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Bigley RB, Payumo AY, Alexander JM, Huang GN. Insights into nuclear dynamics using live-cell imaging approaches. WILEY INTERDISCIPLINARY REVIEWS. SYSTEMS BIOLOGY AND MEDICINE 2017; 9:10.1002/wsbm.1372. [PMID: 28078793 PMCID: PMC5315593 DOI: 10.1002/wsbm.1372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 10/27/2016] [Accepted: 10/28/2016] [Indexed: 11/11/2022]
Abstract
The nucleus contains the genetic blueprint of the cell and myriad interactions within this subcellular structure are required for gene regulation. In the current scientific era, characterization of these gene regulatory networks through biochemical techniques coupled with systems-wide 'omic' approaches has become commonplace. However, these strategies are limited because they represent a mere snapshot of the cellular state. To obtain a holistic understanding of nuclear dynamics, relevant molecules must be studied in their native contexts in living systems. Live-cell imaging approaches are capable of providing quantitative assessment of the dynamics of gene regulatory interactions within the nucleus. We survey recent insights into what live-cell imaging approaches have provided the field of nuclear dynamics. In this review, we focus on interactions of DNA with other DNA loci, proteins, RNA, and the nuclear envelope. WIREs Syst Biol Med 2017, 9:e1372. doi: 10.1002/wsbm.1372 For further resources related to this article, please visit the WIREs website.
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Affiliation(s)
- Rachel B. Bigley
- Cardiovascular Research Institute and Department of Physiology, School of Medicine, University of California, San Francisco CA 94158, USA
| | - Alexander Y. Payumo
- Cardiovascular Research Institute and Department of Physiology, School of Medicine, University of California, San Francisco CA 94158, USA
| | - Jeffrey M. Alexander
- Cardiovascular Research Institute and Department of Physiology, School of Medicine, University of California, San Francisco CA 94158, USA
| | - Guo N. Huang
- Cardiovascular Research Institute and Department of Physiology, School of Medicine, University of California, San Francisco CA 94158, USA
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Affiliation(s)
- I F Zhimulev
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
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Affiliation(s)
- I F Zhimulev
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, Novosibirsk, Russia
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Myohara M, Okada M. Puff induction in permeabilized Drosophila salivary glands in a chemically defined medium. Dev Biol 1988; 125:462-5. [PMID: 3123294 DOI: 10.1016/0012-1606(88)90228-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We showed previously that digitonin-permeabilized salivary glands form prominent puffs in response to ecdysterone only when the incubation medium is supplemented with a homogenate of intact glands. To develop a chemically defined medium that supports puff formation in permeabilized salivary glands, we examined the requirement of ribonucleoside triphosphates (NTPs), precursors of RNA synthesis, for puff formation in permeabilized salivary glands. We found that prominent ecdysone puffs were induced in permeabilized salivary glands when the concentration of each NTP in the medium was higher than 0.5 mM. The puff size was significantly reduced if the volume of the medium were more than 2.0 microliter per gland. This suggests the existence of a factor(s), in addition to NTPs, which is required for puff formation and is diffusible from permeabilized glands.
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Affiliation(s)
- M Myohara
- Institute of Biological Sciences, University of Tsukuba, Ibaraki, Japan
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Induction of ecdysterone-stimulated chromosomal puffs in permeabilized Drosophila salivary glands: A new method for assaying the gene-regulating activity of cytoplasm. Dev Biol 1987. [DOI: 10.1016/0012-1606(87)90304-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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BERRY SPENCERJ. Insect Nucleic Acids. Biochemistry 1985. [DOI: 10.1016/b978-0-08-030811-1.50013-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Gregory SP, Maclean N, Pocklington MJ. Artificial modification of nuclear gene activity. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1981; 13:1047-63. [PMID: 6170533 DOI: 10.1016/0020-711x(81)90167-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Plagens U. Effect of salt-treatment on manually isolated polytene chromosomes from Chironomus tentans. Chromosoma 1978; 68:1-19. [PMID: 357113 DOI: 10.1007/bf00330369] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A method for the rapid manual isolation of polytene chromosomes and nuclear membranes from salivary glands of Chironomus tentans is presented and the analysis of some of their RNA and protein components before and after treatment with 2 M salt solutions is summarized.--After salt-incubation the chromosomes still display a considerable number of bands which stain with ethidium bromide and which are sensitive to treatment with DNase, RNase, trypsin, and proteinase K, to a lesser extent with pronase and papain. Analysis of the iodinated residual proteins on SDS gels yield three major and two minor bands (MW between 50,000 and 70,000 dalton) which were also shown to be present in interphase chromosomes of Ehrlich ascites cells which had been treated similarly and are also tightly bound constituents of DNA prepared according to Gross-Bellard et al. (1973). This result indicates the existence of a general class of non-histone proteins involved in keeping the DNA in a supercoiled state. Furthermore their presence in salt-treated nuclear membranes of Chironomus salivary gland cells (and Xenopus oocytes, unpubl.) will be of interest with respect to functional aspects of the nuclear matrix.
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Biessmann H, Levy B, McCarthy BJ. In vitro transcription of heat-shock-specific RNA from chromatin of Drosophila melanogaster cells. Proc Natl Acad Sci U S A 1978; 75:759-63. [PMID: 416440 PMCID: PMC411336 DOI: 10.1073/pnas.75.2.759] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Polyadenylylated RNA synthesized after heat shock was isolated from polysomes of cultured cells of Drosophila melanogaster and used as template to prepare cDNA. An excess of poly(A)-RNA from heat-shocked cells hybridized to 80% of the cDNA, whereas cytoplasmic poly(A)-RNA from cells grown at 25 degrees could drive only half of the cDNA probe into hybrid. These sequences were removed from the cDNA population by annealing to poly(A)-RNA from cells grown at 25 degrees. The unreacted material represented only heat-shock-induced mRNA sequences, as shown by a second cycle of hybridization. Isolated chromatin was transcribed in vitro at 25 degrees with Escherichia coli RNA polymerase, with mercurated UTP as precursor. RNA transcribed from chromatin that was prepared from cells 1 hr after the temperature was shifted to 37 degrees hybridized with 100-fold faster kinetics to the heat-shock-specific cDNA probe than did RNA transcribed from chromatin of cells grown at 25 degrees. Therefore, heat shock results in a change in chromatin structure recognizable by E. coli RNA polymerase.
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Stein H. RNA synthesis with giant chromosomes of isolated Drosophila hydei nuclei as a correlate to the experimentally altered chromosome morphology. Exp Cell Res 1976; 103:1-14. [PMID: 991944 DOI: 10.1016/0014-4827(76)90234-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Santelli RV, Machado-Santelli GM, Lara FJ. In vitro transcription by isolated nuclei of Rhynchosciara americana salivary glands. Characteristics of incorporation and inhibition by alpha-amanitin. Chromosoma 1976; 56:69-84. [PMID: 976015 DOI: 10.1007/bf00293731] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A method for the isolation of polytene nuclei from salivary glands cells of the Diptera Rhynchosciara americana is described. The stage-specific morphological pattern of the chromosome is maintained during the isolation. The isolated nuclei show two distinct RNA polymerase activities, namely I and II, characterized on the basis of ionic requirements and alpha-amanitin sensitivity. Studies of the product under the incubation conditions show that the system allows the synthesis of high-molecular weight RNA, beside a low molecular weight peak which may comprise pre-4S and 5S RNAs. Autoradiographic studies carried out in the presence or absence of the toxin alpha-amanitin showed that micronucleoli contain products of RNA polymerase type I activity (ribosomal RNA) and that the DNA puffs are engaged in alpha-amanitin sensitive RNA synthesis and thus are sites of polymerase type II activity.
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Abstract
It is reported that chromatin can be prepared from highly purified polytene nuclei from the salivary glands of third instar larvae of Drosophila hydei; such chromatin differs from that of diploid nuclei mainly by deficiencies in certain nonhistone chromosomal proteins. It is suggested that these proteins are important components of constitutive heterochromatin, which is severely underrepresented in polytene chromosomes. Chromosome morphology, including the pattern of induced puffs, is maintained throughout the mass isolation of glands and sucrose gradient purification of nuclei, as indicated by studies on temperature-shocked and control larvae. No significant alteration in the chromosomal proteins following puff induction by heat shock could be detected on analysis of the isolated protein fractions by disc gel electrophoresis. More sensitive techniques must be developed to study the apparent rearrangement or accumulation of protein at puff sites, and to elucidate the role of this protein in gene activation.
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Sekeris CE, Richter KH, Marx R. Isolation of nuclei from epidermis cells of larvae of the blowfly Calliphora vicina R.-D. Exp Cell Res 1974; 88:105-10. [PMID: 4418019 DOI: 10.1016/0014-4827(74)90623-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Fristrom JW, Yund MA. Genetic programming for development in Drosophila. CRC CRITICAL REVIEWS IN BIOCHEMISTRY 1973; 1:537-70. [PMID: 4201069 DOI: 10.3109/10409237309105442] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Boyd JB, Presley JM. Deoxyribonucleic acid synthesis in isolated polytene nuclei of Drosophila hydei. Biochem Genet 1973; 9:309-25. [PMID: 4747550 DOI: 10.1007/bf00486067] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Sederoff R, Clynes R, Poncz M, Hachtel S. RNA synthesis by exogenous RNA polymerase on cytological preparations of chromosomes. J Biophys Biochem Cytol 1973; 57:538-50. [PMID: 4572295 PMCID: PMC2108978 DOI: 10.1083/jcb.57.2.538] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Cytological preparations of Drosophila polytene chromosomes serve as templates for RNA synthesis carried out by exogenous RNA polymerase (Escherichia coli). Incorporation of labeled ribonucleoside triphosphates into RNA may be observed directly by autoradiography. Because of the effects of rifampicin, actinomycin D, ribonuclease, high salt, and the requirement for all four nucleoside triphosphates, we conclude that the labeling observed over chromosomes is due to DNA-dependent RNA polymerase activity. Using this method, one can observe RNA synthesis in vitro on specific chromosome regions due to the activity of exogenous RNA polymerase. We find that much of the RNA synthesis in this system occurs on DNA sequences which appear to be in a nondenatured state.
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Helmsing PJ, van Eupen O. Chromatin of Drosophila: isolation and characterization of chromatin of two larval cell types. BIOCHIMICA ET BIOPHYSICA ACTA 1973; 308:154-60. [PMID: 4722906 DOI: 10.1016/0005-2787(73)90132-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Alonso C. The influence of molting hormone on RNA synthesis in isolated polytene nuclei of Drosophila. Dev Biol 1972; 28:372-81. [PMID: 5031806 DOI: 10.1016/0012-1606(72)90020-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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Helmsing PJ. Induced accumulation of non-histone proteins in polytene nuclei of Drosophila hydei. II. Accumulation of proteins in polytene nuclei and chromatin of different larval tissues. CELL DIFFERENTIATION 1972; 1:19-24. [PMID: 4670873 DOI: 10.1016/0045-6039(72)90109-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Dickson E, Boyd JB, Laird CD. Sequence diversity of polytene chromosome DNA from Drosophila hydei. J Mol Biol 1971; 61:615-27. [PMID: 5133116 DOI: 10.1016/0022-2836(71)90067-2] [Citation(s) in RCA: 104] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Helmsing PJ, Berendes HD. Induced accumulation of nonhistone proteins in polytene nuclei of Drosophila hydei. J Cell Biol 1971; 50:893-6. [PMID: 5098869 PMCID: PMC2108304 DOI: 10.1083/jcb.50.3.893] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
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Helmsing PJ. Isolation and partial characterization of the labeled product from polytene nuclei incubated in vitro with amino acids. BIOCHIMICA ET BIOPHYSICA ACTA 1971; 232:733-5. [PMID: 5556853 DOI: 10.1016/0005-2787(71)90765-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Leenders HJ, Wullems GJ, Berendes HD. Competitive interaction of adenosine 3',5'-monophosphate on gene activation by ecdysterone. Exp Cell Res 1970; 63:159-64. [PMID: 4322177 DOI: 10.1016/0014-4827(70)90344-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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Lezzi M. Differential gene activation in isolated chromosomes. INTERNATIONAL REVIEW OF CYTOLOGY 1970; 29:127-68. [PMID: 4930417 DOI: 10.1016/s0074-7696(08)60034-0] [Citation(s) in RCA: 51] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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32
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Ecdysonbindende Proteinfraktionen in den Speicheldr�sen von Drosophila hydei. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 1970. [DOI: 10.1007/bf00297737] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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33
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Derksen J, Berendes HD. Polytene chromosome structure at the submicroscopic level. II. Length distribution of DNA molecules from polytene chromosomes of Drosophila melanogaster and D. hydei. Chromosoma 1970; 31:468-77. [PMID: 5490312 DOI: 10.1007/bf00285837] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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