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Wang S, Chen B, Dragovich P, Pillow T, Staben L, Guo J, Su D, Zhang C, Bobba S, Ma Y, Wang J, Sangaraju D, Wei B, Phillips GL, Khojasteh C, Zhang D. A Novel Depurination Methodology to Assess DNA Alkylation of Chloro-Bis-Seco-Cyclopropylbenzoindoles Allowed for Comparison of Minor-Groove Reactivity. Drug Metab Dispos 2019; 47:547-555. [DOI: 10.1124/dmd.118.085209] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/25/2019] [Indexed: 01/14/2023] Open
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Chang YC, Chiu CC, Yuo CY, Chan WL, Chang YS, Chang WH, Wu SM, Chou HL, Liu TC, Lu CY, Yang WK, Chang JG. An XIST-related small RNA regulates KRAS G-quadruplex formation beyond X-inactivation. Oncotarget 2016; 7:86713-86729. [PMID: 27880931 PMCID: PMC5349948 DOI: 10.18632/oncotarget.13433] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 10/31/2016] [Indexed: 12/31/2022] Open
Abstract
X-inactive-specific transcript (XIST), a long non-coding RNA, is essential for the initiation of X-chromosome inactivation. However, little is known about other roles of XIST in the physiological process in eukaryotic cells. In this study, the bioinformatics approaches revealed XIST could be processed into a small non-coding RNA XPi2. The XPi2 RNA was confirmed by a northern blot assay; its expression was gender-independent, suggesting the role of XPi2 was beyond X-chromosome inactivation. The pull-down assay combined with LC-MS-MS identified two XPi2-associated proteins, nucleolin and hnRNP A1, connected to the formation of G-quadruplex. Moreover, the microarray data showed the knockdown of XPi2 down-regulated the KRAS pathway. Consistently, we tested the expression of ten genes, including KRAS, which was correlated with a G-quadruplex formation and found the knockdown of XPi2 caused a dramatic decrease in the transcription level of KRAS among the ten genes. The results of CD/NMR assay also supported the interaction of XPi2 and the polypurine-polypyrimidine element of KRAS. Accordingly, XPi2 may stimulate the KRAS expression by attenuating G-quadruplex formation. Our present work sheds light on the novel role of small RNA XPi2 in modulating the G-quadruplex formation which may play some essential roles in the KRAS- associated carcinogenesis.
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Affiliation(s)
- Yuli C. Chang
- Graduate Institutes of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Division of Cytogenetics, Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Chien-Chih Chiu
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Chung-Yee Yuo
- Graduate Institutes of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wen-Ling Chan
- Epigenome Research Center, China Medical University and Hospital, Taichung, Taiwan
- Department of Bioinformatics and Medical Engineering, Asia University
| | - Ya-Sian Chang
- Epigenome Research Center, China Medical University and Hospital, Taichung, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
| | - Wen-Hsin Chang
- Graduate Institutes of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Division of Hematology/Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Shou-Mei Wu
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Han-Lin Chou
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ta-Chih Liu
- Graduate Institutes of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Division of Cytogenetics, Department of Laboratory Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
- Division of Hematology/Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Chi-Yu Lu
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Taiwan
| | - Wen-Kuang Yang
- Cell/Gene Therapy Research Laboratory, Department of Medical Research, China Medical University Hospital, Taichung, Taiwan
| | - Jan-Gowth Chang
- Epigenome Research Center, China Medical University and Hospital, Taichung, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
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Banerjee A, Sanyal S, Dutta S, Chakraborty P, Das PP, Jana K, Vasudevan M, Das C, Dasgupta D. The plant alkaloid chelerythrine binds to chromatin, alters H3K9Ac and modulates global gene expression. J Biomol Struct Dyn 2016; 35:1491-1499. [PMID: 27494525 DOI: 10.1080/07391102.2016.1188154] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Chelerythrine (CHL), a plant alkaloid, possesses antimicrobial, anti-inflammatory, and antitumor properties. Although CHL influences several key signal transduction pathways, its ability to interact directly with nucleoprotein complex chromatin, in eukaryotic cells has so far not been looked into. Here we have demonstrated its association with hierarchically assembled chromatin components, viz. long chromatin, chromatosome, nucleosome, chromosomal DNA, and histone H3 and the consequent effect on chromatin structure. CHL was found to repress acetylation at H3K9. It is more target-specific in terms of gene expression alteration and less cytotoxic compared to its structural analog sanguinarine.
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Affiliation(s)
- Amrita Banerjee
- a Biophysics and Structural Genomics Division , Saha Institute of Nuclear Physics , Block - AF Sector-I, Bidhan Nagar, Kolkata 700064 , India
| | - Sulagna Sanyal
- a Biophysics and Structural Genomics Division , Saha Institute of Nuclear Physics , Block - AF Sector-I, Bidhan Nagar, Kolkata 700064 , India
| | - Shreyasi Dutta
- a Biophysics and Structural Genomics Division , Saha Institute of Nuclear Physics , Block - AF Sector-I, Bidhan Nagar, Kolkata 700064 , India
| | - Payal Chakraborty
- b Genome Informatics Research Group , Bionivid Technology Pvt Ltd. , Bangalore 560043 , India
| | - Prajna Paramita Das
- a Biophysics and Structural Genomics Division , Saha Institute of Nuclear Physics , Block - AF Sector-I, Bidhan Nagar, Kolkata 700064 , India
| | - Kuladip Jana
- c Division of Molecular Medicine, Centre for Translational Animal Research , Bose Institute , P 1/12, C. I. T. Road, Scheme - VIIM, Kolkata 700054 , India
| | - Madavan Vasudevan
- b Genome Informatics Research Group , Bionivid Technology Pvt Ltd. , Bangalore 560043 , India
| | - Chandrima Das
- a Biophysics and Structural Genomics Division , Saha Institute of Nuclear Physics , Block - AF Sector-I, Bidhan Nagar, Kolkata 700064 , India
| | - Dipak Dasgupta
- a Biophysics and Structural Genomics Division , Saha Institute of Nuclear Physics , Block - AF Sector-I, Bidhan Nagar, Kolkata 700064 , India
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Banerjee A, Sanyal S, Majumder P, Chakraborty P, Jana K, Das C, Dasgupta D. Recognition of chromatin by the plant alkaloid, ellipticine as a dual binder. Biochem Biophys Res Commun 2015; 462:352-7. [PMID: 25960297 DOI: 10.1016/j.bbrc.2015.04.140] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 04/29/2015] [Indexed: 11/29/2022]
Abstract
Recognition of core histone components of chromatin along with chromosomal DNA by a class of small molecule modulators is worth examining to evaluate their intracellular mode of action. A plant alkaloid ellipticine (ELP) which is a putative anticancer agent has so far been reported to function via DNA intercalation, association with topoisomerase II and binding to telomere region. However, its effect upon the potential intracellular target, chromatin is hitherto unreported. Here we have characterized the biomolecular recognition between ELP and different hierarchical levels of chromatin. The significant result is that in addition to DNA, it binds to core histone(s) and can be categorized as a 'dual binder'. As a sequel to binding with histone(s) and core octamer, it alters post-translational histone acetylation marks. We have further demonstrated that it has the potential to modulate gene expression thereby regulating several key biological processes such as nuclear organization, transcription, translation and histone modifications.
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Affiliation(s)
- Amrita Banerjee
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Sulagna Sanyal
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Parijat Majumder
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | | | - Kuladip Jana
- Division of Molecular Medicine, Centre for Translational Animal Research, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, West Bengal, India
| | - Chandrima Das
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India.
| | - Dipak Dasgupta
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India.
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Banerjee A, Sanyal S, Kulkarni KK, Jana K, Roy S, Das C, Dasgupta D. Anticancer drug mithramycin interacts with core histones: An additional mode of action of the DNA groove binder. FEBS Open Bio 2014; 4:987-95. [PMID: 25473595 PMCID: PMC4247356 DOI: 10.1016/j.fob.2014.10.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 09/23/2014] [Accepted: 10/12/2014] [Indexed: 01/13/2023] Open
Abstract
Mithramycin (MTR) is a clinically approved DNA-binding antitumor antibiotic currently in Phase 2 clinical trials at National Institutes of Health for treatment of osteosarcoma. In view of the resurgence in the studies of this generic antibiotic as a human medicine, we have examined the binding properties of MTR with the integral component of chromatin - histone proteins - as a part of our broad objective to classify DNA-binding molecules in terms of their ability to bind chromosomal DNA alone (single binding mode) or both histones and chromosomal DNA (dual binding mode). The present report shows that besides DNA, MTR also binds to core histones present in chromatin and thus possesses the property of dual binding in the chromatin context. In contrast to the MTR-DNA interaction, association of MTR with histones does not require obligatory presence of bivalent metal ion like Mg(2+). As a consequence of its ability to interact with core histones, MTR inhibits histone H3 acetylation at lysine 18, an important signature of active chromatin, in vitro and ex vivo. Reanalysis of microarray data of Ewing sarcoma cell lines shows that upon MTR treatment there is a significant down regulation of genes, possibly implicating a repression of H3K18Ac-enriched genes apart from DNA-binding transcription factors. Association of MTR with core histones and its ability to alter post-translational modification of histone H3 clearly indicates an additional mode of action of this anticancer drug that could be implicated in novel therapeutic strategies.
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Key Words
- BAC, benzalkonium chloride
- BSA, bovine serum albumin
- CBP, CREB-binding protein
- CD, circular dichroism
- Core histones
- Dual binding mode
- EM, electron microscopy
- EWS-FLI1, transcription factor with a DNA binding domain FLI1 and a transcription enhancer domain EWS
- Epigenetic modulator
- FACS, fluorescence activated cell sorting
- H3K18 acetylation
- H3K18Ac, histone H3 lysine 18 acetylation
- HAT, histone acetyltransferase
- HD, Huntington’s disease
- ITC, isothermal titration calorimetry
- M2+, bivalent metal ion such as Mg2+
- MTR, mithramycin
- MTT, 3-(4-5 dimethylthiazol-2-yl) 2-5diphenyl-tetrazolium bromide
- Mithramycin
- NIH, National Institutes of Health
- PBS, phosphate-buffered saline
- PTM, post-translational modification
- SGR, sanguinarine
- TBST, Tris-buffered saline Tween-20
- TCA, trichloroacetic acid
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Affiliation(s)
- Amrita Banerjee
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Sulagna Sanyal
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Kirti K Kulkarni
- Bionivid Technology Pvt Ltd, Kasturi Nagar, Bangalore 560043, India
| | - Kuladip Jana
- Division of Molecular Medicine, Centre for Translational Animal Research, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, West Bengal, India
| | - Siddhartha Roy
- Structural Biology and Bioinformatics, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Chandrima Das
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Dipak Dasgupta
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
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Banerjee A, Majumder P, Sanyal S, Singh J, Jana K, Das C, Dasgupta D. The DNA intercalators ethidium bromide and propidium iodide also bind to core histones. FEBS Open Bio 2014; 4:251-9. [PMID: 24649406 PMCID: PMC3958746 DOI: 10.1016/j.fob.2014.02.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 02/11/2014] [Accepted: 02/11/2014] [Indexed: 01/17/2023] Open
Abstract
Eukaryotic DNA is compacted in the form of chromatin, in a complex with histones and other non-histone proteins. The intimate association of DNA and histones in chromatin raises the possibility that DNA-interactive small molecules may bind to chromatin-associated proteins such as histones. Employing biophysical and biochemical techniques we have characterized the interaction of a classical intercalator, ethidium bromide (EB) and its structural analogue propidium iodide (PI) with hierarchical genomic components: long chromatin, chromatosome, core octamer and chromosomal DNA. Our studies show that EB and PI affect both chromatin structure and function, inducing chromatin compaction and disruption of the integrity of the chromatosome. Calorimetric studies and fluorescence measurements of the ligands demonstrated and characterized the association of these ligands with core histones and the intact octamer in absence of DNA. The ligands affect acetylation of histone H3 at lysine 9 and acetylation of histone H4 at lysine 5 and lysine 8 ex vivo. PI alters the post-translational modifications to a greater extent than EB. This is the first report showing the dual binding (chromosomal DNA and core histones) property of a classical intercalator, EB, and its longer analogue, PI, in the context of chromatin.
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Affiliation(s)
- Amrita Banerjee
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Parijat Majumder
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Sulagna Sanyal
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Jasdeep Singh
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Kuladip Jana
- Division of Molecular Medicine, Centre for Translational Animal Research, Bose Institute, P-1/12 C.I.T. Scheme VIIM, Kolkata 700054, West Bengal, India
| | - Chandrima Das
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
| | - Dipak Dasgupta
- Biophysics & Structural Genomics Division, Saha Institute of Nuclear Physics, Block-AF, Sector-1, Bidhan Nagar, Kolkata 700064, West Bengal, India
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Molecular basis of recognition of quadruplexes human telomere and c-myc promoter by the putative anticancer agent sanguinarine. Biochim Biophys Acta Gen Subj 2013; 1830:4189-201. [DOI: 10.1016/j.bbagen.2013.03.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/19/2013] [Accepted: 03/26/2013] [Indexed: 01/24/2023]
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Ghosh S, Kar A, Chowdhury S, Dasgupta D. Ellipticine binds to a human telomere sequence: an additional mode of action as a putative anticancer agent? Biochemistry 2013; 52:4127-37. [PMID: 23697684 DOI: 10.1021/bi400080t] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Polyguanine sequences fold into G-quadruplex structures in the presence of monovalent cations. It is accepted that the telomeric DNA region consists of G-quadruplex structure. There are reports that potential G-quadruplex forming motifs are also present in the promoter region of some proto-oncogenes such as c-myc, c-kit, KRAS, etc. Small molecules with the potential to stabilize the telomeric DNA quadruplex have emerged as potential anticancer agents. We have studied the interaction of ellipticine, a putative anticancer agent from a plant source, with a human telomeric DNA sequence (H24). Spectroscopic and calorimetric studies indicate that the association of ellipticine with H24 is an entropically driven phenomenon with a 2:3 (H24:ellipticine) stoichiometry. Though ellipticine binding does not induce any major structural perturbation in H24, the association leads to formation of a complex with enhanced thermal stability. An assay with the telomerase repeat amplification protocol shows that ellipticine inhibits telomerase activity in MDAMB-231 breast cancer cell line extracts. This is the first report of the quadruplex binding ability of ellipticine. Using the results, we propose that along with DNA intercalation and/or topoisomerase II inhibition, interaction with the telomeric DNA region and the resultant inhibition of telomerase activity might be an additional mode of action for its anticancer property.
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Affiliation(s)
- Saptaparni Ghosh
- Biophysics Division, Saha Institute of Nuclear Physics , Block-AF, Sector- I, Bidhan Nagar, Kolkata 700064, India
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Synthesis, in vitro antitumor evaluation and DNA-binding study of novel tetrahydroquinolines and some derived tricyclic and tetracyclic ring systems. Eur J Med Chem 2013; 63:133-43. [DOI: 10.1016/j.ejmech.2013.02.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Revised: 02/04/2013] [Accepted: 02/07/2013] [Indexed: 11/24/2022]
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Mithramycin interacts with core histones and modulates epigenetic modifications. Epigenetics Chromatin 2013. [PMCID: PMC3620573 DOI: 10.1186/1756-8935-6-s1-p106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Dasgupta D, Majumder P, Banerjee A. A revisit of the mode of interaction of small transcription inhibitors with genomic DNA. J Biosci 2012; 37:475-81. [PMID: 22750984 DOI: 10.1007/s12038-012-9211-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
One class of small molecules with therapeutic potential for treatment of cancer functions as transcription inhibitors via interaction with double-stranded DNA. Majority of the studies of the interaction with DNA have so far been reported under conditions nonexistent in vivo. Inside the cell, DNA is present in the nucleus as a complex with proteins known as chromatin. For the last few years we have been studying the interaction of these DNA-binding small molecules at the chromatin level with emphasis on the drug-induced structural alterations in chromatin. Our studies have shown that at the chromatin level these molecules could be classified in two broad categories: single-binding and dual-binding molecules. Single-binding molecules access only DNA in the chromatin, while the dual-binding molecules could bind to both DNA and the associated histone(s). Structural effects of the DNA-binding molecules upon chromatin in light of the above broad categories and the associated biological implications of the two types of binding are discussed.
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Affiliation(s)
- Dipak Dasgupta
- Biophysics Division, Saha Institute of Nuclear Physics, Bidhan Nagar, Kolkata 700 064, India.
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