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Defossez PA. Chromatin and transcription in Nucleic Acids Research: the first 50 years. Nucleic Acids Res 2024; 52:13485-13489. [PMID: 39607690 DOI: 10.1093/nar/gkae1151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Accepted: 11/12/2024] [Indexed: 11/29/2024] Open
Affiliation(s)
- Pierre-Antoine Defossez
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, 35 Rue H. Brion, F-75013 Paris, France
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2
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Manickavinayaham S, Velez-Cruz R, Biswas AK, Chen J, Guo R, Johnson DG. The E2F1 transcription factor and RB tumor suppressor moonlight as DNA repair factors. Cell Cycle 2020; 19:2260-2269. [PMID: 32787501 PMCID: PMC7513849 DOI: 10.1080/15384101.2020.1801190] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/19/2020] [Accepted: 07/06/2020] [Indexed: 02/08/2023] Open
Abstract
The E2F1 transcription factor and RB tumor suppressor are best known for their roles in regulating the expression of genes important for cell cycle progression but, they also have transcription-independent functions that facilitate DNA repair at sites of damage. Depending on the type of DNA damage, E2F1 can recruit either the GCN5 or p300/CBP histone acetyltransferases to deposit different histone acetylation marks in flanking chromatin. At DNA double-strand breaks, E2F1 also recruits RB and the BRG1 ATPase to remodel chromatin and promote loading of the MRE11-RAD50-NBS1 complex. Knock-in mouse models demonstrate important roles for E2F1 post-translational modifications in regulating DNA repair and physiological responses to DNA damage. This review highlights how E2F1 moonlights in DNA repair, thus revealing E2F1 as a versatile protein that recruits many of the same chromatin-modifying enzymes to sites of DNA damage to promote repair that it recruits to gene promoters to regulate transcription.
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Affiliation(s)
- Swarnalatha Manickavinayaham
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
| | - Renier Velez-Cruz
- Department of Biochemistry and Molecular Genetics, College of Graduate Studies, Midwestern University, Downers Grove, IL, USA
| | - Anup K. Biswas
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Jie Chen
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
| | - Ruifeng Guo
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - David G. Johnson
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX, USA
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Abstract
Eukaryotic genomes are packaged into chromatin, which is the physiological substrate for all DNA transactions, including DNA damage and repair. Chromatin organization imposes major constraints on DNA damage repair and thus undergoes critical rearrangements during the repair process. These rearrangements have been integrated into the "access-repair-restore" (ARR) model, which provides a molecular framework for chromatin dynamics in response to DNA damage. Here, we take a historical perspective on the elaboration of this model and describe the molecular players involved in damaged chromatin reorganization in human cells. In particular, we present our current knowledge of chromatin assembly coupled to DNA damage repair, focusing on the role of histone variants and their dedicated chaperones. Finally, we discuss the impact of chromatin rearrangements after DNA damage on chromatin function and epigenome maintenance.
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4
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Hsieh YH, Chang YY, Su IJ, Yen CJ, Liu YR, Liu RJ, Hsieh WC, Tsai HW, Wang LHC, Huang W. Hepatitis B virus pre-S2 mutant large surface protein inhibits DNA double-strand break repair and leads to genome instability in hepatocarcinogenesis. J Pathol 2015; 236:337-47. [PMID: 25775999 DOI: 10.1002/path.4531] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 02/25/2015] [Accepted: 03/09/2015] [Indexed: 12/27/2022]
Abstract
Although hepatitis B virus (HBV) has been established to cause hepatocellular carcinoma (HCC), the exact mechanism remains to be clarified. Type II ground glass hepatocytes (GGHs) harbouring the HBV pre-S2 mutant large surface protein (LHBS) have been recognized as a morphologically distinct hallmark of HCC in the advanced stages of chronic HBV infection. Considering its preneoplastic nature, we hypothesized that type II GGH may exhibit high genomic instability, which is important for the carcinogenic process in chronic HBV carriers. In this study we found that pre-S2 mutant LHBS directly interacted with importin α1, the key factor that recognizes cargos undergoing nuclear transportation mediated by the importin α/β-associated nuclear pore complex (NPC). By interacting with importin α1, which inhibits its function as an NPC factor, pre-S2 mutant LHBS blocked nuclear transport of an essential DNA repair and recombination factor, Nijmegen breakage syndrome 1 (NBS1), upon DNA damage, thereby delaying the formation of nuclear foci at the sites of DNA double-strand breaks (DSBs). Pre-S2 mutant LHBS was also found to block NBS1-mediated homologous recombination repair and induce multi-nucleation of cells. In addition, pre-S2 mutant LHBS transgenic mice showed genomic instability, indicated by increased global gene copy number variations (CNVs), which were significantly higher than those in hepatitis B virus X mice, indicating that pre-S2 mutant LHBS is the major viral oncoprotein inducing genomic instability in HBV-infected hepatocytes. Consistently, the human type II GGHs in HCC patients exhibited increased DNA DSBs representing significant genomic instability. In conclusion, type II GGHs harbouring HBV pre-S2 mutant oncoprotein represent a high-risk marker for the loss of genome integrity in chronic HBV carriers and explain the complex chromosome changes in HCCs. Mouse array CGH raw data: GEO Accession No. GSE61378 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE61378).
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Affiliation(s)
- Yi-Hsuan Hsieh
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Ying Chang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ih-Jen Su
- Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan, Taiwan
| | - Chia-Jui Yen
- Department of Haematology and Oncology, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Yi-Ru Liu
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Ren-Jei Liu
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Chuan Hsieh
- Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan, Taiwan
| | - Hung-Wen Tsai
- Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan
| | - Lily Hui-Ching Wang
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu, Taiwan
| | - Wenya Huang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Institute of Basic Medicine, National Cheng Kung University, Tainan, Taiwan.,Centre of Infectious Disease and Signalling Research, National Cheng Kung University, Tainan, Taiwan
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5
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Abstract
The removal of DNA damage from the eukaryotic genome requires DNA repair enzymes to operate within the complex environment of chromatin. We review the evidence for chromatin rearrangements during nucleotide excision repair and discuss the extent and possible molecular mechanisms of these rearrangements, focusing on events at the nucleosome level of chromatin structure.
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Affiliation(s)
- J G Moggs
- Dynamique de la Chromatine, Institut Curie, Section de Recherche, UMR 144, Paris, France
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6
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Cleaver JE, Jen J, Charles WC, Mitchell DL. Cyclobutane dimers and (6-4) photoproducts in human cells are mended with the same patch sizes. Photochem Photobiol 1991; 54:393-402. [PMID: 1784640 DOI: 10.1111/j.1751-1097.1991.tb02033.x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The size of excision repair patches corresponding to excision of (6-4) pyrimidine-pyrimidone photoproducts and (5-5, 6-6) cyclobutane dimers have been independently determined by using bromodeoxyuridine substitution and density increases in isopycnic gradients of small DNA fragments. The two classes of photoproducts were distinguished by using (a) a xeroderma pigmentosum (XP) revertant cell line that excises (6-4) photoproducts normally, but does not excise cyclobutane dimers from bulk DNA or from an actively transcribed sequence; (b) an XP cell line containing the denV gene of bacteriophage T4, which repairs only cyclobutane dimers by a unique glycosylase mechanism, and (c) normal cells analyzed during time intervals in which cyclobutane dimer repair is the main repair process in action. The patch sizes for the two lesions were similar under all conditions and were estimated to be approximately 30-40 bases. These values are slightly large than corresponding estimates for Escherichia coli and Saccharomyces cerevisiae but close to estimates from in vitro experiments with human cell extracts. The size of 30 bases may consequently be very close to the actual distance between cleavage sites made on either side of a photoproduct during repair.
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Affiliation(s)
- J E Cleaver
- Laboratory of Radiobiology and Environmental Health, University of California, San Francisco 94143-0750
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7
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Mathis GA, Althaus FR. Isolation of 8-methoxypsoralen accessible DNA domains from chromatin of intact cells. Cell Biol Toxicol 1990; 6:35-45. [PMID: 2334867 DOI: 10.1007/bf00135025] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The chromatin organization of living mammalian cells was probed using 8-methoxypsoralen (MOP). In intact cells, MOP intercalates into DNA domains which are also preferentially accessible to micrococcal nuclease. After UV365 nm irradiation of MOP-treated cells, this chemical forms bifunctional adducts crosslinking the two strands of DNA. Following extraction of cellular DNA, heat denaturation and renaturation at low temperature, the fraction of crosslinked DNA is obtained following enzymatic hydrolysis of unhybridized, non-crosslinked DNA by nuclease S1 treatment. An application of this procedure in the isolation of 8-methoxypsoralen-accessible DNA domains during DNA excision repair is shown.
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Affiliation(s)
- G A Mathis
- University of Zürich-Tierspital, Institute of Pharmacology and Biochemistry, Switzerland
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8
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Telford DJ, Stewart BW. Micrococcal nuclease: its specificity and use for chromatin analysis. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1989; 21:127-37. [PMID: 2663558 DOI: 10.1016/0020-711x(89)90100-6] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- D J Telford
- Children's Leukaemia and Cancer Research Unit, Prince of Wales Children's Hospital, Randwick, NSW, Australia
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9
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Telford DJ, Stewart BW. Characteristics of chromatin release during digestion of nuclei with micrococcal nuclease: preferential solubilization of nascent RNA at low enzyme concentration. THE INTERNATIONAL JOURNAL OF BIOCHEMISTRY 1989; 21:1235-40. [PMID: 2482203 DOI: 10.1016/0020-711x(89)90009-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
1. Extensive digestion of nuclei with micrococcal nuclease (MNase), commonly used in the analysis of chromatin structure, results in the production of mono- and dinucleosomal chromatin fragments. 2. Digestion of nuclei from a range of cell types with low enzyme concentrations solubilized high molecular weight polynucleosomal fragments, some greater than 22 kb long. 3. Such digestion conditions also resulted in extensive solubilization of nascent RNA which contributed considerably to the nucleic acid content of the soluble fraction. 4. We conclude that the contribution of RNA to total nucleic acid content of the soluble fraction should be taken into consideration when nuclei are digested with low concentrations of MNase.
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Affiliation(s)
- D J Telford
- Children's Leukaemia and Cancer Research Unit, Prince of Wales Children's Hospital, Randwick, NSW, Australia
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10
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Affiliation(s)
- V A Bohr
- Laboratory of Molecular Pharmacology, National Cancer Institute, Bethesda, Maryland 20892
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11
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Abstract
The limited DNA excision repair that occurs in the chromatin of UV-irradiated growth arrested cells isolated from a xeroderma pigmentosum (XP) complementation group C patient is clustered in localized regions. The repaired DNA was found to be more sensitive to nicking by endogenous nucleases than the bulk of the DNA. The extra-sensitivity does not change with increasing amounts of DNA damage or repair activity in the locally-repaired regions and is retained through a 24-h chase period. We suggest that these results are due to the occurrence of DNA repair limited to pre-existing, non-transient chromatin fractions that contain actively transcribed DNA. A similar extra-sensitivity of repaired DNA was not detected in cells of normal or XP complementation group A strains that exhibit either normal or limited repair located randomly throughout their genomes. The association between endogenous nuclease sensitivity and clustered repair probably defines a normal excision repair pathway that is specific for selected chromatin domains. The repair defect in XP-C strains may be one in pathways targeted for other endogenous nuclease-resistant domains.
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12
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Guo XC, Morgan WF, Cleaver JE. Hoechst 33258 dye generates DNA-protein cross-links during ultraviolet light-induced photolysis of bromodeoxyuridine in replicated and repaired DNA. Photochem Photobiol 1986; 44:131-6. [PMID: 2430309 DOI: 10.1111/j.1751-1097.1986.tb03576.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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13
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Kaysen JH, Amari NM, Lambert MW. Enhancement of two apurinic/apyrimidinic endonuclease activities from normal but not xeroderma pigmentosum lymphoblastoid cells by nucleosome structure. Mutat Res 1986; 165:221-31. [PMID: 2422553 DOI: 10.1016/0167-8817(86)90057-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The influence of nucleosomes on the activity of two chromatin-associated apurinic/apyrimidinic (AP) DNA endonuclease activities, pIs 9.2 and 9.8, from normal and xeroderma pigmentosum, complementation group A (XPA), lymphoblastoid cells was examined. These AP endonuclease activities were studied on non-nucleosomal and nucleosomal plasmid pWT830/pBR322 DNA which had been reconstituted with core (H2A, H2B, H3, H4) or total (core plus H1) histones from normal or XPA cells. Both nucleosomal and non-nucleosomal DNA was rendered partially AP by alkylation with 12.5 mM methyl methanesulfonate, followed by heating it at 70 degrees C, to produce approximately three AP sites per DNA molecule. The activities of both normal lymphoblastoid AP endonuclease activities on nucleosomal AP DNA, reconstituted with core histones, was approximately 2.5 times greater than that on non-nucleosomal AP DNA. When histone H1 was added to the system, this increase was reduced. XPA AP endonuclease activities, on the other hand, did not show any increase in activity on nucleosomal AP DNA reconstituted with core histones. These differences between normal and XPA endonuclease activities on AP nucleosomal DNA were the same regardless of whether histones from normal or XPA cells were used in the reconstituted system.
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14
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Periodic changes of chromatin organization associated with rearrangement of repair patches accompany DNA excision repair of mammalian cells. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(17)38447-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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15
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Modulation of chromatin superstructure induced by poly(ADP-ribose) synthesis and degradation. J Biol Chem 1986. [DOI: 10.1016/s0021-9258(19)62715-8] [Citation(s) in RCA: 132] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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16
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Dresler SL. Stimulation of deoxyribonucleic acid excision repair in human fibroblasts pretreated with sodium butyrate. Biochemistry 1985; 24:6861-9. [PMID: 4074730 DOI: 10.1021/bi00345a019] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The effect of pretreatment with sodium butyrate on DNA excision repair was studied in intact and permeable confluent (i.e., growth-inhibited) diploid human fibroblasts. Exposure to 20 mM sodium butyrate for 48 h increased subsequent ultraviolet (UV)-induced [methyl-3H]thymidine incorporation by intact AG1518 fibroblasts by 1.8-fold and by intact IMR-90 fibroblasts by 1.2-1.3-fold. UV-induced incorporation of deoxy[5-3H]cytidine, deoxy[6-3H]cytidine, and deoxy[6-3H]uridine, however, showed lesser degrees of either stimulation or inhibition in butyrate-pretreated cells. This result suggested that measurements of butyrate's effect on DNA repair synthesis in intact cells are confounded by simultaneous changes in nucleotide metabolism. The effect of butyrate on excision repair was also studied in permeable human fibroblasts in which excision repair is dependent on exogenous nucleotides. Butyrate pretreatment stimulated UV-induced repair synthesis by 1.3-1.7-fold in permeable AG1518 cells and by 1.5-2-fold in permeable IMR-90 cells. This stimulation of repair synthesis was not due to changes in repair patch size or composition or in the efficiency of DNA damage production but rather resulted from a butyrate-induced increase in the rate of damage-specific incision of DNA. The increased rate of incision in butyrate-pretreated cells could be due either to increased levels of enzymes mediating steps in excision repair at or before incision or to alterations in chromatin structure making damage sites in DNA more accessible to repair enzymes.
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Cleaver JE, Killpack S, Gruenert DC. Formation and repair of psoralen-DNA adducts and pyrimidine dimers in human DNA and chromatin. ENVIRONMENTAL HEALTH PERSPECTIVES 1985; 62:127-134. [PMID: 3002774 PMCID: PMC1568663 DOI: 10.1289/ehp.8562127] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2023]
Abstract
DNA damage and repair in human cells exposed to ultraviolet light (254 nm) or to psoralen derivatives plus 360 nm light were compared by means of a variety of analytic techniques. The two kinds of damage show considerable structural similarity; both involve cyclobutyl bonds to 5,6 positions of pyrimidines as major products and have various minor products. In purified DNA, pyrimidine dimers, but not psoralen adducts, cause structural distortions that are substances for digestion with single-strand-specific nucleases. Whereas pyrimidine dimers are randomly produced in chromatin, psoralen adducts, are concentrated approximately 2- to 4-fold in linker regions of chromatin at doses that are not highly lethal. Chromatin shows considerable mobility; assignment of DNA to linker or core regions is not permanent, and psoralen adducts initially concentrated in linker regions become randomized after 10 hr. Pyrimidine dimers and psoralen adducts are excised by normal cells but not by repair-deficient xeroderma pigmentosum cells. This repair process requires DNA polymerase alpha, but its rate in ultraviolet-damaged cells is twice that in psoralen-damaged cells. Conversion of monoadducts to DNA-DNA crosslinks reduces the rate of repair because of the increased complexity of the damaged site.
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Hunting DJ, Dresler SL, Lieberman MW. Multiple conformational states of repair patches in chromatin during DNA excision repair. Biochemistry 1985; 24:3219-26. [PMID: 3927974 DOI: 10.1021/bi00334a022] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In mammalian cells, newly synthesized DNA repair patches are highly sensitive to digestion by staphylococcal nuclease (SN), but with time, they acquire approximately the same nuclease resistance as the DNA in bulk chromatin. We refer to the process which restores native SN sensitivity to repaired DNA as chromatin rearrangement. We find that during repair of ultraviolet damage in human fibroblasts, repair patch synthesis and ligation occur at approximately the same rate, with ligation delayed by about 4 min, but that chromatin rearrangement is only 75% as rapid. Thus, repair-incorporated nucleotides can exist in at least three distinct states: unligated/unrearranged, ligated/unrearranged, and ligated/rearranged. Inhibition of repair patch synthesis by aphidicolin or hydroxyurea results in inhibition of both patch ligation and chromatin rearrangement, confirming that repair patch completion and/or ligation are prerequisites for rearrangement. We also analyze the kinetics of SN digestion of repair-incorporated nucleotides at various extents of rearrangement and find the data to be consistent with the existence of two or more forms of unrearranged repair patch which have different sensitivities to digestion by SN. These data indicate that the chromatin rearrangement which restores native SN sensitivity to repaired DNA is a multistep process. The multiple forms of unrearranged chromatin with different SN sensitivities may include the unligated/unrearranged and ligated/unrearranged states. If so, the differences in SN sensitivity must arise from differences in chromatin structure, because SN does not differentiate between ligated and unligated repair patches in naked DNA.
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Cleaver JE. Chromatin dynamics. Fast and slow modes of nucleosome movement revealed through psoralen binding and repair. BIOCHIMICA ET BIOPHYSICA ACTA 1985; 824:163-73. [PMID: 3970931 DOI: 10.1016/0167-4781(85)90093-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Psoralen adducts, when formed in DNA at low frequencies that permit extensive survival of normal and repair-deficient cells, are found in both linker and core regions of nucleosomes, but are slightly enriched in the linker sites. The relative frequencies of adducts obtained with 5-methylisopsoralen and angelicin, which form only monoadducts, and 8-methoxypsoralen and trimethylpsoralen, which form monoadducts and cross-links, represent an enrichment in linker DNA that is approx. 2-3-fold higher per nucleotide than in core DNA. 5-Methylisopsoralen monoadducts, which are initially in linker DNA, become randomized during 12 h of growth. This suggests a slow lateral movement of nucleosomes with respect to DNA and implies that linker and core regions of DNA are not permanent assignments. Randomization of 5-methylisopsoralen adducts is independent of the synthesis of DNA, RNA, protein, or poly(ADP-ribose) and is also independent of DNA repair. Excision repair of these adducts, in contrast, causes rapid local changes in nucleosome conformation and an initial increase in staphylococcal nuclease sensitivity that reverts to the sensitivity of bulk chromatin in less than 1 h. Chromatin, therefore, can undergo at least two distinct dynamic changes under physiological conditions: a slow randomization of the nucleosomes with respect to DNA, and a rapid but transient local rearrangement to facilitate repair.
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Nairn RS, Mitchell DL, Clarkson JM. Role of chromatin structure in the repair of DNA photoproducts in mammalian cells. INTERNATIONAL JOURNAL OF RADIATION BIOLOGY AND RELATED STUDIES IN PHYSICS, CHEMISTRY, AND MEDICINE 1985; 47:181-9. [PMID: 3872272 DOI: 10.1080/09553008514550251] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Chinese hamster ovary cells were irradiated with u.v. light and chromatin was isolated and fractionated according to magnesium-solubility in low ionic strength conditions. The minor, magnesium-soluble chromatin fraction was demonstrated to be enriched by over three-fold in transcriptionally active sequences and had proteins associated with it characteristic of transcriptionally active chromatin. Using a sensitive radioimmunoassay for u.v.-induced DNA photoproducts, we have shown that there are no differences in either induction or repair of u.v. DNA photoproducts in chromatin fractions from cells irradiated at low u.v. fluence.
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21
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Niedergang CP, de Murcia G, Ittel ME, Pouyet J, Mandel P. Time course of polynucleosome relaxation and ADP-ribosylation. Correlation between relaxation and histone H1 hyper-ADP-ribosylation. EUROPEAN JOURNAL OF BIOCHEMISTRY 1985; 146:185-91. [PMID: 3917919 DOI: 10.1111/j.1432-1033.1985.tb08637.x] [Citation(s) in RCA: 36] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Isolated rat pancreatic polynucleosomes were poly(ADP-ribosylated) with purified calf thymus poly(ADP-ribose) polymerase. A time course study was performed using an NAD concentration of 200 microM and changes in nucleosomal structure were investigated by means of electron microscopy visualization and sedimentation velocity determinations. In parallel, analyses of histone H1 poly(ADP-ribosylation) and determinations of DNA polymerase alpha activity on ADP-ribosylated polynucleosomes were done at different time intervals. A direct kinetic correlation between ADP-ribose incorporation, polynucleosome relaxation amd histone H1 hyper-ADP-ribosylation was established. In addition, DNA polymerase alpha activity was highly stimulated on ADP-ribosylated polynucleosomes as compared to control ones, suggesting increased accessibility of DNA to enzymatic action. Because of the strong evidence implicating histone H1 in the maintenance of higher-ordered chromatin structures, the present study may provide a basis for the interpretation of the involvement of the histone H1 ADP-ribosylation reaction in DNA rearrangements during DNA repair, replication or gene expression.
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22
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23
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24
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Mondello C, Zei G, Nuzzo F. Correlation between unscheduled DNA synthesis and chromosome condensation in mitoses from human lymphocytes. Mutat Res 1985; 142:45-8. [PMID: 3974598 DOI: 10.1016/s0165-7992(85)80011-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The correlation between chromosome condensation and amount of repair synthesis after UV irradiation was studied in PHA-stimulated human lymphocytes. The length of selected chromosomes and the number of autoradiographic grains were determined in cells from late prophase to middle metaphase. The statistical analysis of data indicates a highly significant correlation between the two variables and a positive linear regression of the number of grains on chromosome length.
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25
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Chiu SM, Sokany NM, Friedman LR, Oleinick NL. Differential processing of ultraviolet or ionizing radiation-induced DNA-protein cross-links in Chinese hamster cells. INTERNATIONAL JOURNAL OF RADIATION BIOLOGY AND RELATED STUDIES IN PHYSICS, CHEMISTRY, AND MEDICINE 1984; 46:681-90. [PMID: 6335496 DOI: 10.1080/09553008414551921] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The yield and repairability of DNA-protein cross-links have been compared after gamma- or U.V.-irradiation of Chinese hamster V79-379 lung fibroblasts. Using a filter-binding assay, cross-linked DNA can be specifically isolated after doses between 10 and 100 Gy of gamma-radiation and fluences between 20 and 300 J/m2 of U.V.-radiation. After ionizing radiation, the majority of DNA cross-linked to protein is released with biphasic kinetics, requiring 1 h for removal of 50 per cent of the cross-linked DNA and 24 h for 90 per cent release. In these cells, U.V.-induced cross-linked DNA is not removed; on the contrary, the yield of apparent DNA-protein complexes increases during postirradiation incubation. Prior gamma-irradiation, to initiate the associated repair system, does not stimulate release of U.V.-induced cross-linked DNA. Inhibition of protein synthesis by cycloheximide affects neither the removal of gamma-ray-induced cross-linked DNA nor the increase in U.V.-induced cross-linked DNA. 3-Aminobenzamide, an inhibitor of poly(ADP-ribose) polymerase, slows the second phase of release after gamma-irradiation as well as the increase in apparent cross-links after U.V.-irradiation. Thus, even though both types of DNA-protein cross-links can be detected by the same assay, their structures or other factors must be substantially different, since the repair system for one type does not recognize the other.
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Cleaver JE, Gruenert DC. Repair of psoralen adducts in human DNA: differences among xeroderma pigmentosum complementation groups. J Invest Dermatol 1984; 82:311-5. [PMID: 6707485 DOI: 10.1111/1523-1747.ep12260596] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Angelicin and 5-methylangelicin formed photoadducts in DNA after illumination with 360-nm radiation that were excised rapidly from normal cells; 80-90% of the initial angelicin adducts and 65% of the initial 5-methylangelicin adducts were excised within 24 h. Xeroderma pigmentosum group A cells excised about 20% of the angelicin adducts, group D cells excised 55-60%, and group E, 80%. This extent of excision resembles that reported for pyrimidine dimers in these complementation groups, except for group D. Repair of psoralen adducts may not, therefore, be identical in every respect to repair of pyrimidine dimers. Group D cells seem exceptionally able to repair angelicin adducts in comparison to their repair of pyrimidine dimers, suggesting that these cells lack a gene product that is required to a greater extent for the repair of pyrimidine dimers than for the repair of angelicin adducts.
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Requirement of ATP for specific incision of ultraviolet-damaged DNA during excision repair in permeable human fibroblasts. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(17)44169-x] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Nose K, Okamoto H. Detection of carcinogen-induced DNA breaks by nick translation in permeable cells. Biochem Biophys Res Commun 1983; 111:383-9. [PMID: 6188463 DOI: 10.1016/0006-291x(83)90317-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
A nick-translation reaction with E. coli DNA polymerase I (pol. I) was used to detect in situ DNA breaks produced by chemical carcinogens. Normal human fibroblasts treated with N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) in various doses were permeabilized with lysolecithin, and were nick translated in the presence of [3H]dCTP and pol. I. The radioactivity incorporated increased with MNNG concentration, and was directly proportional to the poly(ADP-ribose) synthetase activity. Other DNA-damaging agents such as bleomycin or 4-nitroquinoline 1-oxide also caused the nick translation rate to increase. When MNNG-treated cells were cultured in fresh medium containing no MNNG, the increase in the rate of nick translation in permeable cells became less and this decrease was abolished by addition of aphidicolin or cytosine arabinoside. The nick translation method described here may be a useful means for estimating intrinsic DNA breaks in cells treated with carcinogens.
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Abstract
Cockayne syndrome (CS) is a genetic disorder showing cellular sensitivity to the lethal effects of UV-irradiation. No defects in unscheduled DNA synthesis or in daughter-strand repair have been detected after UV-irradiation of CS cells. We have studied several aspects of excision repair, particularly at early times after UV-irradiation, and with one exception, we have not been able to detect any difference in the response of normal and CS cells to UV-irradiation, by measuring: (1) the rate of formation of incision breaks in the presence of 1-beta-D-arabinofuranosylcytosine (araC); (2) the amount of repair replication as measured by equilibrium centrifugation; (3) the ligation of repaired DNA to pre-existing DNA; (4) the digestibility of repaired DNA after treatment of nuclei with micrococcal nuclease. The single exception was a pair of CS strains from sibling donors in which the rate of uncoupled incision due to the presence of either araC or the specific inhibitor of DNA polymerase alpha, aphidicolin, was slightly faster than in other cells studied. This effect was absent in the heterozygous parents. However, since this was not seen in two other CS strains in the same genetic complementation group, we can not attribute this increased rate of incision to the defective CS gene. We conclude that, within the limits of resolution of these techniques, CS cells do not have a detectable defect in excision repair.
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Zolan ME, Smith CA, Calvin NM, Hanawalt PC. Rearrangement of mammalian chromatin structure following excision repair. Nature 1982; 299:462-4. [PMID: 7121585 DOI: 10.1038/299462a0] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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32
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Smerdon MJ, Watkins JF, Lieberman MW. Effect of histone H1 removal on the distribution of ultraviolet-induced deoxyribonucleic acid repair synthesis within chromatin. Biochemistry 1982; 21:3879-85. [PMID: 7138811 DOI: 10.1021/bi00259a024] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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33
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Ishiwata K, Oikawa A. Chromatin structure interferes with excision of abnormal bases from DNA. BIOCHIMICA ET BIOPHYSICA ACTA 1982; 698:15-21. [PMID: 6288101 DOI: 10.1016/0167-4781(82)90178-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Cell-free extracts of human lymphoblastoid cells NL3 excised almost all uracil residues from free DNA with misincorporated dUMP, but only about half the uracil residues from nuclei, chromatin and reconstituted chromatin with dUMP-misincorporated DNA. This difference in susceptibility to uracil-DNA glycosylase of free and complexed DNAs was similar to the difference in susceptibility of free and complexed methylated DNAs to 3-methyladenine-DNA glycosylase. Methylated poly(dA-dT) was also protected by formation of complexes with calf thymus chromosomal proteins. It seems that the nucleosome structure prevents the action of DNA glycosylases. The very high sensitivity of PBS1 phage DNA, which contains uracil as a natural component, in complexes with calf thymus chromosomal proteins as well as in the free form [1] was confirmed. This high sensitivity seems ascribable to the high uracil content of PBS1 DNA. Methylated nucleosome monomers and dimers, and reconstituted nucleosome monomers containing methylated DNA of about 150 bp length, were considerably more resistant to 3-methyladenine-DNA glycosylase than chromatin reconstituted from methylated DNA of longer chain length. This may be due to the lower proportion of linker regions of free form stretches of the DNA chain in nucleosome oligomers.
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34
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Cleaver JE. Normal reconstruction of DNA supercoiling and chromatin structure in cockayne syndrome cells during repair of damage from ultraviolet light. Am J Hum Genet 1982; 34:566-75. [PMID: 7102674 PMCID: PMC1685362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
The chromatin of human cells undergoes structural rearrangements during excision repair of ultraviolet damage in DNA that were detected by transient relaxation of DNA supercoiling and increased staphylococcal nuclease digestibility of repaired sites. Inhibition of polymerization and/or ligation of repaired regions with inhibitors of DNA polymerase alpha (cytosine arabinoside and aphidicolin) resulted in the accumulation of single-strand breaks, delayed reconstruction of DNA supercoiling, and maintenance of the staphylococcal nuclease digestibility. These observations suggest that reconstruction of the native chromatin state requires completion of repaired regions with covalent ligation into the DNA strands. Although previous claims have been made that a late stage associated with ligation of repaired regions may be defective in cells from patients with Cockayne syndrome, complete reconstruction of the native chromatin occurred in cells from three unrelated patients after ultraviolet irradiation. No abnormality in repair was therefore detected in Cockayne syndrome cells. The hypersensitivity of cell survival and semiconservative DNA replication to damage by ultraviolet light in this human disorder must therefore be regarded as features of a primary defect in DNA metabolism unrelated to DNA repair.
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Hamlet SM, Lavin MF, Jennings PA. Increased rate of repair of ultraviolet-induced DNA strand breaks in mitogen stimulated lymphocytes. INTERNATIONAL JOURNAL OF RADIATION BIOLOGY AND RELATED STUDIES IN PHYSICS, CHEMISTRY, AND MEDICINE 1982; 41:483-91. [PMID: 6980198 DOI: 10.1080/09553008214550561] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Previous results from this laboratory have shown that phytohaemagglutinin-stimulated bovine lymphocytes exhibit a peak of ultraviolet-induced DNA repair synthesis 3 to 4 days after addition of mitogen. The level of repair synthesis was approximately tenfold higher than that in unstimulated lymphocytes. We have extended these studies to examine the rate of repair of strand breaks in U.V.-irradiated bovine lymphocytes. The extent of breakage of DNA was shown to be the same in mitogen-stimulated and unstimulated lymphocytes from two breeds of cattle, when determined by sedimentation of nucleoids on sucrose gradients. However, in mitogen-stimulated cells the time taken to repair DNA strand breaks was 6 hours compared to 12 hours in stationary phase lymphocytes after a U.V. dose of 5 J/m2. These results suggest that the increased rate of repair of strand breaks is due to the induction of enzymes involved at the post-incision stage of DNA repair. Thus the increased level of repair synthesis observed in earlier work correlates with an increased rate of repair of DNA strand breaks in phytohaemagglutinin-stimulated bovine lymphocytes.
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Althaus FR, Lawrence SD, Sattler GL, Pitot HC. ADP-ribosyltransferase activity in cultured hepatocytes. Interactions with DNA repair. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(19)83809-7] [Citation(s) in RCA: 80] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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37
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Niggli HJ, Cerutti PA. Nucleosomal distribution of thymine photodimers following far- and near-ultraviolet irradiation. Biochem Biophys Res Commun 1982; 105:1215-23. [PMID: 7092895 DOI: 10.1016/0006-291x(82)91098-1] [Citation(s) in RCA: 56] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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38
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Lipetz PD, Galsky AG, Stephens RE. Relationship of DNA tertiary and quaternary structure to carcinogenic processes. Adv Cancer Res 1982; 36:165-210. [PMID: 6751038 DOI: 10.1016/s0065-230x(08)60425-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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39
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Hanawalt PC, Cooper PK, Ganesan AK, Lloyd RS, Smith CA, Zolan ME. Repair responses to DNA damage: enzymatic pathways in E coli and human cells. J Cell Biochem 1982; 18:271-83. [PMID: 7040432 DOI: 10.1002/jcb.1982.240180303] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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40
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Chiu SM, Oleinick NL. The sensitivity of active and inactive chromatin to ionizing radiation-induced DNA strand breakage. INTERNATIONAL JOURNAL OF RADIATION BIOLOGY AND RELATED STUDIES IN PHYSICS, CHEMISTRY, AND MEDICINE 1982; 41:71-7. [PMID: 6800971 DOI: 10.1080/09553008214550061] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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41
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Musich PR, Brown FL, Maio JJ. Nucleosome phasing and micrococcal nuclease cleavage of African green monkey component alpha DNA. Proc Natl Acad Sci U S A 1982; 79:118-22. [PMID: 6275381 PMCID: PMC345673 DOI: 10.1073/pnas.79.1.118] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The micrococcal nuclease cleavage of intact nuclear chromatin from African green monkey cells and of the completely deproteinized sequences was studied by using high-resolution analytical and DNA sequencing gels and secondary restriction enzyme analysis. When deproteinized component alpha DNA was used as substrate, not all phosphodiester bonds in the 172-base-pair repeat units were cleaved with equal frequency by the nuclease. A distinct preference for the cleavage of A-T rather than G-C bonds was observed; however, A + T-richness in itself did not confer susceptibility to cleavage by micrococcal nuclease. The results suggested that, in deproteinized DNA, nuclease cleavage at particular dinucleotides may be influenced more by the effect of adjacent sequences than by the composition of the dinucleotide. In contrast to complex cleavage patterns of the deproteinized component alpha DNA which arose because of multiple cleavage sites in the repeat unit, micrococcal nuclease cleaved component alpha nuclear chromatin at one site per nucleosome repeat, near position 126 in the nucleotide sequence. This simple chromatin cleavage pattern is consistent with the discrete nucleosomal structure of component alpha in chromatin and a direct phase relationship between the component alpha DNA sequence repeats and the nucleosome protein structural repeats.
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42
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Lieberman MW. Alterations in chromatin structure during DNA excision repair. BASIC LIFE SCIENCES 1982; 20:303-14. [PMID: 7115269 DOI: 10.1007/978-1-4613-3476-7_20] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Work from a number of laboratories recently has demonstrated that alterations in chromatin structure occur during excision repair in mammalian cells. It is now clear that when cells are damaged with a wide variety of chemical agents or ultraviolet radiation, almost all of the repair synthesis is initially sensitive to staphylococcal nuclease. With time, there is a redistribution of the counts incorporated during excision repair synthesis so that many of them become nuclease resistant and associated with nucleosome core length DNA. In our laboratory, we have demonstrated this phenomenon in human cells damaged with N-acetoxy-2-acetylaminofluorene, 7-bromomethylbenz[a]anthracene, and ultraviolet radiation. It is clear from the work of others that the phenomenon is not unique to human cells since African green monkey cells damaged with either ultraviolet radiation or angelicin also show an initial nuclease sensitivity of repair-incorporated nucleotides follow by rearrangement. Two models to explain these observations have been proposed; one suggests that there is an unfolding of nucleosomes during excision repair followed by a refolding, while the other suggests that sliding of core proteins with respect to DNA occurs during excision repair. These models, as well as recent data bearing on them, will be discussed.
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