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En A, Watanabe K, Ayusawa D, Fujii M. The key role of a basic domain of histone H2B N-terminal tail in the action of 5-bromodeoxyuridine to induce cellular senescence. FEBS J 2023; 290:692-711. [PMID: 35882390 DOI: 10.1111/febs.16584] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 06/28/2022] [Accepted: 07/25/2022] [Indexed: 02/04/2023]
Abstract
5-Bromodeoxyuridine (BrdU), a thymidine analogue, is an interesting reagent that modulates various biological phenomena. BrdU, upon incorporation into DNA, causes destabilized nucleosome positioning which leads to changes in heterochromatin organization and gene expression in cells. We have previously shown that BrdU effectively induces cellular senescence, a phenomenon of irreversible growth arrest in mammalian cells. Identification of the mechanism of action of BrdU would provide a novel insight into the molecular mechanisms of cellular senescence. Here, we showed that a basic domain in the histone H2B N-terminal tail, termed the HBR (histone H2B repression) domain, is involved in the action of BrdU. Notably, deletion of the HBR domain causes destabilized nucleosome positioning and derepression of gene expression, as does BrdU. We also showed that the genes up-regulated by BrdU significantly overlapped with those by deletion of the HBR domain, the result of which suggested that BrdU and deletion of the HBR domain act in a similar way. Furthermore, we showed that decreased HBR domain function induced cellular senescence or facilitated the induction of cellular senescence. These findings indicated that the HBR domain is crucially involved in the action of BrdU, and also suggested that disordered nucleosome organization may be involved in the induction of cellular senescence.
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Affiliation(s)
- Atsuki En
- Graduate School of Nanobioscience, Yokohama City University, Japan
| | - Kazuaki Watanabe
- Graduate School of Nanobioscience, Yokohama City University, Japan
| | - Dai Ayusawa
- Graduate School of Nanobioscience, Yokohama City University, Japan
| | - Michihiko Fujii
- Graduate School of Nanobioscience, Yokohama City University, Japan
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2
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Kondalaji SG, Bowman GD. In Vitro Mapping of Nucleosome Positions at Base-Pair Resolution Using Ortho-Phenanthroline. Curr Protoc 2022; 2:e518. [PMID: 35943282 PMCID: PMC9373710 DOI: 10.1002/cpz1.518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The positions of nucleosomes along genomic DNA play a role in defining patterns of gene expression and chromatin organization. Determination of nucleosome positions in vivo and in vitro, as revealed by the locations of histones on DNA, has provided insight into mechanisms of nucleosome sliding, spacing, assembly, and disassembly. Here, we describe methods for the in vitro determination of histone-DNA contacts at base-pair (bp) resolution. The protocol involves the labeling of histones with ortho-phenanthroline (OP), site-specific cleavage of nucleosomal DNA, and processing and analysis of the resulting DNA fragments. This methodology provides an efficient and high-resolution means for studying kinetics and behavior of enzymes that alter nucleosome structure and/or positioning, and can be used to identify preferred distributions of nucleosomes on natural DNA sequences. © 2022 Wiley Periodicals LLC. Basic Protocol 1: Cysteine-specific chemical modification of folded histones with ortho-phenanthroline (OP) Basic Protocol 2: Nucleosome sliding assay adapted for OP mapping of histone-DNA contacts Basic Protocol 3: OP-mediated cleavage, processing, and analysis of DNA fragments using a sequencing gel Support Protocol 1: Preparation of dideoxy sequencing ladders Support Protocol 2: Preparation and running of a denaturing DNA sequencing gel.
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Affiliation(s)
| | - Gregory D Bowman
- T. C. Jenkins Department of Biophysics, Johns Hopkins
University, Baltimore, Maryland 21218
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3
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Prusov AN, Smirnova TA, Kolomijtseva GY. Thermodynamic Study of Interactions of Distamycin A with Chromatin in Rat Liver Nuclei in the Presence of Polyamines. BIOCHEMISTRY (MOSCOW) 2018; 83:1231-1244. [PMID: 30472960 DOI: 10.1134/s0006297918100085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We studied the thermodynamics of melting of isolated rat liver nuclei with different degrees of chromatin condensation determined by the concentration of polyamines (PA) and the solution ionic strength, as well as the effect of the antibiotic distamycin A (DM) on melting. Differential scanning calorimetry (DSC) profiles of nuclear preparations contained three peaks that reflected melting of three main chromatin domains. The number of peaks did not depend on the degree of condensation; however, nuclei with more condensed chromatin had a higher total enthalpy. DM stabilized peaks II and III corresponding to the melting of relaxed and topologically strained DNA, respectively, but destabilized peak I corresponding to the melting of nucleosome core histones. At the saturating concentration (DM/DNA molar ratio = 0.1), DM increased Tm of peaks II and III by ~5°C and decreased Tm of peak I by ~2.5°C. Based on the dependence of ΔH on DM concentration, we established that at low DM/DNA ratio (≤0.03), when DM interacted predominantly with AT-rich DNA regions, the enthalpy of peak II decreased in parallel with the increase in the enthalpy of peak III, which indicated that DM induces structural transitions in the nuclear chromatin associated with the increase in torsional stress in DNA. An increase in free energy under saturation conditions was equal to the change in the free energy of DM interaction with DNA. However, the increase in the enthalpy of melting of the nuclei in the presence of DM was much greater than the enthalpy of titration of nuclei with DM. This indicates a significant increase in the strength of interaction between the two DNA strands apparently due, among other things, to changes in the torsional stress of DNA in the nuclei. Titration of the nuclei with increasing PA concentrations resulted in the decrease in the number of DM-binding sites and the non-monotonous dependence of the enthalpy and entropy contribution to the binding free energy on the PA content. We suggested that the observed differences in the thermodynamic parameters were due to the different width of the minor groove in the nuclear chromatin DNA, which depends on PA concentration.
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Affiliation(s)
- A N Prusov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - T A Smirnova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.,Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - G Ya Kolomijtseva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
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4
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Minor Groove Binder Distamycin Remodels Chromatin but Inhibits Transcription. PLoS One 2013; 8:e57693. [PMID: 23460895 PMCID: PMC3584068 DOI: 10.1371/journal.pone.0057693] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2012] [Accepted: 01/28/2013] [Indexed: 11/19/2022] Open
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5
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Dasgupta D, Majumder P, Banerjee A. A revisit of the mode of interaction of small transcription inhibitors with genomic DNA. J Biosci 2012; 37:475-81. [PMID: 22750984 DOI: 10.1007/s12038-012-9211-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
One class of small molecules with therapeutic potential for treatment of cancer functions as transcription inhibitors via interaction with double-stranded DNA. Majority of the studies of the interaction with DNA have so far been reported under conditions nonexistent in vivo. Inside the cell, DNA is present in the nucleus as a complex with proteins known as chromatin. For the last few years we have been studying the interaction of these DNA-binding small molecules at the chromatin level with emphasis on the drug-induced structural alterations in chromatin. Our studies have shown that at the chromatin level these molecules could be classified in two broad categories: single-binding and dual-binding molecules. Single-binding molecules access only DNA in the chromatin, while the dual-binding molecules could bind to both DNA and the associated histone(s). Structural effects of the DNA-binding molecules upon chromatin in light of the above broad categories and the associated biological implications of the two types of binding are discussed.
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Affiliation(s)
- Dipak Dasgupta
- Biophysics Division, Saha Institute of Nuclear Physics, Bidhan Nagar, Kolkata 700 064, India.
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6
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Majumder P, Dasgupta D. Effect of DNA groove binder distamycin A upon chromatin structure. PLoS One 2011; 6:e26486. [PMID: 22046291 PMCID: PMC3202541 DOI: 10.1371/journal.pone.0026486] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Accepted: 09/27/2011] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Distamycin A is a prototype minor groove binder, which binds to B-form DNA, preferentially at A/T rich sites. Extensive work in the past few decades has characterized the binding at the level of double stranded DNA. However, effect of the same on physiological DNA, i.e. DNA complexed in chromatin, has not been well studied. Here we elucidate from a structural perspective, the interaction of distamycin with soluble chromatin, isolated from Sprague-Dawley rat. METHODOLOGY/PRINCIPAL FINDINGS Chromatin is a hierarchical assemblage of DNA and protein. Therefore, in order to characterize the interaction of the same with distamycin, we have classified the system into various levels, according to the requirements of the method adopted, and the information to be obtained. Isothermal titration calorimetry has been employed to characterize the binding at the levels of chromatin, chromatosome and chromosomal DNA. Thermodynamic parameters obtained thereof, identify enthalpy as the driving force for the association, with comparable binding affinity and free energy for chromatin and chromosomal DNA. Reaction enthalpies at different temperatures were utilized to evaluate the change in specific heat capacity (ΔCp), which, in turn, indicated a possible binding associated structural change. Ligand induced structural alterations have been monitored by two complementary methods--dynamic light scattering, and transmission electron microscopy. They indicate compaction of chromatin. Using transmission electron microscopy, we have visualized the effect of distamycin upon chromatin architecture at di- and trinucleosome levels. Our results elucidate the simultaneous involvement of linker bending and internucleosomal angle contraction in compaction process induced by distamycin. CONCLUSIONS/SIGNIFICANCE We summarize here, for the first time, the thermodynamic parameters for the interaction of distamycin with soluble chromatin, and elucidate its effect on chromatin architecture. The study provides insight into a ligand induced compaction phenomenon, and suggests new mechanisms of chromatin architectural alteration.
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Affiliation(s)
- Parijat Majumder
- Biophysics Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India
| | - Dipak Dasgupta
- Biophysics Division, Saha Institute of Nuclear Physics, Kolkata, West Bengal, India
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7
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Role of structure-proteins in the porphyrin-DNA interaction. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2009; 96:207-15. [PMID: 19604705 DOI: 10.1016/j.jphotobiol.2009.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 06/17/2009] [Accepted: 06/18/2009] [Indexed: 11/22/2022]
Abstract
We studied the complexation of meso-tetrakis(4-N-methylpyridyl)porphyrin (TMPyP) with HeLa nucleosomes and compared it to our earlier results on T7 phage nucleoprotein complex (NP) and isolated DNA. To identify binding modes and relative concentrations of the bound TMPyP forms, the porphyrin absorption spectra were analyzed at various base pair/porphyrin ratios. Spectral decomposition and circular dichroism measurements proved that the two main binding modes of TMPyP, i.e., external binding and intercalation occur also in the nucleosomes. The DNA superstructure maintained by the proteins decreases its accessibility for TMPyP similarly in both nucleoproteins. A difference is observed between the partitioning of the two binding modes: in the case of nucleosome the ratio of intercalation to groove-binding is changed from 60/40 to 40/60 as determined for T7 NP and for isolated DNA-s. Using UV and CD melting studies, we revealed that TMPyP destabilizes the DNA-protein interaction in the nucleosomes but not in the T7 phage. Lastly, photoinduced reaction of bound TMPyP caused alterations in DNA structures and DNA-protein interactions within both nucleoprotein complexes; the nucleosomes were found to be more sensitive to the photoreaction.
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8
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Human chromosome fragility. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2008; 1779:3-16. [DOI: 10.1016/j.bbagrm.2007.10.005] [Citation(s) in RCA: 150] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2007] [Revised: 10/02/2007] [Accepted: 10/03/2007] [Indexed: 11/21/2022]
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9
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Tawar U, Bansal S, Shrimal S, Singh M, Tandon V. Nuclear condensation and free radical scavenging: a dual mechanism of bisbenzimidazoles to modulate radiation damage to DNA. Mol Cell Biochem 2007; 305:221-33. [PMID: 17619948 DOI: 10.1007/s11010-007-9546-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Accepted: 06/21/2007] [Indexed: 10/23/2022]
Abstract
The complexing of histones with DNA and the resulting condensation of chromatin protects mammalian cell, from radiation-induced strand breakage. In the present study, benzimidazoles DMA and TBZ showed marked radioprotection through drug-induced compaction of chromatin and direct quenching of free radicals generated by radiation. The mammalian cells were incubated with 100 microM concentration of DMA and TBZ and irradiated at 5 Gy; both the ligands showed nuclei condensation suggesting a probable mechanism to protect DNA from radiation damage. The bisubstituted analogs of Hoechst 33342 are found to be better free radical scavengers and protect DNA against radiation-induced damage at a lower concentration than the parent molecule. Both the ligands also quenched free radicals in isolated free radical system suggesting their dual mode of action against radiation-induced damage to DNA. Molecules binding to the chromatin alter gene expression, whereas in this study both the ligands have not shown any profound effect on the nucleosome assembly and gene expression in vitro and in vivo. Both ligands afford a 2-fold protection by altering DNA structure as well as through direct free radical quenching in bulk solution in comparison to the parent ligand, which acts only through quenching of free radicals.
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Affiliation(s)
- Urmila Tawar
- Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, Delhi, 110007, India
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10
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Majumder P, Pradhan SK, Devi PG, Pal S, Dasgupta D. Chromatin as a target for the DNA-binding anticancer drugs. Subcell Biochem 2007; 41:145-89. [PMID: 17484128 PMCID: PMC7121056 DOI: 10.1007/1-4020-5466-1_8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Chemotherapy has been a major approach to treat cancer. Both constituents of chromatin, chromosomal DNA and the associated chromosomal histone proteins are the molecular targets of the anticancer drugs. Small DNA binding ligands, which inhibit enzymatic processes with DNA substrate, are well known in cancer chemotherapy. These drugs inhibit the polymerase and topoisomerase activity. With the advent in the knowledge of chromatin chemistry and biology, attempts have shifted from studies of the structural basis of the association of these drugs or small ligands (with the potential of drugs) with DNA to their association with chromatin and nucleosome. These drugs often inhibit the expression of specific genes leading to a series of biochemical events. An overview will be given about the latest understanding of the molecular basis of their action. We shall restrict to those drugs, synthetic or natural, whose prime cellular targets are so far known to be chromosomal DNA.
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Affiliation(s)
- Parijat Majumder
- Biophysics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-I, Bidhannagar, Kolkata-700 064, India
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11
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Trzupek JD, Gottesfeld JM, Boger DL. Alkylation of duplex DNA in nucleosome core particles by duocarmycin SA and yatakemycin. Nat Chem Biol 2006; 2:79-82. [PMID: 16415862 DOI: 10.1038/nchembio761] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2005] [Accepted: 12/08/2005] [Indexed: 11/09/2022]
Abstract
(+)-Yatakemycin (1, Fig. 1) and (+)-duocarmycin SA (2) are exceptionally potent, naturally occurring antitumor agents that derive their biological properties through a characteristic sequence-selective DNA-alkylation reaction. Studies have shown that both the AT-rich binding selectivity (shape-selective recognition) and the alkylation catalysis (shape-dependent catalysis) that contribute to the alkylation selectivity are dependent on the DNA minor groove shape and size characteristics of an AT-rich sequence (ref. 6 and references therein; refs. 7,8). Here we report the alkylation properties of yatakemycin and duocarmycin SA on free DNA (alpha-satellite DNA) and the same sequence bound in a nucleosome core particle (NCP) modeling the state of DNA in eukaryotic cells. Both compounds showed a clear, relatively unaltered ability to alkylate DNA packaged in NCPs in terms of both alkylating efficiency and sequence selectivity, despite the steric and conformational perturbations imposed by NCP packaging. These findings highlight the dynamic nature of NCP-bound DNA and illustrate that cell- and protein-free DNA-alkylation studies of members of this class of antitumor drugs provide valuable insights into their properties.
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Affiliation(s)
- John D Trzupek
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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12
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Lemke K, Wojciechowski M, Laine W, Bailly C, Colson P, Baginski M, Larsen AK, Skladanowski A. Induction of unique structural changes in guanine-rich DNA regions by the triazoloacridone C-1305, a topoisomerase II inhibitor with antitumor activities. Nucleic Acids Res 2005; 33:6034-47. [PMID: 16254080 PMCID: PMC1270948 DOI: 10.1093/nar/gki904] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Revised: 09/29/2005] [Accepted: 09/29/2005] [Indexed: 11/12/2022] Open
Abstract
We recently reported that the antitumor triazoloacridone, compound C-1305, is a topoisomerase II poison with unusual properties. In this study we characterize the DNA interactions of C-1305 in vitro, in comparison with other topoisomerase II inhibitors. Our results show that C-1305 binds to DNA by intercalation and possesses higher affinity for GC- than AT-DNA as revealed by surface plasmon resonance studies. Chemical probing with DEPC indicated that C-1305 induces structural perturbations in DNA regions with three adjacent guanine residues. Importantly, this effect was highly specific for C-1305 since none of the other 22 DNA interacting drugs tested was able to induce similar structural changes in DNA. Compound C-1305 induced stronger structural changes in guanine triplets at higher pH which suggested that protonation/deprotonation of the drug is important for this drug-specific effect. Molecular modeling analysis predicts that the zwitterionic form of C-1305 intercalates within the guanine triplet, resulting in widening of both DNA grooves and aligning of the triazole ring with the N7 atoms of guanines. Our results show that C-1305 binds to DNA and induces very specific and unusual structural changes in guanine triplets which likely plays an important role in the cytotoxic and antitumor activity of this unique compound.
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Affiliation(s)
- Krzysztof Lemke
- Laboratory of Cellular and Molecular Pharmacology, Department of Pharmaceutical Technology and Biochemistry, Gdansk University of TechnologyGdansk, Poland
- Group of Biology and Pharmacogenetics of Human Tumors, INSERM U673, Université Pierre et Marie Curie (UPMC-Paris 6), Hôpital Saint-AntoineParis, 75571 Paris 12, France
| | - Marcin Wojciechowski
- Laboratory of Cellular and Molecular Pharmacology, Department of Pharmaceutical Technology and Biochemistry, Gdansk University of TechnologyGdansk, Poland
| | - William Laine
- INSERM U-524 et Laboratoire de Pharmacologie Antitumorale du Centre Oscar Lambret, IRCL59045 Lille Cedex, France
| | - Christian Bailly
- INSERM U-524 et Laboratoire de Pharmacologie Antitumorale du Centre Oscar Lambret, IRCL59045 Lille Cedex, France
| | - Pierre Colson
- Biospectroscopy and Physical Chemistry Unit, Department of Chemistry and Natural and Synthetic Drugs Research Center, University of LiègeSart-Tilman, 4000, Liège, Belgium
| | - Maciej Baginski
- Laboratory of Cellular and Molecular Pharmacology, Department of Pharmaceutical Technology and Biochemistry, Gdansk University of TechnologyGdansk, Poland
| | - Annette K. Larsen
- Group of Biology and Pharmacogenetics of Human Tumors, INSERM U673, Université Pierre et Marie Curie (UPMC-Paris 6), Hôpital Saint-AntoineParis, 75571 Paris 12, France
| | - Andrzej Skladanowski
- Laboratory of Cellular and Molecular Pharmacology, Department of Pharmaceutical Technology and Biochemistry, Gdansk University of TechnologyGdansk, Poland
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13
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Wang YH. Chromatin structure of human chromosomal fragile sites. Cancer Lett 2005; 232:70-8. [PMID: 16229940 DOI: 10.1016/j.canlet.2005.07.040] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2005] [Accepted: 07/30/2005] [Indexed: 02/07/2023]
Abstract
Cytological appearance of fragile sites as non-staining gaps in metaphase chromosomes suggests an abnormality in chromatin structure. Studies of fragile sites at three levels of chromosome organization: (1) examining the ability of DNA derived from fragile sites to form nucleosomes-the basic structural element of chromosomes, (2) probing the arrangement of nucleosome arrays over fragile sites in fragile site-expressing cell lines, and (3) visualizing fragile sites in higher-order chromatin organization, reveal an unusual chromatin structure associated with fragile sites. This fragile site-associated chromatin structure might play an active role in DNA metabolic processes such as replication, transcription, repair and recombination, which are closely linked to the instability of fragile sites.
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Affiliation(s)
- Yuh-Hwa Wang
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, 675 Hoes Lane, Piscataway, NJ 08854, USA
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14
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Felbor U, Feichtinger W, Schmid M. The rare human fragile site 16B. Cytogenet Genome Res 2003; 100:85-8. [PMID: 14526167 DOI: 10.1159/000072841] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2002] [Accepted: 12/04/2002] [Indexed: 11/19/2022] Open
Abstract
The rare human fragile site 16B (FRA16B) has been found to occur spontaneously. Its expression in lymphocyte cultures can also be induced or greatly enhanced by addition of chemicals which are known to bind to AT-rich DNA regions. Following optimal treatment with 150 microg/ml berenil 24 h prior to fixation, the heterozygote frequency of FRA16B is found to be about 5% in populations of European descent. Thus, FRA16B represents the most common of the rare fragile sites. Consistent with cytogenetic observations, the molecular characterization of FRA16B revealed that it is an amplified 33-base pair AT-rich minisatellite repeat. These interindividually variable, extremely large repeat expansions of 15-70 kb in size do not seem to interfere with the expression of genes essential for human development since heterozygotes and homozygotes for FRA16B are normal.
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Affiliation(s)
- U Felbor
- Institut für Humangenetik, Biozentrum, Würzburg, Germany
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15
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Hsu YY, Wang YH. Human fragile site FRA16B DNA excludes nucleosomes in the presence of distamycin. J Biol Chem 2002; 277:17315-9. [PMID: 11880377 DOI: 10.1074/jbc.m200901200] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human fragile sites are weak staining gaps in chromosomes generated by specific culture conditions. The short CGG repeating DNA derived from folate-sensitive fragile sites has been shown to exclude single nucleosomes. To test whether this nucleosome exclusion model provides a general molecular mechanism for the formation of fragile sites, a different class of fragile site, the 33-base pair AT-rich repeating DNAs derived from the rare distamycin-inducible site, FRA16B, was examined for its ability to assemble single nucleosomes and nucleosome arrays using in vitro nucleosome reconstitution methods. The FRA16B DNA fragments strongly exclude nucleosome assembly only in the presence of distamycin, and increasing the number of 33-bp repeats increases the effect of distamycin in the destabilization of the nucleosome formation, suggesting a common mechanism for the formation of fragile sites.
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Affiliation(s)
- Ying Ying Hsu
- Department of Biochemistry, Robert Wood Johnson Medical School, University of Medicine and Dentistry of New Jersey, Piscataway, New Jersey 08854, USA
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16
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Affiliation(s)
- J Portugal
- Departamento de Biologia Molecular y Celular, Instituto de Biologia Molecular de Barcelona, CSIC, Barcelona 08034, Spain
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17
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Gottesfeld JM, Melander C, Suto RK, Raviol H, Luger K, Dervan PB. Sequence-specific recognition of DNA in the nucleosome by pyrrole-imidazole polyamides. J Mol Biol 2001; 309:615-29. [PMID: 11397084 DOI: 10.1006/jmbi.2001.4694] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The ability of DNA-binding proteins to recognize their cognate sites in chromatin is restricted by the structure and dynamics of nucleosomal DNA, and by the translational and rotational positioning of the histone octamer. Here, we use six different pyrrole-imidazole polyamides as sequence-specific molecular probes for DNA accessibility in nucleosomes. We show that sites on nucleosomal DNA facing away from the histone octamer, or even partially facing the histone octamer, are fully accessible and that nucleosomes remain fully folded upon ligand binding. Polyamides only failed to bind where sites are completely blocked by interactions with the histone octamer. Removal of the amino-terminal tails of either histone H3 or histone H4 allowed these polyamides to bind. These results demonstrate that much of the DNA in the nucleosome is freely accessible for molecular recognition in the minor groove, and also support a role for the amino-terminal tails of H3 and H4 in modulating accessibility of nucleosomal DNA.
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Affiliation(s)
- J M Gottesfeld
- Department of Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA.
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18
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Foderà R, Caneva R, Canzonetta C, Savino M. DNA accessibility to minor groove ligands in core nucleosome and chromatosome. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2000; 19:1231-40. [PMID: 11097053 DOI: 10.1080/15257770008033046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Using the circular dichroism spectra induced in the visible by the binding to the minor groove of DNA, we found that Hoechst 33258 is able to occupy its specific sites even when these are located inside the nucleosome structure. This high accessibility of the DNA in the nucleosome is not modified by the removal of the amino-terminal domains of the octamer histones and is not reduced by the presence of linker histone. Interesting and reasonable differences were found in the association constants.
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Affiliation(s)
- R Foderà
- CNR Centro di Studio per gli Acidi Nucleici, Università di Roma La Sapienza, Rome, Italy
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19
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Abstract
Transcription regulatory proteins are an integral component of the cell nucleus and a great deal of work has been done to characterize the subnuclear distribution of these proteins. Much of the early work on this subject was done with immunofluorescence. The development of the green fluorescent protein (GFP) as a marker for intracellular protein localization has allowed for the real time study of protein localization and dynamics in living cells. In this review, an overview of the way in which GFP can be utilized to study protein localization is presented.
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Affiliation(s)
- C T Baumann
- Laboratory of Receptor Biology and Gene Expression, NCI/NIH, Building 41, Room B602, 41 Library Drive, MSC 5055, Bethesda, Maryland, 20892-5055, USA
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20
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Abstract
In this review, both cationic and neutral synthetic ligands that bind in the minor groove of DNA are discussed. Certain bis-distamycins and related lexitropsins show activities against human immunodeficiency virus (HIV)-1 and HIV-2 at low nanomolar concentrations. DAPI binds strongly to AT-containing polymers and is located in the minor groove of DNA. DAPI intercalates in DNA sequences that do not contain at least three consecutive AT bp. Berenil can also exhibit intercalative, as well as minor groove binding, properties depending on sequence. Furan-containing analogues of berenil play an important role in their activities against Pneumocystis carinii and Cryptosporidium parvuam infections in vivo. Pt(II)-berenil conjugates show a good activity profile against HL60 and U-937 human leukemic cells. Pt-pentamidine shows higher antiproliferative activity against small cell lung, non-small cell lung, and melanoma cancer cell lines compared with many other tumor cell lines. trans-Butenamidine shows good anti-P. carinii activity in rats. Pentamidine is used against P. carinii pneumonia in individuals infected with HIV who are at high risk from this infection. A comparison of the cytotoxic potencies of adozelesin, bizelesin, carzelesin, cisplatin, and doxorubicin indicates that adozelesin is a potent analog of CC-1065. Naturally occurring pyrrolo[2,1-c][l,4]benzodiazepines such as anthramycin have a 2- to 3-bp sequence specificity, but a synthetic PBD dimer spans 6 bp, actively recognizing a central 5'-GATC sequence. The crosslinking efficiency of PBD dimers is much greater than that of other major groove crosslinkers, such as cisplatin, melphalan, etc. Neothramycin is used clinically for the treatment of superficial carcinoma of the bladder.
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Affiliation(s)
- B S Reddy
- Department of Chemistry, University of Alberta, Edmonton, Canada
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Fitzgerald DJ, Anderson JN. Selective nucleosome disruption by drugs that bind in the minor groove of DNA. J Biol Chem 1999; 274:27128-38. [PMID: 10480928 DOI: 10.1074/jbc.274.38.27128] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Previous studies have shown that drugs which bind in the DNA minor groove reduce the curvature of bent DNA. In this article, we examined the effects of these drugs on the nucleosome assembly of DNA molecules that display different degrees of intrinsic curvature. DAPI (4,6-diamidino-2-phenylindole) inhibited the assembly of a histone octamer onto a 192-base pair circular DNA fragment from Caenorhabditis elegans and destabilized a nucleosome that was previously assembled on this segment. The inhibitory effect was highly selective since it was not seen with nonbent molecules, bent molecules with noncircular shapes, or total genomic DNA. This marked template specificity was attributed to the binding of the ligand to multiple oligo A-tracts distributed over the length of the fragment. A likely mechanism for the effect is that the bound ligand prevents the further compression of the DNA into the minor groove which is required for assembly of DNA into nucleosomes. To further characterize the effects of the drug on chromatin formation, a nucleosome was assembled onto a 322-base pair DNA fragment that contained the circular element and a flanking nonbent segment of DNA. The position of the nucleosome along the fragment was then determined using a variety of nuclease probes including exonuclease III, micrococcal nuclease, DNase I, and restriction enzymes. The results of these studies revealed that the nucleosome was preferentially positioned along the circular element in the absence of DAPI but assembled onto the nonbent flanking sequence in the presence of the drug. DAPI also induced the directional movement of the nucleosome from the circular element onto the nonbent flanking sequence when a nucleosome preassembled onto this template was exposed to the drug under physiologically relevant conditions.
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Affiliation(s)
- D J Fitzgerald
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907-1392, USA
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