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Nuclear distribution of the chromatin-remodeling protein ATRX in mouse early embryogenesis. Acta Histochem 2017; 119:18-25. [PMID: 27863708 DOI: 10.1016/j.acthis.2016.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/03/2016] [Accepted: 11/03/2016] [Indexed: 12/13/2022]
Abstract
The nucleus of mammalian embryos differs by transcriptional activity at different stages of early development. Here, we studied nuclear distribution of the chromatin-remodeling protein ATRX in pre-implantation mouse embryos. Immunofluorescent staining revealed the changes of ATRX nuclear distribution at the initial stages of early mouse development. At the stage of early zygote, a diffuse ATRX distribution pattern was prevalent. During the course of zygotic genome activation (ZGA), zones of increased ATRX concentration are observed, and they are most expressed in the nuclei of late 2-cell embryos. In the morula stage, the ATRX distribution becomes diffuse again. In zygotes, the patterns of ATRX distribution differ between male and female pronuclei. At all the stages, ATRX concentrates in the DAPI-positive areas of condensed chromatin. The level of colocalization between ATRX and heterochromatin was found the highest at the late 2-cell stage. When transcription was artificially suppressed, the pattern of intranuclear ATRX distribution was mostly determined by the mechanism of inhibitor action rather than the decreased level of transcriptional activity. Thus, the obvious changes of ATRX distribution occur and partially correlate with the main stages of ZGA during mouse early development, but these changes seem to be determined by other processes of structural and functional rearrangements of blastomere nuclei.
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Galati A, Micheli E, Alicata C, Ingegnere T, Cicconi A, Pusch MC, Giraud-Panis MJ, Gilson E, Cacchione S. TRF1 and TRF2 binding to telomeres is modulated by nucleosomal organization. Nucleic Acids Res 2015; 43:5824-37. [PMID: 25999344 PMCID: PMC4499135 DOI: 10.1093/nar/gkv507] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 05/04/2015] [Indexed: 01/22/2023] Open
Abstract
The ends of eukaryotic chromosomes need to be protected from the activation of a DNA damage response that leads the cell to replicative senescence or apoptosis. In mammals, protection is accomplished by a six-factor complex named shelterin, which organizes the terminal TTAGGG repeats in a still ill-defined structure, the telomere. The stable interaction of shelterin with telomeres mainly depends on the binding of two of its components, TRF1 and TRF2, to double-stranded telomeric repeats. Tethering of TRF proteins to telomeres occurs in a chromatin environment characterized by a very compact nucleosomal organization. In this work we show that binding of TRF1 and TRF2 to telomeric sequences is modulated by the histone octamer. By means of in vitro models, we found that TRF2 binding is strongly hampered by the presence of telomeric nucleosomes, whereas TRF1 binds efficiently to telomeric DNA in a nucleosomal context and is able to remodel telomeric nucleosomal arrays. Our results indicate that the different behavior of TRF proteins partly depends on the interaction with histone tails of their divergent N-terminal domains. We propose that the interplay between the histone octamer and TRF proteins plays a role in the steps leading to telomere deprotection.
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Affiliation(s)
- Alessandra Galati
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, 00185 Rome, Italy Institute Pasteur-Fondazione Cenci-Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Emanuela Micheli
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, 00185 Rome, Italy Institute Pasteur-Fondazione Cenci-Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | - Claudia Alicata
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, 00185 Rome, Italy
| | - Tiziano Ingegnere
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, 00185 Rome, Italy
| | - Alessandro Cicconi
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, 00185 Rome, Italy Institute Pasteur-Fondazione Cenci-Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
| | | | - Marie-Josèphe Giraud-Panis
- Institute for Research on Cancer and Aging, Nice (IRCAN) CNRS UMR 7284/INSERM U1081, University of Nice Sophia Antipolis, 06107 Nice, France
| | - Eric Gilson
- Institute for Research on Cancer and Aging, Nice (IRCAN) CNRS UMR 7284/INSERM U1081, University of Nice Sophia Antipolis, 06107 Nice, France Department of Medical Genetics, Hospital, CHU of Nice, 06202 Nice, France
| | - Stefano Cacchione
- Department of Biology and Biotechnology 'Charles Darwin', Sapienza University of Rome, 00185 Rome, Italy Institute Pasteur-Fondazione Cenci-Bolognetti, Sapienza University of Rome, 00185 Rome, Italy
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Caneva R, Rossetti L, Savino M. DNA minor groove accessibility in the nucleosome core deduced from specific interactions with DAPI. BIOCHIMICA ET BIOPHYSICA ACTA 1996; 1306:117-21. [PMID: 8634325 DOI: 10.1016/0167-4781(96)00015-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Equilibrium binding properties of DAPI for purified nucleosome cores were derived from fluorescence intensity enhancement. Both the affinity and the number of sites of the primary, minor groove binding are preserved with respect to the corresponding isolated DNA, suggesting that the capacity for specific interactions of the minor groove may well be exerted in chromatin.
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Affiliation(s)
- R Caneva
- Centro di Studio per gli Acidi Nucleici del CNR, Dipartimento di Genetica e Biologia Molecolare, Rome,Italy
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Loborg H, Lindén E, Lönn A, Skoglund P, Rundquist I. High affinity binding of 7-aminoactinomycin D and 4',6-diamidino-2-phenylindole to human neutrophilic granulocytes and lymphocytes. CYTOMETRY 1995; 20:296-306. [PMID: 7587717 DOI: 10.1002/cyto.990200405] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The binding behavior of the DNA binding dyes 7-aminoactinomycin D (7-AAMD) and 4',6-diamidino-2-phenylindole (DAPI) to human neutrophilic granulocytes and lymphocytes was studied by image cytofluorometry. Peripheral blood leukocytes were prefixed in paraformaldehyde (PFA) and attached to cover glasses. Different fixation, permeabilization, and acid extraction method were applied before the cells were stained to equilibrium using varying concentrations of 7-AAMD or DAPI. The apparent association constant and number of high affinity dye binding sites were estimated for the different cell types, dyes, and treatments. Acid-extracted cells, supposedly containing nucleosome-free DNA, were chosen to represent maximal dye binding. Only about 10% of the 7-AAMD binding sites remained in the unextracted PFA-fixed cells, and the apparent dye affinity was also reduced. We found no major difference in high affinity binding between the cell types, but granulocytes showed more fluorescence from less specifically bound 7-AAMD compared to lymphocytes. DAPI had a much higher affinity than 7-AAMD, independent of the preparation method. It showed a cooperative binding behavior with an apparent saturation of the high affinity binding sites at a dye concentration of about 50 nM. We conclude that both dyes may be useful as probes for chromatin structure in intact cells and that our new technique may contribute to such studies since it allows determination of dye affinities and numbers of high affinity binding sites in situ.
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Affiliation(s)
- H Loborg
- Department of Cell Biology, Faculty of Health Sciences, University of Linköping, Sweden
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5
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Rundquist I. Equilibrium binding of DAPI and 7-aminoactinomycin D to chromatin of cultured cells. CYTOMETRY 1993; 14:610-7. [PMID: 8404367 DOI: 10.1002/cyto.990140605] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The binding of 4',6-diamidino-2-phenylindole (DAPI) and 7-aminoactinomycin D (7-AAMD) to chromatin of intact cultured fibroblast nuclei was studied by cytofluorometry. Staining was performed at equilibrium at varying dye concentrations. By using large volumes of dye solutions, the free dye concentration became approximately equal to total dye concentration, and the estimation of affinity and number of binding sites was performed by Scatchard analysis. Since all Scatchard plots showed a definite curvature, indicating more than one class of binding sites, a two component regression was performed, although only the highest affinity binding sites were determined. The observed affinity constants did not change substantially between different preparational procedures for any of the dyes. The number of DAPI binding sites increased about 30% after detergent extraction. No such increase was observed for 7-AAMD. Fixation in formaldehyde, instead of ethanol, after detergent extraction had no effect on DAPI binding, but decreased the number of 7-AAMD binding sites with about 50%. Extraction of basic proteins with HCl resulted in about 100% increase of the number of binding sites for both dyes. It should be feasible to use this technique as an assay for the identification of proteins or other nuclear components important for the maintenance of chromatin structure.
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Affiliation(s)
- I Rundquist
- Department of Cell Biology, Faculty of Health Sciences, University of Linköping, Sweden
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Bordin F, Cacchione S, Savino M, Tufillaro A. Different superstructural features of the complexes between spermine and the light responsive elements of the two pea genes rbcS-3A and rbcS-3.6. Gel electrophoresis and circular dichroism studies. Biophys Chem 1992; 44:99-112. [PMID: 1391610 DOI: 10.1016/0301-4622(92)85042-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Two light responsive elements (LREs), DNA sequences, 62 base pairs long, relevant to the light control during transcription of the pea genes rbcS-3A and rbcS-3.6, were synthesized and ligated to obtain multimers with defined superstructural features. Their gel electrophoretic mobilities were studied in the presence of the tetracation, spermine, since it was previously suggested, on the basis of theoretical analysis, that spermine can increase DNA bending and thus could be useful in revealing DNA superstructural features. In fact, the difference between the curvatures of the two LREs, derived from gel electrophoresis retardation ratios, increases in the presence of spermine. Circular dichroism spectra of the complexes between spermine and the two LREs, at different neutralization ratios, show that the polyamine is able to induce the formation of asymmetric arrangements of complexes of molecules. The chirality of these complexes appears dramatically different for the two LREs, suggesting that their different superstructural features give rise to different interactions with the polyamine.
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Affiliation(s)
- F Bordin
- Dipartimento di Genetica e Biologia Molecolare, Università degli Studi di Roma La Sapienza, Italy
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Bumma C, Cacchione S, Caneva R, Savino M. Specific interactions of 4'-6-diamidino-2-phenylindole with nucleosome. Biochem Pharmacol 1988; 37:1865-6. [PMID: 3377856 DOI: 10.1016/0006-2952(88)90485-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- C Bumma
- Dpt Genet. Biol. Mol., CS Acidi Nucleici CNR, Università Roma I
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Caffarelli E, De Santis P, Leoni L, Palleschi A, Savino M. Preferential positioning of nucleosomes on pBR322 as evaluated via Fourier transform of data from electron microscopy. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 171:497-501. [PMID: 3345744 DOI: 10.1111/j.1432-1033.1988.tb13817.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Nucleosome positioning on pBR322 DNA has been evaluated by electron microscopy visualization, after psoralen cross-linking. The distribution function of nucleosomes on pBR322 DNA has been calculated analyzing the data of the electron microscopy via Fourier transform. This function shows definite maxima, which indicate differential interactions of the histone octamer to different DNA sequences.
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Affiliation(s)
- E Caffarelli
- Centro di Studio per gli Acidi Nucleici del Consiglio Nazionale delle Ricerche, Roma, Italy
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Portugal J, Waring MJ. Analysis of the effects of antibiotics on the structure of nucleosome core particles determined by DNAase I cleavage. Biochimie 1987; 69:825-40. [PMID: 3122845 DOI: 10.1016/0300-9084(87)90209-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Patterns of sensitivity to DNAase I cleavage have been analysed in order to investigate the effects of anti-tumour antibiotics and related drugs on nucleosome core particles containing different DNA restriction fragments. In this article, we review the experimental results which show that after controlled digestion of defined-sequence core particles, new cleavage products appear in the enzyme digestion patterns which lie approximately mid-way between the strong bands characteristic of native nucleosome core particles. The effects of the antibiotics, which include bis-intercalators as well as minor groove-binding ligands (but not monofunctional intercalators), are explained in terms of an induced change in rotational setting (phasing) of the core DNA. The new rotational positioning of DNA induced by antibiotic binding appears to be almost independent of DNA sequence, although some differences can be observed with the various pieces of DNA, most likely reflecting the exact number and disposition of antibiotic binding sites.
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Affiliation(s)
- J Portugal
- University of Cambridge Department of Pharmacology, England
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