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Kim M, Kreig A, Lee CY, Rube HT, Calvert J, Song JS, Myong S. Quantitative analysis and prediction of G-quadruplex forming sequences in double-stranded DNA. Nucleic Acids Res 2016; 44:4807-17. [PMID: 27095201 PMCID: PMC4889947 DOI: 10.1093/nar/gkw272] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 04/05/2016] [Indexed: 11/16/2022] Open
Abstract
G-quadruplex (GQ) is a four-stranded DNA structure that can be formed in guanine-rich sequences. GQ structures have been proposed to regulate diverse biological processes including transcription, replication, translation and telomere maintenance. Recent studies have demonstrated the existence of GQ DNA in live mammalian cells and a significant number of potential GQ forming sequences in the human genome. We present a systematic and quantitative analysis of GQ folding propensity on a large set of 438 GQ forming sequences in double-stranded DNA by integrating fluorescence measurement, single-molecule imaging and computational modeling. We find that short minimum loop length and the thymine base are two main factors that lead to high GQ folding propensity. Linear and Gaussian process regression models further validate that the GQ folding potential can be predicted with high accuracy based on the loop length distribution and the nucleotide content of the loop sequences. Our study provides important new parameters that can inform the evaluation and classification of putative GQ sequences in the human genome.
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Affiliation(s)
- Minji Kim
- Department of Electrical and Computer Engineering, University of Illinois; 306 N. Wright St. Urbana, IL 61801, USA Institute for Genomic Biology; 1206 Gregory Drive, Urbana, IL 61801, USA
| | - Alex Kreig
- Department of Bioengineering, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA
| | - Chun-Ying Lee
- Department of Biophysics, Johns Hopkins University; 3400 N. Charles St. Baltimore, MD 21218 USA
| | - H Tomas Rube
- Institute for Genomic Biology; 1206 Gregory Drive, Urbana, IL 61801, USA Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Jacob Calvert
- Department of Bioengineering, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA School of Mathematics, University of Bristol; University Walk, Bristol BS8 1TW, UK
| | - Jun S Song
- Institute for Genomic Biology; 1206 Gregory Drive, Urbana, IL 61801, USA Department of Bioengineering, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA Department of Physics, University of Illinois; 1110 West Green Street, Urbana, IL 61801-3080, USA Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 W. Green St. Urbana, IL 61801, USA
| | - Sua Myong
- Institute for Genomic Biology; 1206 Gregory Drive, Urbana, IL 61801, USA Department of Bioengineering, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA Department of Biophysics, Johns Hopkins University; 3400 N. Charles St. Baltimore, MD 21218 USA Physics Frontier Center (Center for Physics of Living Cells), University of Illinois, 1110 W. Green St. Urbana, IL 61801, USA
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Bell R, Rube HT, Kreig A, Mancini A, Fouse S, Nagarajan R, Choi S, Hong C, He D, Pekmezci M, Wiencke J, Wrensch M, Chang S, Walsh K, Myong S, Song J, Costello J. GENO-07A MECHANISM OF MUTANT TERT PROMOTER ACTIVATION SHARED ACROSS CANCER TYPES. Neuro Oncol 2015. [DOI: 10.1093/neuonc/nov215.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Abstract
G-quadruplexes (GQs) are alternative DNA secondary structures that can form throughout the human genome and control the replication and transcription of important regulatory genes. Here, we established an ensemble fluorescence assay by employing two GQ-interacting compounds, N-methyl mesoporphyrin IX (NMM) and Crystal Violet (CV). This enables quantitative measurement of the GQ folding propensity and conformation specificity in both single strand (ss) and double strand (ds) DNA. Our GQ mapping indicates that the likelihood of GQ formation is substantially diminished in dsDNA, likely due to the competition from the Watson-Crick base pairing. Unlike GQ folding sequence in ssDNA which forms both parallel and antiparallel GQs, dsDNA displays only parallel folding. Additionally, we employed single molecule FRET to obtain a direct quantitation of stably formed-, weakly folded and unfolded GQ conformations. The findings of this study and the method developed here will enable identifying and classifying potential GQ-forming sequences in human genome.
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Affiliation(s)
- Alex Kreig
- Bioengineering Department, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA
| | - Jacob Calvert
- Bioengineering Department, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA
| | - Janet Sanoica
- Bioengineering Department, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA
| | - Emily Cullum
- Bioengineering Department, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA
| | - Ramreddy Tipanna
- Bioengineering Department, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA
| | - Sua Myong
- Bioengineering Department, University of Illinois; 1304 W. Springfield Ave. Urbana, IL 61801, USA Biophysics and Computational Biology; 1110 W. Green St. Urbana, IL 61801, USA Institute for Genomic Biology; 1206 Gregory Drive, Urbana, IL 61801, USA Physics Frontier Center (Center of Physics for Living Cells), University of Illinois; 1110 W. Green St. Urbana, IL 61801, USA
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Bell RJA, Rube HT, Kreig A, Mancini A, Fouse SD, Nagarajan RP, Choi S, Hong C, He D, Pekmezci M, Wiencke JK, Wrensch MR, Chang SM, Walsh KM, Myong S, Song JS, Costello JF. Cancer. The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer. Science 2015; 348:1036-9. [PMID: 25977370 PMCID: PMC4456397 DOI: 10.1126/science.aab0015] [Citation(s) in RCA: 389] [Impact Index Per Article: 43.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/04/2015] [Indexed: 12/12/2022]
Abstract
Reactivation of telomerase reverse transcriptase (TERT) expression enables cells to overcome replicative senescence and escape apoptosis, which are fundamental steps in the initiation of human cancer. Multiple cancer types, including up to 83% of glioblastomas (GBMs), harbor highly recurrent TERT promoter mutations of unknown function but specific to two nucleotide positions. We identified the functional consequence of these mutations in GBMs to be recruitment of the multimeric GA-binding protein (GABP) transcription factor specifically to the mutant promoter. Allelic recruitment of GABP is consistently observed across four cancer types, highlighting a shared mechanism underlying TERT reactivation. Tandem flanking native E26 transformation-specific motifs critically cooperate with these mutations to activate TERT, probably by facilitating GABP heterotetramer binding. GABP thus directly links TERT promoter mutations to aberrant expression in multiple cancers.
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Affiliation(s)
- Robert J A Bell
- Department of Neurological Surgery, University of California, San Francisco, CA. Department of Biostatistics and Epidemiology, University of California, San Francisco, CA
| | - H Tomas Rube
- Department of Physics, University of Illinois, Urbana-Champaign, IL. Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL
| | - Alex Kreig
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL. Department of Bioengineering, University of Illinois, Urbana-Champaign, IL
| | - Andrew Mancini
- Department of Neurological Surgery, University of California, San Francisco, CA
| | - Shaun D Fouse
- Department of Neurological Surgery, University of California, San Francisco, CA
| | - Raman P Nagarajan
- Department of Neurological Surgery, University of California, San Francisco, CA
| | - Serah Choi
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA
| | - Chibo Hong
- Department of Neurological Surgery, University of California, San Francisco, CA
| | - Daniel He
- Department of Neurological Surgery, University of California, San Francisco, CA
| | - Melike Pekmezci
- Department of Anatomic Pathology, University of California San Francisco Medical School, San Francisco, CA 94143, USA
| | - John K Wiencke
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA. Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Margaret R Wrensch
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA. Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco, CA
| | - Kyle M Walsh
- Division of Neuroepidemiology, Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Sua Myong
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL. Department of Bioengineering, University of Illinois, Urbana-Champaign, IL
| | - Jun S Song
- Department of Biostatistics and Epidemiology, University of California, San Francisco, CA. Department of Physics, University of Illinois, Urbana-Champaign, IL. Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL. Department of Bioengineering, University of Illinois, Urbana-Champaign, IL.
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, CA.
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Calvert JS, Kreig A, Sinha S, Myong S. Computational Prediction of G-Quadruplex Formation. Biophys J 2015. [DOI: 10.1016/j.bpj.2014.11.098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Hwang H, Kreig A, Calvert J, Lormand J, Kwon Y, Daley JM, Sung P, Opresko PL, Myong S. Telomeric overhang length determines structural dynamics and accessibility to telomerase and ALT-associated proteins. Structure 2014; 22:842-53. [PMID: 24836024 DOI: 10.1016/j.str.2014.03.013] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Revised: 02/07/2014] [Accepted: 03/04/2014] [Indexed: 02/03/2023]
Abstract
The G-rich single-stranded DNA at the 3' end of human telomeres can self-fold into G-quaduplex (GQ). However, telomere lengthening by telomerase or the recombination-based alternative lengthening of telomere (ALT) mechanism requires protein loading on the overhang. Using single-molecule fluorescence spectroscopy, we discovered that lengthening the telomeric overhang also increased the rate of dynamic exchanges between structural conformations. Overhangs with five to seven TTAGGG repeats, compared with four repeats, showed much greater dynamics and accessibility to telomerase binding and activity and loading of the ALT-associated proteins RAD51, WRN, and BLM. Although the eight repeats are highly dynamic, they can fold into two GQs, which limited protein accessibility. In contrast, the telomere-specific protein POT1 is unique in that it binds independently of repeat number. Our results suggest that the telomeric overhang length and dynamics may contribute to the regulation of telomere extension via telomerase action and the ALT mechanism.
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Affiliation(s)
- Helen Hwang
- Bioengineering Department, University of Illinois, 1304 West Springfield Avenue, Urbana, IL 61801, USA; Medical Scholars Program, University of Illinois, 506 South Matthews Avenue, Urbana, IL 61801, USA
| | - Alex Kreig
- Bioengineering Department, University of Illinois, 1304 West Springfield Avenue, Urbana, IL 61801, USA
| | - Jacob Calvert
- Bioengineering Department, University of Illinois, 1304 West Springfield Avenue, Urbana, IL 61801, USA
| | - Justin Lormand
- Department of Environmental and Occupational Health, University of Pittsburgh, 100 Technology Drive, Suite 326, BRIDG, Pittsburgh, PA 15219, USA
| | - Yongho Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar Street, P.O. Box 208024, New Haven, CT 06520, USA
| | - James M Daley
- Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar Street, P.O. Box 208024, New Haven, CT 06520, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar Street, P.O. Box 208024, New Haven, CT 06520, USA
| | - Patricia L Opresko
- Department of Environmental and Occupational Health, University of Pittsburgh, 100 Technology Drive, Suite 326, BRIDG, Pittsburgh, PA 15219, USA
| | - Sua Myong
- Bioengineering Department, University of Illinois, 1304 West Springfield Avenue, Urbana, IL 61801, USA; Institute for Genomic Biology, University of Illinois, 1206 West Gregory Street, Urbana, IL 61801, USA; Physics Frontier Center (Center of Physics for Living Cells), University of Illinois, 1110 West Green Street, Urbana, IL 61801, USA.
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Kreig A, Calvert J, Tippana R, Myong SA. G-Quadruplex DNA Folding and Dynamics within Duplex DNA. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Darai G, Flügel RM, Zöller L, Matz B, Kreig A, Gelderblom H, Delius H, Leach RH. The plaque-forming factor for mink lung cells present in cytomegalovirus and herpes-zoster virus stocks identified as Mycoplasma hyorhinis. J Gen Virol 1981; 55:201-5. [PMID: 6271903 DOI: 10.1099/0022-1317-55-1-201] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Previous investigation of the ability of cytomegalovirus and varicella-zoster virus to replicate in a variety of cell lines suggested that both virus types plaqued with high efficiency in mink lung cells. However, many of the virus isolates used appeared to be contaminated with mycoplasma. We now report that the observed cytopathic effect is due to a mycoplasma which grows lytically to high titre in mink lung cells, but is difficult to cultivate in cell-free media. The mycoplasma was plaque-purified and shown to contain DNA with a buoyant density of 1.684 g/ml, with restriction endonuclease patterns identical to the porcine mycoplasma M. hyorhinis. This was confirmed by serological identification.
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