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Role of Histone Tails and Single Strand DNA Breaks in Nucleosomal Arrest of RNA Polymerase. Int J Mol Sci 2023; 24:ijms24032295. [PMID: 36768621 PMCID: PMC9917218 DOI: 10.3390/ijms24032295] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/13/2023] [Accepted: 01/19/2023] [Indexed: 01/26/2023] Open
Abstract
Transcription through nucleosomes by RNA polymerases (RNAP) is accompanied by formation of small intranucleosomal DNA loops (i-loops). The i-loops form more efficiently in the presence of single-strand breaks or gaps in a non-template DNA strand (NT-SSBs) and induce arrest of transcribing RNAP, thus allowing detection of NT-SSBs by the enzyme. Here we examined the role of histone tails and extranucleosomal NT-SSBs in i-loop formation and arrest of RNAP during transcription of promoter-proximal region of nucleosomal DNA. NT-SSBs present in linker DNA induce arrest of RNAP +1 to +15 bp in the nucleosome, suggesting formation of the i-loops; the arrest is more efficient in the presence of the histone tails. Consistently, DNA footprinting reveals formation of an i-loop after stalling RNAP at the position +2 and backtracking to position +1. The data suggest that histone tails and NT-SSBs present in linker DNA strongly facilitate formation of the i-loops during transcription through the promoter-proximal region of nucleosomal DNA.
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Structure of an Intranucleosomal DNA Loop That Senses DNA Damage during Transcription. Cells 2022; 11:cells11172678. [PMID: 36078089 PMCID: PMC9454427 DOI: 10.3390/cells11172678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/22/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
Transcription through chromatin by RNA polymerase II (Pol II) is accompanied by the formation of small intranucleosomal DNA loops containing the enzyme (i-loops) that are involved in survival of core histones on the DNA and arrest of Pol II during the transcription of damaged DNA. However, the structures of i-loops have not been determined. Here, the structures of the intermediates formed during transcription through a nucleosome containing intact or damaged DNA were studied using biochemical approaches and electron microscopy. After RNA polymerase reaches position +24 from the nucleosomal boundary, the enzyme can backtrack to position +20, where DNA behind the enzyme recoils on the surface of the histone octamer, forming an i-loop that locks Pol II in the arrested state. Since the i-loop is formed more efficiently in the presence of SSBs positioned behind the transcribing enzyme, the loop could play a role in the transcription-coupled repair of DNA damage hidden in the chromatin structure.
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Mhamdi-Ghodbani M, Starzonek C, Degenhardt S, Bender M, Said M, Greinert R, Volkmer B. UVB damage response of dermal stem cells as melanocyte precursors compared to keratinocytes, melanocytes, and fibroblasts from human foreskin. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2021; 220:112216. [PMID: 34023595 DOI: 10.1016/j.jphotobiol.2021.112216] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/21/2021] [Accepted: 05/14/2021] [Indexed: 02/09/2023]
Abstract
Ultraviolet B (UVB) radiation induces mutagenic DNA photolesions in skin cells especially in form of cyclobutane pyrimidine dimers (CPDs). Protection mechanisms as DNA repair and apoptosis are of great importance in order to prevent skin carcinogenesis. In human skin, neural crest-derived precursors of melanocytes, the dermal stem cells (DSCs), are discussed to be at the origin of melanoma. Although they are constantly exposed to solar UV radiation, it is still not investigated how DSCs cope with UV-induced DNA damage. Here, we report a comparative study of the DNA damage response after irradiation with a physiological relevant UVB dose in DSCs in comparison to fibroblasts, melanocytes and keratinocytes isolated from human foreskin. Within our experimental settings, DSCs were able to repair DNA photolesions as efficient as the other skin cell types with solely keratinocytes repairing significantly faster. Interestingly, only fibroblasts showed significant alterations in cell cycle distribution in terms of a transient S phase arrest following irradiation. Moreover, with the applied UVB dose none of the examined cell types was prone to UVB-induced apoptosis. This may cause persistent genomic alterations and in case of DSCs it may have severe consequences for their daughter cells, the differentiated melanocytes. Altogether, this is the first study demonstrating a similar UV response in dermal stem cells compared to differentiated skin cells.
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Affiliation(s)
- Mouna Mhamdi-Ghodbani
- Skin Cancer Center, Division of Molecular Cell Biology, Elbe Klinikum Buxtehude, 21614 Buxtehude, Germany
| | - Christin Starzonek
- Skin Cancer Center, Division of Molecular Cell Biology, Elbe Klinikum Buxtehude, 21614 Buxtehude, Germany
| | - Sarah Degenhardt
- Skin Cancer Center, Division of Molecular Cell Biology, Elbe Klinikum Buxtehude, 21614 Buxtehude, Germany
| | - Marc Bender
- Skin Cancer Center, Division of Molecular Cell Biology, Elbe Klinikum Buxtehude, 21614 Buxtehude, Germany
| | | | - Rüdiger Greinert
- Skin Cancer Center, Division of Molecular Cell Biology, Elbe Klinikum Buxtehude, 21614 Buxtehude, Germany
| | - Beate Volkmer
- Skin Cancer Center, Division of Molecular Cell Biology, Elbe Klinikum Buxtehude, 21614 Buxtehude, Germany.
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Valente WJ, Ericson NG, Long AS, White PA, Marchetti F, Bielas JH. Mitochondrial DNA exhibits resistance to induced point and deletion mutations. Nucleic Acids Res 2016; 44:8513-8524. [PMID: 27550180 PMCID: PMC5062989 DOI: 10.1093/nar/gkw716] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/04/2016] [Indexed: 12/17/2022] Open
Abstract
The accumulation of somatic mitochondrial DNA (mtDNA) mutations contributes to the pathogenesis of human disease. Currently, mitochondrial mutations are largely considered results of inaccurate processing of its heavily damaged genome. However, mainly from a lack of methods to monitor mtDNA mutations with sufficient sensitivity and accuracy, a link between mtDNA damage and mutation has not been established. To test the hypothesis that mtDNA-damaging agents induce mtDNA mutations, we exposed MutaTMMouse mice to benzo[a]pyrene (B[a]P) or N-ethyl-N-nitrosourea (ENU), daily for 28 consecutive days, and quantified mtDNA point and deletion mutations in bone marrow and liver using our newly developed Digital Random Mutation Capture (dRMC) and Digital Deletion Detection (3D) assays. Surprisingly, our results demonstrate mutagen treatment did not increase mitochondrial point or deletion mutation frequencies, despite evidence both compounds increase nuclear DNA mutations and demonstrated B[a]P adduct formation in mtDNA. These findings contradict models of mtDNA mutagenesis that assert the elevated rate of mtDNA mutation stems from damage sensitivity and abridged repair capacity. Rather, our results demonstrate induced mtDNA damage does not readily convert into mutation. These findings suggest robust mitochondrial damage responses repress induced mutations after mutagen exposure.
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Affiliation(s)
- William J Valente
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Medical Scientist Training Program, University of Washington School of Medicine, Seattle, WA 98195, USA Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA
| | - Nolan G Ericson
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Alexandra S Long
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Paul A White
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Francesco Marchetti
- Environmental Health Science and Research Bureau, Health Canada, Ottawa, ON K1A 0K9, Canada
| | - Jason H Bielas
- Translational Research Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA Department of Pathology, University of Washington, Seattle, WA 98195, USA Human Biology Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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Pestov NA, Gerasimova NS, Kulaeva OI, Studitsky VM. Structure of transcribed chromatin is a sensor of DNA damage. SCIENCE ADVANCES 2015; 1:e1500021. [PMID: 26601207 PMCID: PMC4646769 DOI: 10.1126/sciadv.1500021] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 05/03/2015] [Indexed: 06/05/2023]
Abstract
Early detection and repair of damaged DNA is essential for cell functioning and survival. Although multiple cellular systems are involved in the repair of single-strand DNA breaks (SSBs), it remains unknown how SSBs present in the nontemplate strand (NT-SSBs) of DNA organized in chromatin are detected. The effect of NT-SSBs on transcription through chromatin by RNA polymerase II was studied. NT-SSBs localized in the promoter-proximal region of nucleosomal DNA and hidden in the nucleosome structure can induce a nearly quantitative arrest of RNA polymerase downstream of the break, whereas more promoter-distal SSBs moderately facilitate transcription. The location of the arrest sites on nucleosomal DNA suggests that formation of small intranucleosomal DNA loops causes the arrest. This mechanism likely involves relief of unconstrained DNA supercoiling accumulated during transcription through chromatin by NT-SSBs. These data suggest the existence of a novel chromatin-specific mechanism that allows the detection of NT-SSBs by the transcribing enzyme.
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Affiliation(s)
- Nikolay A. Pestov
- Department of Pharmacology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
| | | | - Olga I. Kulaeva
- Biology Faculty, Lomonosov Moscow State University, Moscow, Russia
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
| | - Vasily M. Studitsky
- Department of Pharmacology, Rutgers Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA
- Biology Faculty, Lomonosov Moscow State University, Moscow, Russia
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
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Multiple roles of ubiquitination in the control of nucleotide excision repair. Mech Ageing Dev 2011; 132:355-65. [DOI: 10.1016/j.mad.2011.03.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2010] [Revised: 03/10/2011] [Accepted: 03/16/2011] [Indexed: 11/19/2022]
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The origin of a derived superkingdom: how a gram-positive bacterium crossed the desert to become an archaeon. Biol Direct 2011; 6:16. [PMID: 21356104 PMCID: PMC3056875 DOI: 10.1186/1745-6150-6-16] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Accepted: 02/28/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The tree of life is usually rooted between archaea and bacteria. We have previously presented three arguments that support placing the root of the tree of life in bacteria. The data have been dismissed because those who support the canonical rooting between the prokaryotic superkingdoms cannot imagine how the vast divide between the prokaryotic superkingdoms could be crossed. RESULTS We review the evidence that archaea are derived, as well as their biggest differences with bacteria. We argue that using novel data the gap between the superkingdoms is not insurmountable. We consider whether archaea are holophyletic or paraphyletic; essential to understanding their origin. Finally, we review several hypotheses on the origins of archaea and, where possible, evaluate each hypothesis using bioinformatics tools. As a result we argue for a firmicute ancestry for archaea over proposals for an actinobacterial ancestry. CONCLUSION We believe a synthesis of the hypotheses of Lake, Gupta, and Cavalier-Smith is possible where a combination of antibiotic warfare and viral endosymbiosis in the bacilli led to dramatic changes in a bacterium that resulted in the birth of archaea and eukaryotes. REVIEWERS This article was reviewed by Patrick Forterre, Eugene Koonin, and Gáspár Jékely.
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Al-Moghrabi NM, Al-Sharif IS, Aboussekhra A. The RAD9-dependent gene trans-activation is required for excision repair of active genes but not for repair of non-transcribed DNA. Mutat Res 2009; 663:60-8. [PMID: 19428371 DOI: 10.1016/j.mrfmmm.2009.01.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 01/20/2009] [Accepted: 01/26/2009] [Indexed: 10/21/2022]
Abstract
The Saccharomyces cerevisiae RAD9 and RAD24 are two cell cycle checkpoint genes required for UV-dependent up-regulation of a battery of genes involved in different metabolic pathways. RAD9 is also implicated in nucleotide excision repair (NER); however, its precise role is still unclear. For the present study, we made use of the high-resolution primer extension technique to show that the RAD9-deleted cells are deficient in the repair of both strands of the URA3 gene. Interestingly, this defect was suppressed by over-expressing the RAD24 gene, suggesting that the role of RAD9 in NER is indirect probably through the UV-dependent trans-activation of some NER factors. Accordingly, we present evidence that the inhibition of UV-related de novo protein synthesis by cycloheximide has no effect on the rad9Delta mutant while it suppresses the correcting effect of RAD24 over-expression. Importantly, we have also shown that RAD9 has no role in repair of transcriptionally inactive DNA sequences (URA3 promoter and transcriptionally silent GAL10 gene). Furthermore, de novo protein synthesis was not required for NER in the absence of transcription-coupled NER. This implies that RAD9-dependent gene up-regulation is required for NER only when this process is coupled to transcription.
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Affiliation(s)
- Nisreen M Al-Moghrabi
- King Faisal Specialist Hospital & Research Center, Department of Biological and Medical Research, Riyadh, Saudi Arabia
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Li B, Si J, DeWille JW. Ultraviolet radiation (UVR) activates p38 MAP kinase and induces post-transcriptional stabilization of the C/EBPδ mRNA in G0 growth arrested mammary epithelial cells. J Cell Biochem 2008; 103:1657-69. [PMID: 17902160 DOI: 10.1002/jcb.21554] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The G(0) growth arrest (quiescent) state is highly conserved in evolution to promote survival under adverse environmental conditions. To maintain viability, G(0) growth arrested cells limit gene expression to essential growth control and pro-survival genes. CCAAT enhancer binding protein delta (C/EBPdelta), a member of the C/EBP family of nuclear proteins, is highly expressed in G(0) growth arrested mammary epithelial cells (MECs). Although C/EBPdelta gene transcription is elevated during G(0) growth arrest, C/EBPdelta mRNA and protein are relatively short lived, suggesting tight control of the cellular C/EBPdelta content in unstressed, quiescent cells. Treatment of G(0) growth arrested MECs with ultraviolet radiation (UVR) dramatically increases the C/EBPdelta mRNA half-life (approximately 4-fold) and protein content (approximately 3-fold). The mRNA stabilizing effects of UVR treatment are mediated by the C/EBPdelta mRNA 3'untranslated region, which contains an AU rich element. UVR increased p38 MAP kinase (MAPK) activation and SB203580, a p38 MAPK inhibitor, blocked UVR-induced C/EBPdelta mRNA stabilization. UVR increased the nuclear to cytoplasmic translocation of HuR, an ARE-binding protein that functions in mRNA stabilization. Finally, HuR siRNA treatment blocked UVR-induced stabilization of the C/EBPdelta and C/EBPbeta mRNAs but had no effect on C/EBPzeta (CHOP) mRNA stability. In summary, G(0) growth arrested MECs respond to UVR treatment by activating p38 MAPK, increasing HuR translocation and HuR/C/EBPdelta mRNA binding and stabilizing the C/EBPdelta mRNA. These results identify post-transcriptional stabilization of the C/EBPdelta mRNA as a mechanism to increase C/EBPdelta levels in the stress response of quiescent cells to UVR.
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Affiliation(s)
- Bin Li
- Department of Veterinary Biosciences, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio 43210, USA
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Foresti M, Avallone B. Only complete rejoining of DNA strand breaks after UVC allows K562 cell proliferation and DMSO induction of erythropoiesis. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2007; 90:8-16. [PMID: 18032060 DOI: 10.1016/j.jphotobiol.2007.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2006] [Revised: 05/10/2007] [Accepted: 05/17/2007] [Indexed: 11/30/2022]
Abstract
DNA strand breaks are early intermediates of the repair of UVC-induced DNA damage, however, since they severely impair cellular activities, their presence should be limited in time. In this study, the effects of incomplete repair of UVC-induced DNA strand breaks are investigated on K562 cell growth and the induction of erythroid differentiation by addition of DMSO to the cell culture medium. The kinetics were followed after UV irradiation by single cell gel electrophoresis, and in total cell population by alkaline or neutral agarose gel electrophoresis. Shortly after exposure, an extensive fragmentation occurred in DNA; DNA double strand breaks were negatively correlated with recovery time for DNA integrity. DNA damage induced by UVC 9J/m2 rapidly triggered necrosis in a large fraction of irradiated K562 cells, and only 40% of treated cells resumed growth at a very low rate within 24h of culture. The addition of DMSO to the culture medium of cells 15min after UVC, when DNA strand break repair was not yet complete, produced apoptosis in >70% of surviving cells, as determined by TUNEL assay. Conversely, if DMSO was added when the resealing of DNA strand breaks was complete, surviving K562 cells retained full growth capacity, and their progeny underwent erythroid differentiation with normal levels of erythroid proteins, delta-aminolevulinic acid dehydrase and hemoglobin. This study shows that the extent of DNA strand break repair influences cell proliferation and the DMSO induced erythroid program, and the same UVC dose can have opposite effects depending on cellular status.
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Affiliation(s)
- Magda Foresti
- University of Naples Federico II, Department of Biological Sciences, Section of Genetics and Molecular Biology, via Mezzocannone 8, 80134 Naples, Italy.
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Nouspikel TP, Hyka-Nouspikel N, Hanawalt PC. Transcription domain-associated repair in human cells. Mol Cell Biol 2006; 26:8722-30. [PMID: 17015469 PMCID: PMC1636821 DOI: 10.1128/mcb.01263-06] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nucleotide excision repair (NER), which is arguably the most versatile DNA repair system, is strongly attenuated in human cells of the monocytic lineage when they differentiate into macrophages. Within active genes, however, both DNA strands continue to be proficiently repaired. The proficient repair of the nontranscribed strand cannot be explained by the dedicated subpathway of transcription-coupled repair (TCR), which is targeted to the transcribed strand in expressed genes. We now report that the previously termed differentiation-associated repair (DAR) depends upon transcription, but not simply upon RNA polymerase II (RNAPII) encountering a lesion: proficient repair of both DNA strands can occur in a part of a gene that the polymerase never reaches, and even if the translocation of RNAPII is blocked with transcription inhibitors. This suggests that DAR may be a subset of global NER, restricted to the subnuclear compartments or chromatin domains within which transcription occurs. Downregulation of selected NER genes with small interfering RNA has confirmed that DAR relies upon the same genes as global genome repair, rather than upon TCR-specific genes. Our findings support the general view that the genomic domains within which transcription is active are more accessible than the bulk of the genome to the recognition and repair of lesions through the global pathway and that TCR is superimposed upon that pathway of NER.
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Affiliation(s)
- Thierry P Nouspikel
- Institute for Cancer Studies, University of Sheffield Medical School, Beech Hill Road, Sheffield S10 2RX, United Kingdom.
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