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Bai G, Dhillon N, Felton C, Meissner B, Saint-John B, Shelansky R, Meyerson E, Hrabeta-Robinson E, Hodjat B, Boeger H, Brooks AN. Probing chromatin accessibility with small molecule DNA intercalation and nanopore sequencing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.20.585815. [PMID: 38562899 PMCID: PMC10983977 DOI: 10.1101/2024.03.20.585815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Genome-wide identification of chromatin organization and structure has been generally probed by measuring accessibility of the underlying DNA to nucleases or methyltransferases. These methods either only observe the positioning of a single nucleosome or rely on large enzymes to modify or cleave the DNA. We developed adduct sequencing (Add-seq), a method to probe chromatin accessibility by treating chromatin with the small molecule angelicin, which preferentially intercalates into DNA not bound to core nucleosomes. We show that Nanopore sequencing of the angelicin-modified DNA is possible and allows visualization and analysis of long single molecules with distinct chromatin structure. The angelicin modification can be detected from the Nanopore current signal data using a neural network model trained on unmodified and modified chromatin-free DNA. Applying Add-seq to Saccharomyces cerevisiae nuclei, we identified expected patterns of accessibility around annotated gene loci in yeast. We also identify individual clusters of single molecule reads displaying different chromatin structure at specific yeast loci, which demonstrates heterogeneity in the chromatin structure of the yeast population. Thus, using Add-seq, we are able to profile DNA accessibility in the yeast genome across long molecules.
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Affiliation(s)
- Gali Bai
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, 95064, United States of America
| | - Namrita Dhillon
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, 95064, United States of America
| | - Colette Felton
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, 95064, United States of America
| | - Brett Meissner
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, 95064, United States of America
| | - Brandon Saint-John
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, 95064, United States of America
| | - Robert Shelansky
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, 95064, United States of America
| | - Elliot Meyerson
- Cognizant AI Labs, San Francisco, California, 94105, United States of America
| | - Eva Hrabeta-Robinson
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, 95064, United States of America
| | - Babak Hodjat
- Cognizant AI Labs, San Francisco, California, 94105, United States of America
| | - Hinrich Boeger
- Department of Molecular, Cell, and Developmental Biology, University of California, Santa Cruz, Santa Cruz, California, 95064, United States of America
| | - Angela N. Brooks
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, 95064, United States of America
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Ataur Rahman M, Kim NH, Yang H, Huh SO. Angelicin induces apoptosis through intrinsic caspase-dependent pathway in human SH-SY5Y neuroblastoma cells. Mol Cell Biochem 2012; 369:95-104. [DOI: 10.1007/s11010-012-1372-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 06/20/2012] [Indexed: 12/22/2022]
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Komura JI, Ikehata H, Mori T, Ono T. Fully functional global genome repair of (6-4) photoproducts and compromised transcription-coupled repair of cyclobutane pyrimidine dimers in condensed mitotic chromatin. Exp Cell Res 2012; 318:623-31. [PMID: 22248875 DOI: 10.1016/j.yexcr.2012.01.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2011] [Revised: 12/09/2011] [Accepted: 01/03/2012] [Indexed: 12/27/2022]
Abstract
During mitosis, chromatin is highly condensed, and activities such as transcription and semiconservative replication do not occur. Consequently, the condensed condition of mitotic chromatin is assumed to inhibit DNA metabolism by impeding the access of DNA-transacting proteins. However, about 40 years ago, several researchers observed unscheduled DNA synthesis in UV-irradiated mitotic chromosomes, suggesting the presence of excision repair. We re-examined this subject by directly measuring the removal of UV-induced DNA lesions by an ELISA and by a Southern-based technique in HeLa cells arrested at mitosis. We observed that the removal of (6-4) photoproducts from the overall genome in mitotic cells was as efficient as in interphase cells. This suggests that global genome repair of (6-4) photoproducts is fully functional during mitosis, and that the DNA in mitotic chromatin is accessible to proteins involved in this mode of DNA repair. Nevertheless, not all modes of DNA repair seem fully functional during mitosis. We also observed that the removal of cyclobutane pyrimidine dimers from the dihydrofolate reductase and c-MYC genes in mitotic cells was very slow. This suggests that transcription-coupled repair of cyclobutane pyrimidine dimers is compromised or non-functional during mitosis, which is probably the consequence of mitotic transcriptional repression.
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Affiliation(s)
- Jun-ichiro Komura
- Department of Cell Biology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan.
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Tamanini A, Borgatti M, Finotti A, Piccagli L, Bezzerri V, Favia M, Guerra L, Lampronti I, Bianchi N, Dall'Acqua F, Vedaldi D, Salvador A, Fabbri E, Mancini I, Nicolis E, Casavola V, Cabrini G, Gambari R. Trimethylangelicin reduces IL-8 transcription and potentiates CFTR function. Am J Physiol Lung Cell Mol Physiol 2011; 300:L380-90. [DOI: 10.1152/ajplung.00129.2010] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Chronic inflammatory response in the airway tract of patients affected by cystic fibrosis is characterized by an excessive recruitment of neutrophils to the bronchial lumina, driven by the chemokine interleukin (IL)-8. We previously found that 5-methoxypsoralen reduces Pseudomonas aeruginosa -dependent IL-8 transcription in bronchial epithelial cell lines, with an IC50 of 10 μM (Nicolis E, Lampronti I, Dechecchi MC, Borgatti M, Tamanini A, Bezzerri V, Bianchi N, Mazzon M, Mancini I, Giri MG, Rizzotti P, Gambari R, Cabrini G. Int Immunopharmacol 9: 1411–1422, 2009). Here, we extended the investigation to analogs of 5-methoxypsoralen, and we found that the most potent effect is obtained with 4,6,4′-trimethylangelicin (TMA), which inhibits P. aeruginosa -dependent IL-8 transcription at nanomolar concentration in IB3–1, CuFi-1, CFBE41o−, and Calu-3 bronchial epithelial cell lines. Analysis of phosphoproteins involved in proinflammatory transmembrane signaling evidenced that TMA reduces the phosphorylation of ribosomal S6 kinase-1 and AKT2/3, which we found indeed involved in P. aeruginosa -dependent activation of IL-8 gene transcription by testing the effect of pharmacological inhibitors. In addition, we found a docking site of TMA into NF-κB by in silico analysis, whereas inhibition of the NF-κB/DNA interactions in vitro by EMSA was observed at high concentrations (10 mM TMA). To further understand whether NF-κB pathway should be considered a target of TMA, chromatin immunoprecipitation was performed, and we observed that TMA (100 nM) preincubated in whole living cells reduced the interaction of NF-κB with the promoter of IL-8 gene. These results suggest that TMA could inhibit IL-8 gene transcription mainly by intervening on driving the recruitment of activated transcription factors on IL-8 gene promoter, as demonstrated here for NF-κB. Although the complete understanding of the mechanism of action of TMA deserves further investigation, an activity of TMA on phosphorylating pathways was already demonstrated by our study. Finally, since psoralens have been shown to potentiate cystic fibrosis transmembrane conductance regulator (CFTR)-mediated chloride transport, TMA was tested and found to potentiate CFTR-dependent chloride efflux. In conclusion, TMA is a dual-acting compound reducing excessive IL-8 expression and potentiating CFTR function.
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Affiliation(s)
- Anna Tamanini
- Laboratory of Molecular Pathology, Laboratory of Clinical Chemistry and Haematology, University-Hospital, Verona
| | - Monica Borgatti
- BioPharmaNet, ER-GenTech, Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara
| | - Alessia Finotti
- BioPharmaNet, ER-GenTech, Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara
| | - Laura Piccagli
- BioPharmaNet, ER-GenTech, Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara
| | - Valentino Bezzerri
- Laboratory of Molecular Pathology, Laboratory of Clinical Chemistry and Haematology, University-Hospital, Verona
| | - Maria Favia
- Department of General and Environmental Physiology, University of Bari, Bari
| | - Lorenzo Guerra
- Department of General and Environmental Physiology, University of Bari, Bari
| | - Ilaria Lampronti
- BioPharmaNet, ER-GenTech, Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara
| | - Nicoletta Bianchi
- BioPharmaNet, ER-GenTech, Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara
| | | | - Daniela Vedaldi
- Department of Pharmaceutical Sciences, University of Padova, Padova; and
| | - Alessia Salvador
- Department of Pharmaceutical Sciences, University of Padova, Padova; and
| | - Enrica Fabbri
- BioPharmaNet, ER-GenTech, Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara
| | - Irene Mancini
- BioPharmaNet, ER-GenTech, Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara
| | - Elena Nicolis
- Laboratory of Molecular Pathology, Laboratory of Clinical Chemistry and Haematology, University-Hospital, Verona
| | - Valeria Casavola
- Department of General and Environmental Physiology, University of Bari, Bari
| | - Giulio Cabrini
- Laboratory of Molecular Pathology, Laboratory of Clinical Chemistry and Haematology, University-Hospital, Verona
| | - Roberto Gambari
- BioPharmaNet, ER-GenTech, Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara
- Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara, Italy
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Increase in gamma-globin mRNA content in human erythroid cells treated with angelicin analogs. Int J Hematol 2009; 90:318-327. [PMID: 19777196 DOI: 10.1007/s12185-009-0422-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2009] [Revised: 08/27/2009] [Accepted: 08/30/2009] [Indexed: 10/20/2022]
Abstract
The aim of the present study was to identify molecular analogs of angelicin (ANG) able to increase erythroid differentiation of K562 cells and expression of gamma-globin genes in human erythroid precursor cells, with low effects on apoptosis. ANG-like molecules are well-known photosensitizers largely used for their antiproliferative activity in the treatment of different skin diseases (i.e., psoriasis, vitiligo, eczema, and mycosis fungoides). To verify the activity of these derivatives, we employed three experimental cell systems: (1) the human leukemic K562 cell line, (2) K562 cell clones stably transfected with a pCCL construct carrying green-EGFP under the gamma-globin gene promoter, and (3) the two-phase liquid culture of human erythroid progenitors isolated from normal donors and beta-thalassemia patients. The results of our study suggest that trimethyl ANG is a powerful inducer of erythroid differentiation, compared with known inducers, such as ANG, cytosine arabinoside, mithramycin, and cisplatin. These data could have practical relevance, because pharmacologically mediated regulation of human gamma-globin gene expression, with the consequent induction of fetal hemoglobin, is considered a potential therapeutic approach in hematological disorders including beta-thalassemia and sickle cell anemia.
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7
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Chen HH, Lebon J, Riggs AD. Analysis of RNA structure and RNA-protein interactions in mammalian cells by use of terminal transferase-dependent PCR. Methods Mol Biol 2008; 488:319-41. [PMID: 18982300 DOI: 10.1007/978-1-60327-475-3_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Terminal transferase-dependent polymerase chain reaction (TDPCR) can be used after reverse transcription (RT) to analyze RNA. This method (RT-TDPCR) has been used for study of RNA structure and RNA-protein interactions at nucleotide-level resolution. A detailed protocol of RT-TDPCR is presented here with examples of its use with ribonuclease T1 in mammalian cells for detecting (1) RNA structure and protein footprints of the human ferritin heavy-chain messenger RNA and (2) in vivo structure of exon 4 of human XIST (X chromosome inactivation-specific transcript) RNA.
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Affiliation(s)
- Hsiu-Hua Chen
- Beckman Research Institute of the City of Hope, Duarte, California, USA
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8
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Bianchi N, Zuccato C, Lampronti I, Borgatti M, Gambari R. Fetal Hemoglobin Inducers from the Natural World: A Novel Approach for Identification of Drugs for the Treatment of {beta}-Thalassemia and Sickle-Cell Anemia. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2007; 6:141-51. [PMID: 18955291 PMCID: PMC2686630 DOI: 10.1093/ecam/nem139] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The objective of this review is to present examples of lead compounds identified from biological material (fungi, plant extracts and agro-industry material) and of possible interest in the field of a pharmacological approach to the therapy of beta-thalassemia using molecules able to stimulate production of fetal hemoglobin (HbF) in adults. Concerning the employment of HbF inducers as potential drugs for pharmacological treatment of beta-thalassemia, the following conclusions can be reached: (i) this therapeutic approach is reasonable, on the basis of the clinical parameters exhibited by hereditary persistence of fetal hemoglobin patients, (ii) clinical trials (even if still limited) employing HbF inducers were effective in ameliorating the symptoms of beta-thalassemia patients, (iii) good correlation of in vivo and in vitro results of HbF synthesis and gamma-globin mRNA accumulation indicates that in vitro testing might be predictive of in vivo responses and (iv) combined use of different inducers might be useful to maximize HbF, both in vitro and in vivo. In this review, we present three examples of HbF inducers from the natural world: (i) angelicin and linear psoralens, contained in plant extracts from Angelica arcangelica and Aegle marmelos, (ii) resveratrol, a polyphenol found in grapes and several plant extracts and (iii) rapamycin, isolated from Streptomyces hygroscopicus.
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Affiliation(s)
- Nicoletta Bianchi
- GenTech-for-Thal, Laboratory for the Development of Pharmacological and Pharmacogenomic Therapy of Thalassaemia, Biotechnology Centre, Ferrara, Italy.
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9
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Fernández-Miragall O, Martínez-Salas E. In vivo footprint of a picornavirus internal ribosome entry site reveals differences in accessibility to specific RNA structural elements. J Gen Virol 2007; 88:3053-3062. [PMID: 17947530 DOI: 10.1099/vir.0.83218-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Internal ribosome entry site (IRES) elements were described in picornaviruses as an essential region of the viral RNA. Understanding of IRES function requires a detailed knowledge of each step involved in the internal initiation process, from RNA folding and IRES-protein interaction to ribosome recruitment. Thus, deciphering IRES accessibility to external agents due to RNA structural features, as well as RNA-protein protection within living cells, is of primary importance. In this study, two chemical reagents, dimethylsulfate (DMS) and aminomethylpsoralen, have been used to footprint the entire IRES of foot-and-mouth disease virus (FMDV) in living cells; these reagents enter the cell membrane and interact with nucleic acids in a structure-dependent manner. For FMDV, as in other picornaviruses, viral infection is dependent on the correct function of the IRES; therefore, the IRES region itself constitutes a useful target of antiviral drugs. Here, the in vivo footprint of a picornavirus IRES element in the context of a biologically active mRNA is shown for the first time. The accessibility of unpaired adenosine and cytosine nucleotides in the entire FMDV IRES was first obtained in vitro by DMS probing; subsequently, this information was used to interpret the footprint data obtained in vivo for the mRNA encompassing the IRES element in the intercistronic space. The results of DMS accessibility and UV-psoralen cross-linking studies in the competitive cellular environment provided evidence for differences in RNA structure from data obtained in vitro, and provided essential information to identify appropriate targets within the FMDV IRES aimed at combating this important pathogen.
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Affiliation(s)
- Olga Fernández-Miragall
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Encarnación Martínez-Salas
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas - Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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Komura JI, Ikehata H, Ono T. Chromatin fine structure of the c-MYC insulator element/DNase I-hypersensitive site I is not preserved during mitosis. Proc Natl Acad Sci U S A 2007; 104:15741-6. [PMID: 17890321 PMCID: PMC2000435 DOI: 10.1073/pnas.0702363104] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
During mitosis in higher eukaryotic cells, transcription is silenced and transcription complexes are absent from promoters in the condensed chromosomes; however, epigenetic information concerning the pattern of expressed and silent genes must be preserved. Recently, it has been reported that CTCF, a major protein in vertebrate insulator elements, remains associated with mitotic chromatin. If the structure of insulators is preserved during mitosis, then it is possible that insulators can function as components or elements of the mechanism involved in the transfer of epigenetic information through the mitotic phase and can help guide the reconstitution of domain structure and nuclear organization after the completion of this phase. We have studied the chromatin structure of the insulator upstream of the c-MYC gene in mitotic HeLa cells. The region of the insulator corresponds to the DNase I hypersensitive site I, but Southern blot analysis revealed that hypersensitivity was lost during mitosis. High resolution in vivo footprinting analysis using dimethyl sulfate, UV light, psoralen, and DNase I also demonstrated the disappearance of the sequence-specific direct binding of CTCF and the absence of detectable structures during mitosis. Thus, it appears that the nucleoprotein complex involving this insulator element must be reassembled de novo with each new cell generation.
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Affiliation(s)
- Jun-Ichiro Komura
- Department of Cell Biology, Tohoku University Graduate School of Medicine, Sendai, Miyagi 980-8575, Japan.
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11
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Rowther FB, Rodrigues C, Mehta AP, Deshmukh MS, Kapadia FN, Hegde A, Joshi VR. An improved method of elimination of DNA from PCR reagents. ACTA ACUST UNITED AC 2005; 9:53-7. [PMID: 16137180 DOI: 10.1007/bf03260072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
OBJECTIVE The presence of exogenous DNA in commercially available polymerase chain reaction (PCR) reagent preparations is a serious problem when amplifying conserved regions of bacteria. The preferred and currently in-use method of decontamination using 8-methoxypsoralen (8-MOP) and UVA requires re-standardization of decontamination with increasing concentrations of 8-MOP and UVA irradiation timings, if the DNA load of reagents is high due to lot-to-lot differences. The objective of this study was to develop a decontamination method, which would (i) work at the minimum reported concentration of 8-MOP and UVA irridation timings; and (ii) take care of inter-batch DNA-load variability of reagents. MATERIALS AND METHODS The improved method described here was formulated after studying the exact molecular mechanism of action of 8-MOP with DNA. The successful working of the method was experimentally proven and validated with 6-7 new batches of PCR reagents. The sensitivity of eubacterial PCR, after using the new method of decontamination, to be used clinically was checked with both the spiked specimens and the actual clinical specimens. RESULTS AND DISCUSSION The new method was found to work at the same starting parameters of 8-MOP and UVA in such situations. The increased efficiency of this method was found to be due to the synergistic effect of both the selective treatment of Taq DNA polymerase and the split-irradiation approach.
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Affiliation(s)
- Farjana B Rowther
- Research laboratories, P.D. Hinduja National Hospital and MRC, Mumbai, India
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12
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Lee W, St.Onge RP, Proctor M, Flaherty P, Jordan MI, Arkin AP, Davis RW, Nislow C, Giaever G. Genome-wide requirements for resistance to functionally distinct DNA-damaging agents. PLoS Genet 2005; 1:e24. [PMID: 16121259 PMCID: PMC1189734 DOI: 10.1371/journal.pgen.0010024] [Citation(s) in RCA: 131] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2005] [Accepted: 07/01/2005] [Indexed: 11/18/2022] Open
Abstract
The mechanistic and therapeutic differences in the cellular response to DNA-damaging compounds are not completely understood, despite intense study. To expand our knowledge of DNA damage, we assayed the effects of 12 closely related DNA-damaging agents on the complete pool of approximately 4,700 barcoded homozygous deletion strains of Saccharomyces cerevisiae. In our protocol, deletion strains are pooled together and grown competitively in the presence of compound. Relative strain sensitivity is determined by hybridization of PCR-amplified barcodes to an oligonucleotide array carrying the barcode complements. These screens identified genes in well-characterized DNA-damage-response pathways as well as genes whose role in the DNA-damage response had not been previously established. High-throughput individual growth analysis was used to independently confirm microarray results. Each compound produced a unique genome-wide profile. Analysis of these data allowed us to determine the relative importance of DNA-repair modules for resistance to each of the 12 profiled compounds. Clustering the data for 12 distinct compounds uncovered both known and novel functional interactions that comprise the DNA-damage response and allowed us to define the genetic determinants required for repair of interstrand cross-links. Further genetic analysis allowed determination of epistasis for one of these functional groups.
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Affiliation(s)
- William Lee
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
| | | | - Michael Proctor
- Department of Biochemistry, Stanford University School of Medicine, Stanford Genome Technology Center, Palo Alto, California, United States of America
| | - Patrick Flaherty
- Department of Electrical Engineering and Computer Science, University of California, Berkeley, California, United States of America
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Michael I Jordan
- Division of Computer Science, Department of Statistics, University of California, Berkeley, California, United States of America
| | - Adam P Arkin
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
- Howard Hughes Medical Institute, Department of Bioengineering, University of California, Berkeley, California, United States of America
| | - Ronald W Davis
- Department of Genetics, Stanford University School of Medicine, Stanford, California, United States of America
- Department of Biochemistry, Stanford University School of Medicine, Stanford Genome Technology Center, Palo Alto, California, United States of America
| | - Corey Nislow
- Department of Biochemistry, Stanford University School of Medicine, Stanford Genome Technology Center, Palo Alto, California, United States of America
| | - Guri Giaever
- Department of Biochemistry, Stanford University School of Medicine, Stanford Genome Technology Center, Palo Alto, California, United States of America
- *To whom correspondence should be addressed. E-mail:
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Komura JI, Ono T. Disappearance of nucleosome positioning in mitotic chromatin in vivo. J Biol Chem 2005; 280:14530-5. [PMID: 15705567 DOI: 10.1074/jbc.m500637200] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
During mitosis, transcription is silenced and most transcription factors are displaced from their recognition sequences. By in vivo footprinting analysis, we have confirmed and extended previous studies showing loss of transcription factors from an RNA polymerase II promoter (c-FOS) and, for the first time, an RNA polymerase III promoter (U6) in HeLa cells. Because little was known about nucleosomal organization in mitotic chromosomes, we performed footprinting analysis for nucleosomes on these promoters in interphase and mitotic cells. During interphase, each of the promoters had a positioned nucleosome in the region intervening between proximal promoter elements and distal enhancer elements, but the strong nucleosome positioning disappeared during mitosis. Thus, the nucleosomal organization that appears to facilitate transcription in interphase cells may be lost in mitotic cells, and nucleosome positioning during mitosis does not seem to be a major component of the epigenetic mechanisms to mark genes for rapid reactivation after this phase.
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Affiliation(s)
- Jun-ichiro Komura
- Department of Cell Biology, Tohoku University Graduate School of Medicine, Sendai 980-8575, Japan.
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Lampronti I, Bianchi N, Borgatti M, Fibach E, Prus E, Gambari R. Accumulation of gamma-globin mRNA in human erythroid cells treated with angelicin. Eur J Haematol 2003; 71:189-95. [PMID: 12930320 DOI: 10.1034/j.1600-0609.2003.00113.x] [Citation(s) in RCA: 71] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The aim of the present study was to determine whether angelicin is able to increase the expression of gamma-globin genes in human erythroid cells. Angelicin is structurally related to psoralens, a well-known chemical class of photosensitizers used for their antiproliferative activity in treatment of different skin diseases (i.e., psoriasis and vitiligo). To verify the activity of angelicin, we employed two experimental cell systems, the human leukemic K562 cell line and the two-phase liquid culture of human erythroid progenitors isolated from normal donors. The results of our investigation suggest that angelicin, compared with cytosine arabinoside, mithramycin and cisplatin, is a powerful inducer of erythroid differentiation and gamma-globin mRNA accumulation of human leukemia K562 cells. In addition, when normal human erythroid precursors were cultured in the presence of angelicin, increases of gamma-globin mRNA accumulation and fetal hemoglobin (HbF) production, even higher than those obtained using hydroxyurea, were detected. These results could have practical relevance, as pharmacologically-mediated regulation of the expression of human gamma-globin genes, leading to HbF induction, is considered a potential therapeutic approach in hematological disorders, including beta-thalassemia and sickle cell anemia.
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Affiliation(s)
- Ilaria Lampronti
- Department of Biochemistry and Molecular Biology, University of Ferrara, Ferrara, Italy
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Abstract
In order to determine the time required for nucleosomes assembled on the daughter strands of replication forks to assume favoured positions with respect to DNA sequence, psoralen cross-linked replication intermediates purified from preparative two-dimensional agarose gels were analysed by exonuclease digestion or primer extension. Analysis of sites of psoralen intercalation revealed that nucleosomes in the yeast Saccharomyces cerevisiae rDNA intergenic spacer are positioned shortly after passage of the replication machinery. Therefore, both the 'old' randomly segregated nucleosomes as well as the 'new' assembled histone octamers rapidly position themselves (within seconds) on the newly replicated DNA strands, suggesting that the positioning of nucleosomes is an initial step in the chromatin maturation process.
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Affiliation(s)
- Renzo Lucchini
- Institute of Cell Biology, ETH Hönggerberg, CH-8093 Zürich, Switzerland
Present address: Laboratorio Analisi Speciali, via Rovere 8, CH-6932 Breganzona, Switzerland Corresponding author e-mail: R.Lucchini and R.E.Wellinger contributed equally to this work
| | | | - José M. Sogo
- Institute of Cell Biology, ETH Hönggerberg, CH-8093 Zürich, Switzerland
Present address: Laboratorio Analisi Speciali, via Rovere 8, CH-6932 Breganzona, Switzerland Corresponding author e-mail: R.Lucchini and R.E.Wellinger contributed equally to this work
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Wollowitz S. Fundamentals of the psoralen-based Helinx technology for inactivation of infectious pathogens and leukocytes in platelets and plasma. Semin Hematol 2001; 38:4-11. [PMID: 11727280 DOI: 10.1016/s0037-1963(01)90118-0] [Citation(s) in RCA: 83] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Psoralens plus ultraviolet A (UVA) light inactivate viruses and bacteria as well as leukocytes. A system employing the synthetic psoralen compound amotosalen hydrochloride (S-59), in combination with UVA light, is being developed to decontaminate platelet concentrates and plasma in a blood-bank setting. S-59 is a heterocyclic psoralen compound that reacts by a three-step process with nucleic acids (NAs): (1) S-59 intercalates into the double helix; (2) upon illumination with long-wavelength ultraviolet light (UVA), it covalently attaches to a single strand, forming a monoadduct; and (3) additional illumination causes a photoreaction of the monoadduct with the second NA strand, resulting in an interstrand crosslink. The reaction occurs with the genomic material of DNA- and RNA-based viruses and occurs in genomes that are single stranded as well as double stranded. Inactivation rate is related to genome size. Large genomes such as those in leukocytes are far more susceptible to inactivation than are viruses such as hepatitis B virus (HBV), which is inactivated (>10(5) logs) under conditions being developed for blood-bank use. The efficiency of the process is affected by a number of practical considerations such as solution components and light source. The S-59 photochemical treatment process (PCT) has been optimized for platelet concentrates as currently processed for transfusion.
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Affiliation(s)
- S Wollowitz
- Department of Chemical Technology, Cerus Corporation, Concord, CA 94520, USA
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