penetrated the organelles. Together, the interferometry and dextran penetration data show that organelles in the Xenopus GV have a low-density, sponge-like structure that provides access to macromolecules from the nucleoplasm.
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Affiliation(s)
- Korie E Handwerger
- Department of Embryology, Carnegie Institution of Washington, Baltimore, MD 21210, USA
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Gall JG. E. B. Wilson's study of cleavage in the egg of the mollusc Dentalium. J Exp Zool A Comp Exp Biol 2004; 301:613-6. [PMID: 15286940 DOI: 10.1002/jez.a.83] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Affiliation(s)
- Joseph G Gall
- Department of Embryology, Carnegie Institution, Baltimore, Maryland 21210, USA.
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Abstract
The germinal vesicle (GV) of Xenopus laevis is an enormous nucleus that contains 18 giant lampbrush chromosomes and thousands of inclusions. The inclusions are primarily of three types: approximately 1500 extrachromosomal nucleoli, 50-100 Cajal bodies, and several thousand B-snurposomes, which correspond to speckles or interchromatin granule clusters in other nuclei. The large size and abundance of the GV organelles, as well as the ease with which they can be studied both in vivo and in vitro, make the GV an ideal object for analysis of nuclear structure and function.
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Affiliation(s)
- Joseph G Gall
- Department of Embryology, Carnegie Institution, Baltimore, MD 21210, USA.
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Abstract
Cajal bodies (CBs) are complex organelles found in the nuclei of a wide variety of organisms, including vertebrates, invertebrates, plants, and yeast. In most cell types CBs are <1 microm in diameter, severely limiting the range of experimental observations that can be made on them. By contrast, CBs in the amphibian oocyte nucleus (also called the germinal vesicle) are 2-10 microm in diameter. We have taken advantage of this large size to carry out kinetic studies on coilin, a protein that is specifically enriched in CBs. We labeled coilin with photoactivatable green fluorescent protein and analyzed the movement of the protein by confocal microscopy in unfixed germinal vesicles isolated in oil. We showed that coilin leaves the CB relatively slowly (minutes rather than seconds) with kinetics similar to earlier measurements on its entrance. We also showed that coilin diffuses very slowly within the CB, consistent with its being in a large macromolecular complex. Finally, we found that the movement of coilin is not directly affected by the transcriptional state of the nucleus or ongoing nucleocytoplasmic exchange. These data on the kinetics of coilin reinforce the conclusion that CB components are in a constant state of flux, consistent with models that postulate an active role for CBs in nuclear physiology.
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Affiliation(s)
- Svetlana Deryusheva
- Biological Institute, University of St. Petersburg, Stary Peterhof, St. Petersburg 198904, Russia
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Affiliation(s)
- Joseph G Gall
- Department of Embryology, Carnegie Institution of Washington, 115 West University Parkway, Baltimore, Maryland 21210, USA.
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Abstract
Cajal bodies (CBs) are evolutionarily conserved nuclear organelles that contain many factors involved in the transcription and processing of RNA. It has been suggested that macromolecular complexes preassemble or undergo maturation within CBs before they function elsewhere in the nucleus. Most such models of CB function predict a continuous flow of molecules between CBs and the nucleoplasm, but there are few data that directly support this view. We used fluorescence recovery after photobleaching (FRAP) on isolated Xenopus oocyte nuclei to measure the steady-state exchange rate between the nucleoplasm and CBs of three fluorescently tagged molecules: U7 small nuclear RNA, coilin, and TATA-binding protein (TBP). In the nucleoplasm, the apparent diffusion coefficients for the three molecules ranged from 0.26 to 0.40 microm2 s-1. However, in CBs, fluorescence recovery was markedly slower than in the nucleoplasm, and there were at least three kinetic components. The recovery rate within CBs was independent of bleach spot diameter and could not be attributed to high CB viscosity or density. We propose that binding to other molecules and possibly assembly into larger complexes are the rate-limiting steps for FRAP of U7, coilin, and TBP inside CBs.
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Affiliation(s)
- Korie E Handwerger
- Department of Embryology, Carnegie Institution of Washington, Baltimore, MD 21210, USA
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Gall JG. [A role for Cajal bodies in assembly of the nuclear transcription machinery]. Tsitologiia 2003; 45:971-5. [PMID: 14989168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Cajal bodies (CBs) are small nuclear organelles that contain the three eukaryotic RNA polymerases and variety of factors involved in transcription and processing of all types of RNA. A number of these factors, as well as subunits of polymerase (pol) II itself, are rapidly and specifically targeted to CBs when injected into the cell. It is suggested that pol I, pol II and pol III transcription and processing complexes are preassembled in the CBs before transport to the sites of transcription on the chromosomes and in the nucleoli.
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Affiliation(s)
- Joseph G Gall
- Department of Embryology, Carnegie Institution of Washington, Baltimore, MD 21210-3301, USA.
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Abstract
We used immunofluorescence to study the distribution and targeting of RNA polymerase (pol) III subunits and pol III transcription factors in the Xenopus laevis oocyte nucleus. Antibodies against several of these proteins stained Cajal bodies and approximately 90 specific sites on the lampbrush chromosomes. Some of the chromosomal sites had been identified previously by in situ hybridization as the genes for 5S rRNA. The remaining sites presumably encode tRNAs and other pol III transcripts. Pol III sites were often resolvable as loops similar to the much more abundant pol II loops, but without a matrix detectable by phase contrast or differential interference contrast. This morphology is consistent with the transcription of short repeated sequences. Hemagglutinin-tagged transcripts encoding core subunits and transcription factors were injected into the oocyte cytoplasm, and the distribution of newly translated proteins inside the nucleus was monitored by immunostaining. Cajal bodies were preferentially targeted by these proteins, and in some cases the chromosomal sites were also weakly stained. The existence of pol III subunits and pol III transcription factors in Cajal bodies and their targeting to these organelles are consistent with a model of Cajal bodies as sites for preassembly of the nuclear transcription machinery.
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Affiliation(s)
- Christine Murphy
- Department of Embryology, Carnegie Institution, Baltimore, Maryland 21210, USA
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