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Bachurin SS, Kletskii ME, Burov ON, Bibov MY, Dobaeva NM, Berezovskiy DP. Oligonucleotides-transformers for molecular biology and nanoengineering. Gene X 2022; 820:146277. [PMID: 35149154 DOI: 10.1016/j.gene.2022.146277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/14/2022] [Accepted: 02/03/2022] [Indexed: 11/04/2022] Open
Abstract
In the present review, numerous experimental and theoretical data describing the properties of non-canonical DNA structures (NSs) are analyzed. NSs (G-quadruplex, i-motif, hairpin, and triplex) play an important role in epigenetic processes (including the genetic variability of viruses), are prone to energetically low-cost conformational transformations and can very effectively be used in the design of nanoscale devices. Numerous experimental data have been analyzed in connection with the so-called oligonucleotides-transformers (nucleotide sequences that able to fold not only into one, but also into several NSs). These sequences were recently predicted by our calculations using automata and graph theories ("Dafna" algorithm). Possible applications of the oligonucleotides-transformers in nanoengineering and genetic editing of organisms are considered.
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Affiliation(s)
- Stanislav S Bachurin
- Rostov State Medical University, 29 Nakhichevanskiy Lane, Rostov-on-Don 344022, Russian Federation.
| | - Mikhail E Kletskii
- Chemical Department of Southern Federal University, 7 Zorge Str, Rostov-on-Don 344090, Russian Federation
| | - Oleg N Burov
- Chemical Department of Southern Federal University, 7 Zorge Str, Rostov-on-Don 344090, Russian Federation
| | - Mikhail Yu Bibov
- Rostov State Medical University, 29 Nakhichevanskiy Lane, Rostov-on-Don 344022, Russian Federation
| | - Natalya M Dobaeva
- Rostov State Medical University, 29 Nakhichevanskiy Lane, Rostov-on-Don 344022, Russian Federation
| | - Dmitriy P Berezovskiy
- I.M. Sechenov First Moscow State Medical University (Sechenov University), build. 4, 2 Bolshaya Pirogovskaya Str, Moscow 119435, Russian Federation
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2
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Bandyopadhyay D, Mishra PP. Real-Time Monitoring of the Multistate Conformational Dynamics of Polypurine Reverse Hoogsteen Hairpin To Capture Their Triplex-Affinity for Gene Silencing by smFRET Microspectroscopy. J Phys Chem B 2020; 124:8230-8239. [DOI: 10.1021/acs.jpcb.0c05493] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Debolina Bandyopadhyay
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, HBNI Mumbai, 1/AF Bidhannagar, Kolkata 700064, India
| | - Padmaja P. Mishra
- Single-Molecule Biophysics Lab, Chemical Sciences Division, Saha Institute of Nuclear Physics, HBNI Mumbai, 1/AF Bidhannagar, Kolkata 700064, India
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3
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Abstract
G-quadruplexes (G4s) have become one of the most exciting nucleic acid secondary structures. A noncanonical, four-stranded structure formed in guanine-rich DNA and RNA sequences, G-quadruplexes can readily form under physiologically relevant conditions and are globularly folded structures. DNA is widely recognized as a double-helical structure essential in genetic information storage. However, only ~3% of the human genome is expressed in protein; RNA and DNA may form noncanonical secondary structures that are functionally important. G-quadruplexes are one such example which have gained considerable attention for their formation and regulatory roles in biologically significant regions, such as human telomeres, oncogene-promoter regions, replication initiation sites, and 5'- and 3'-untranslated region (UTR) of mRNA. They are shown to be a regulatory motif in a number of critical cellular processes including gene transcription, translation, replication, and genomic stability. G-quadruplexes are also found in nonhuman genomes, particularly those of human pathogens. Therefore, G-quadruplexes have emerged as a new class of molecular targets for drug development. In addition, there is considerable interest in the use of G-quadruplexes for biomaterials, biosensors, and biocatalysts. The First International Meeting on Quadruplex DNA was held in 2007, and the G-quadruplex field has been growing dramatically over the last decade. The methods used to study G-quadruplexes have been essential to the rapid progress in our understanding of this exciting nucleic acid secondary structure.
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Affiliation(s)
- Danzhou Yang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, Purdue Center for Cancer Research, Purdue Institute for Drug Discovery, West Lafayette, IN USA
| | - Clement Lin
- Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University, West Lafayette, IN USA
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4
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Majumder K, Bassing CH, Oltz EM. Regulation of Tcrb Gene Assembly by Genetic, Epigenetic, and Topological Mechanisms. Adv Immunol 2015; 128:273-306. [PMID: 26477369 DOI: 10.1016/bs.ai.2015.07.001] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The adaptive immune system endows mammals with an ability to recognize nearly any foreign invader through antigen receptors that are expressed on the surface of all lymphocytes. This defense network is generated by V(D)J recombination, a set of sequentially controlled DNA cleavage and repair events that assemble antigen receptor genes from physically separated variable (V), joining (J), and sometimes diversity (D) gene segments. The recombination process itself must be stringently regulated to minimize oncogenic translocations involving chromosomes that harbor immunoglobulin and T cell receptor loci. Indeed, V(D)J recombination is controlled at several levels, including tissue-, developmental stage-, allele-, and gene segment-specificity. These levels of control are imposed by a collection of architectural and regulatory elements that are distributed throughout each antigen receptor locus. Together, the genetic elements regulate developmental changes in chromatin, transcription, and locus topology that promote or disfavor long-range recombination. This chapter focuses on the cross talk between these mechanisms at the T cell receptor beta (Tcrb) locus, and how they sculpt a diverse TCRβ repertoire while maintaining monospecificity of this antigen receptor on each mature T lymphocyte. We also discuss how insights obtained from studies of Tcrb are more generally relevant to our understanding of gene regulation strategies employed by mammals.
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Affiliation(s)
- Kinjal Majumder
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA
| | - Craig H Bassing
- Division of Cancer Pathobiology, Department of Pathology and Laboratory Medicine, Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA; Abramson Family Cancer Research Institute, Cell and Molecular Biology Graduate Program, Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Eugene M Oltz
- Department of Pathology and Immunology, Washington University School of Medicine, Saint Louis, Missouri, USA.
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5
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Axford MM, Wang YH, Nakamori M, Zannis-Hadjopoulos M, Thornton CA, Pearson CE. Detection of slipped-DNAs at the trinucleotide repeats of the myotonic dystrophy type I disease locus in patient tissues. PLoS Genet 2013; 9:e1003866. [PMID: 24367268 PMCID: PMC3868534 DOI: 10.1371/journal.pgen.1003866] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2012] [Accepted: 08/25/2013] [Indexed: 12/16/2022] Open
Abstract
Slipped-strand DNAs, formed by out-of-register mispairing of repeat units on complementary strands, were proposed over 55 years ago as transient intermediates in repeat length mutations, hypothesized to cause at least 40 neurodegenerative diseases. While slipped-DNAs have been characterized in vitro, evidence of slipped-DNAs at an endogenous locus in biologically relevant tissues, where instability varies widely, is lacking. Here, using an anti-DNA junction antibody and immunoprecipitation, we identify slipped-DNAs at the unstable trinucleotide repeats (CTG)n•(CAG)n of the myotonic dystrophy disease locus in patient brain, heart, muscle and other tissues, where the largest expansions arise in non-mitotic tissues such as cortex and heart, and are smallest in the cerebellum. Slipped-DNAs are shown to be present on the expanded allele and in chromatinized DNA. Slipped-DNAs are present as clusters of slip-outs along a DNA, with each slip-out having 1–100 extrahelical repeats. The allelic levels of slipped-DNA containing molecules were significantly greater in the heart over the cerebellum (relative to genomic equivalents of pre-IP input DNA) of a DM1 individual; an enrichment consistent with increased allelic levels of slipped-DNA structures in tissues having greater levels of CTG instability. Surprisingly, this supports the formation of slipped-DNAs as persistent mutation products of repeat instability, and not merely as transient mutagenic intermediates. These findings further our understanding of the processes of mutation and genetic variation. Over 30 diseases are caused by the expansion of a trinucleotide repeat (TNR) in a specific gene, including the most common adult-onset form of muscular dystrophy, myotonic dystrophy (DM1). The mechanistic contributors to this unstable (TNR) expansion are not fully known, although since the discovery of these types of diseases over twenty years ago, the extrusion of the expanded repeats into mutagenic slipped-DNA conformations has been hypothesized. Here, we show the presence of slipped-DNA at the DM1 disease locus in various patient tissues. The allelic amounts of slipped-DNA in tissues correlate with overall levels of repeat instability. Slipped-DNA was also found to form in clusters along a tract of expanded repeats, which has been previously shown in vitro to impede DNA repair. This is the first evidence for slipped-DNA formation at an endogenous disease-causing gene in patient tissues.
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Affiliation(s)
- Michelle M. Axford
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Yuh-Hwa Wang
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
| | - Masayuki Nakamori
- Department of Neurology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Maria Zannis-Hadjopoulos
- Goodman Cancer Research Centre and Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Charles A. Thornton
- Department of Neurology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Christopher E. Pearson
- Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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6
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Kozhevnikova EN, van der Knaap JA, Pindyurin AV, Ozgur Z, van Ijcken WFJ, Moshkin YM, Verrijzer CP. Metabolic enzyme IMPDH is also a transcription factor regulated by cellular state. Mol Cell 2012; 47:133-9. [PMID: 22658723 DOI: 10.1016/j.molcel.2012.04.030] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Revised: 03/13/2012] [Accepted: 04/26/2012] [Indexed: 01/27/2023]
Abstract
Cells need to coordinate gene expression and metabolic state. Inosine monophosphate dehydrogenase (IMPDH) controls the guanine nucleotide pool and, thereby, cell proliferation. We found that Drosophila IMPDH is also a DNA-binding transcriptional repressor. IMPDH attenuates expression of histone genes and E2f, a key driver of cell proliferation. Nuclear IMPDH accumulates during the G2 phase of the cell cycle or following replicative or oxidative stress. Thus, IMPDH can couple the expression of histones and E2F to cellular state. Genome-wide profiling and in vitro binding assays established that IMPDH binds sequence specifically to single-stranded, CT-rich DNA elements. Surprisingly, this DNA-binding function is conserved in E. coli IMPDH. The catalytic function of IMPDH is not required for DNA binding. Yet substitutions that correspond to human retinitis pigmentosa mutations disrupt IMPDH binding to CT-rich, single-stranded DNA elements. By doubling as nucleotide biosynthetic enzyme or transcription factor, IMPDH can either enable or restrict cell proliferation.
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Affiliation(s)
- Elena N Kozhevnikova
- Department of Biochemistry and Center for Biomedical Genetics, Erasmus University Medical Centre, P.O. Box 1738, 3000 DR, Rotterdam, The Netherlands
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7
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Zhao R, Nakamura T, Fu Y, Lazar Z, Spector DL. Gene bookmarking accelerates the kinetics of post-mitotic transcriptional re-activation. Nat Cell Biol 2011; 13:1295-304. [PMID: 21983563 PMCID: PMC3210065 DOI: 10.1038/ncb2341] [Citation(s) in RCA: 188] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Accepted: 08/10/2011] [Indexed: 12/12/2022]
Abstract
Although transmission of the gene expression program from mother to daughter cells has been suggested to be mediated by gene bookmarking, the precise mechanism by which bookmarking mediates post-mitotic transcriptional re-activation has been unclear. Here, we used a real-time gene expression system to quantitatively demonstrate that transcriptional activation of the same genetic locus occurs with a significantly more rapid kinetics in post-mitotic cells versus interphase cells. RNA polymerase II large subunit (Pol II) and bromodomain protein 4 (BRD4) were recruited to the locus in a different sequential order on interphase initiation versus post-mitotic re-activation resulting from the recognition by BRD4 of increased levels of histone H4 Lys 5 acetylation (H4K5ac) on the previously activated locus. BRD4 accelerated the dynamics of messenger RNA synthesis by de-compacting chromatin and hence facilitating transcriptional re-activation. Using a real-time quantitative approach, we identified differences in the kinetics of transcriptional activation between interphase and post-mitotic cells that are mediated by a chromatin-based epigenetic mechanism.
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Affiliation(s)
- Rui Zhao
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, USA
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8
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Abstract
DNA G-quadruplexes are DNA secondary structures formed in specific G-rich sequences. DNA sequences that can form G-quadruplexes have been found in regions with biological significance, such as human telomeres and oncogene-promoter regions. DNA G-quadruplexes have recently emerged as a new class of novel molecular targets for anticancer drugs. Recent progress on structural studies of the biologically relevant G-quadruplexes formed in human telomeres and in the promoter regions of human oncogenes will be discussed, as well as recent advances in the design and development of G-quadruplex-interactive drugs. DNA G-quadruplexes can readily form in solution under physiological conditions and are globularly folded nucleic acid structures. The molecular structures of intramolecular G-quadruplexes appear to differ from one another and, therefore, in principle may be differentially regulated and targeted by different proteins and drugs.
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9
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Qin Y, Fortin JS, Tye D, Gleason-Guzman M, Brooks TA, Hurley LH. Molecular cloning of the human platelet-derived growth factor receptor beta (PDGFR-beta) promoter and drug targeting of the G-quadruplex-forming region to repress PDGFR-beta expression. Biochemistry 2010; 49:4208-19. [PMID: 20377208 DOI: 10.1021/bi100330w] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
To understand the mechanisms controlling platelet-derived growth factor receptor beta (PDGFR-beta) expression in malignancies, we have cloned and characterized the first functional promoter of the human PDGFR-beta gene, which has been confirmed by luciferase reporter gene assays. The transcription initiation sites were mapped by primer extension. Promoter deletion experiments demonstrate that the proximal, highly GC-rich region (positions -165 to -139) of the human PDGFR-beta promoter is crucial for basal promoter activity. This region is sensitive to S1 nuclease and likely to assume a non-B-form DNA secondary structure within the supercoiled plasmid. The G-rich strand in this region contains a series of runs of three or more guanines that can form multiple different G-quadruplex structures, which have been subsequently assessed by circular dichroism. A Taq polymerase stop assay has shown that three different G-quadruplex-interactive drugs can each selectively stabilize different G-quadruplex structures of the human PDGFR-beta promoter. However, in transfection experiments, only telomestatin significantly reduced the human PDGFR-beta basal promoter activity relative to the control. Furthermore, the PDGFR-beta mRNA level in Daoy cells was significantly decreased after treatment with 1 muM telomestatin for 24 h. Therefore, we propose that ligand-mediated stabilization of specific G-quadruplex structures in the human PDGFR-beta promoter can modulate its transcription.
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Affiliation(s)
- Yong Qin
- College of Pharmacy, 1703 East Mabel, University of Arizona, Tucson, Arizona 85721, USA
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10
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Song G, Ren J. Recognition and regulation of unique nucleic acid structures by small molecules. Chem Commun (Camb) 2010; 46:7283-94. [DOI: 10.1039/c0cc01312a] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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11
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Lee HT, Khutsishvili I, Marky LA. DNA Complexes Containing Joined Triplex and Duplex Motifs: Melting Behavior of Intramolecular and Bimolecular Complexes with Similar Sequences. J Phys Chem B 2009; 114:541-8. [DOI: 10.1021/jp9084074] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hui-Ting Lee
- Department of Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, and Eppley Institute for Cancer Research, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025
| | - Irine Khutsishvili
- Department of Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, and Eppley Institute for Cancer Research, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025
| | - Luis A. Marky
- Department of Pharmaceutical Sciences, Department of Biochemistry and Molecular Biology, and Eppley Institute for Cancer Research, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, Nebraska 68198-6025
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12
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Sarge KD, Park-Sarge OK. Mitotic bookmarking of formerly active genes: keeping epigenetic memories from fading. Cell Cycle 2009; 8:818-23. [PMID: 19221503 DOI: 10.4161/cc.8.6.7849] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In order for cell lineages to be maintained, daughter cells must have the same patterns of gene expression as the cells from which they were divided so that they can have the same phenotypes. However, during mitosis transcription ceases, chromosomal DNA is compacted, and most sequence-specific binding factors dissociate from DNA, making it difficult to understand how the "memory" of gene expression patterns is remembered and propagated to daughter cells. The process of remembering patterns of active gene expression during mitosis for transmission to daughter cells is called gene bookmarking. Here we discuss current knowledge concerning the factors and mechanisms involved in mediating gene bookmarking, including recent results on the mechanism by which the general transcription factor TBP participates in the mitotic bookmarking of formerly active genes.
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Affiliation(s)
- Kevin D Sarge
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, USA.
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13
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Baker ES, Dupuis NF, Bowers MT. DNA Hairpin, Pseudoknot, and Cruciform Stability in a Solvent-Free Environment. J Phys Chem B 2009; 113:1722-7. [DOI: 10.1021/jp807529m] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Erin Shammel Baker
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510
| | - Nicholas F. Dupuis
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510
| | - Michael T. Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510
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14
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Unfolding Thermodynamics of DNA Intramolecular Complexes Involving Joined Triple- and Double-Helical Motifs. Methods Enzymol 2009; 466:477-502. [DOI: 10.1016/s0076-6879(09)66020-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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15
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Xing H, Vanderford NL, Sarge KD. The TBP-PP2A mitotic complex bookmarks genes by preventing condensin action. Nat Cell Biol 2008; 10:1318-23. [PMID: 18931662 DOI: 10.1038/ncb1790] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Accepted: 08/12/2008] [Indexed: 11/09/2022]
Abstract
To maintain phenotypes of cell lineages, cells must 'remember' which genes were active before mitosis entry and transmit this information to their daughter cells so that expression patterns can be faithfully re-established in G1. This phenomenon is called gene bookmarking. However, during mitosis transcription ceases, most sequence-specific proteins dissociate from DNA and the chromatin is tightly compacted, making it difficult to understand how gene activity 'memory' is maintained through this stage of the cell cycle. A feature of gene bookmarking is that in mitotic cells, the promoters of formerly active genes lack compaction, but how compaction of these regions is inhibited is unknown. Here we show that during mitosis, TATA-binding protein (TBP), which remains bound to DNA during mitosis, recruits PP2A. TBP also interacts with condensin to allow efficient dephosphorylation and inactivation of condensin near these promoters to inhibit their compaction. Further, ChIP-on-chip data show that TBP is bound to many chromosomal sites during mitosis, and is higher in transcribed regions but low in regions containing pseudogenes and genes whose expression is tissue-restricted. These results suggest that TBP is involved not only in gene transcription during interphase but also in preserving the memory of gene activity through mitosis to daughter cells.
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Affiliation(s)
- Hongyan Xing
- Department of Molecular and Cellular Biochemistry, Chandler Medical Center, University of Kentucky, Lexington, KY 40536, USA
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16
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Yafe A, Shklover J, Weisman-Shomer P, Bengal E, Fry M. Differential binding of quadruplex structures of muscle-specific genes regulatory sequences by MyoD, MRF4 and myogenin. Nucleic Acids Res 2008; 36:3916-25. [PMID: 18511462 PMCID: PMC2475631 DOI: 10.1093/nar/gkn340] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Four myogenic regulatory factors (MRFs); MyoD, Myf-5, MRF4 and Myogenin direct muscle tissue differentiation. Heterodimers of MRFs with E-proteins activate muscle-specific gene expression by binding to E-box motifs d(CANNTG) in their promoters or enhancers. We showed previously that in contrast to the favored binding of E-box by MyoD-E47 heterodimers, homodimeric MyoD associated preferentially with quadruplex structures of regulatory sequences of muscle-specific genes. To inquire whether other MRFs shared the DNA binding preferences of MyoD, the DNA affinities of hetero- and homo-dimeric MyoD, MRF4 and Myogenin were compared. Similarly to MyoD, heterodimers with E47 of MRF4 or Myogenin bound E-box more tightly than quadruplex DNA. However, unlike homodimeric MyoD or MRF4, Myogenin homodimers associated weakly and nonpreferentially with quadruplex DNA. By reciprocally switching basic regions between MyoD and Myogenin we demonstrated dominance of MyoD in determining the quadruplex DNA-binding affinity. Thus, Myogenin with an implanted MyoD basic region bound quadruplex DNA nearly as tightly as MyoD. However, a grafted Myogenin basic region did not diminish the high affinity of homodimeric MyoD for quadruplex DNA. We speculate that the dissimilar interaction of MyoD and Myogenin with tetrahelical domains in muscle gene promoters may differently regulate their myogenic activities.
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Affiliation(s)
- Anat Yafe
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, POB 9649 Bat Galim, Haifa 31096, Israel
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17
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Yagil G. DNA tracts composed of only two bases concentrate in gene promoters. Genomics 2006; 87:591-7. [PMID: 16442774 DOI: 10.1016/j.ygeno.2005.12.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2005] [Revised: 12/04/2005] [Accepted: 12/05/2005] [Indexed: 10/25/2022]
Abstract
We have previously shown that long DNA tracts composed of only two of the bases ("binary DNA") are highly overrepresented in sequenced eukaryotic genomes. Here we examine gene promoter regions, by superposing all genes in a chromosome at their transcription start sites. We find that of the four motifs made of two bases, three are concentrated in gene promoters: Purine/pyrimidine tracts are highly overrepresented in the promoters of yeast chromosome IV, in Caenorhabditis elegans chromosome I, in Arabidopsis thaliana chromosome 2, and in human chromosomes 14, 21, and 22 (a subset). AT-rich tracts (W tracts) are enriched in the same chromosomes, as well as in Drosophila melanogaster chromosome 2R and in an archeon, M. jannaschii. A third motif, K.M tracts, shows some concentration in D. melanogaster promoters. A propensity of binary DNA to unwind is proposed to explain the high presence of the two-base motifs in gene promoters.
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Affiliation(s)
- G Yagil
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot 76100, Israel.
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18
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Sarge KD, Park-Sarge OK. Gene bookmarking: keeping the pages open. Trends Biochem Sci 2005; 30:605-10. [PMID: 16188444 DOI: 10.1016/j.tibs.2005.09.004] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2005] [Revised: 08/12/2005] [Accepted: 09/14/2005] [Indexed: 11/19/2022]
Abstract
'Gene bookmarking' is a mechanism of epigenetic memory that functions to transmit through mitosis the pattern of active genes and/or genes that can be activated to daughter cells. It is thought that, at a point before mitosis, genes that exist in an open, transcriptionally competent state are bound by proteins or marked by some kind of modification event. This is thought to facilitate the assembly of transcription complexes on the promoters in early G1, thereby ensuring that daughter cells have the same pattern of gene expression as the cell from which they derived. Little is known, however, about these 'bookmarking factors' and modifications or the mechanisms by which they mediate the transmission of transcriptional competence after mitosis is complete. Recent findings have provided new insights into the mechanisms, regulation and biological importance of gene bookmarking in eukaryotic cell function.
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Affiliation(s)
- Kevin D Sarge
- Department of Molecular and Cellular Biochemistry, Biomedical/Biological Sciences Research Building, 741 South Limestone Street, Lexington, KY 40536, USA.
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19
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Suswam EA, Li YY, Mahtani H, King PH. Novel DNA-binding properties of the RNA-binding protein TIAR. Nucleic Acids Res 2005; 33:4507-18. [PMID: 16091628 PMCID: PMC1184220 DOI: 10.1093/nar/gki763] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
TIA-1 related protein binds avidly to uridine-rich elements in mRNA and pre-mRNAs of a wide range of genes, including interleukin (IL)-8 and vascular endothelial growth factor (VEGF). The protein has diverse regulatory roles, which in part depend on the locus of binding within the transcript, including translational control, splicing and apoptosis. Here, we observed selective and potent inhibition of TIAR–RNP complex formation with IL-8 and VEGF 3′-untranslated regions (3′-UTRs) using thymidine-rich deoxyoligonucleotide (ODN) sequences derived from the VEFG 3′-UTR. We show by ultraviolet crosslinking and electrophoretic mobility shift assays that TIAR can bind directly to single-stranded, thymidine-rich ODNs but not to double-stranded ODNs containing the same sequence. TIAR had a nearly 6-fold greater affinity for DNA than RNA (Kdapp=1.6×10−9M versus 9.4 × 10−9 M). Truncation of TIAR indicated that the high affinity DNA-binding site overlaps with the RNA-binding site involving RNA recognition motif 2 (RRM2). However, RRM1 alone could also bind to DNA. Finally, we show that TIAR can be displaced from single-stranded DNA by active transcription through the binding site. These results provide a potential mechanism by which TIAR can shuttle between RNA and DNA ligands.
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Affiliation(s)
- Esther A. Suswam
- Department of Neurology, University of AlabamaBirmingham, AL 35295, USA
- Birmingham Veterans Affairs Medical CenterBirmingham, AL 35295, USA
| | - Yan Yan Li
- Department of Neurology, University of AlabamaBirmingham, AL 35295, USA
- Birmingham Veterans Affairs Medical CenterBirmingham, AL 35295, USA
| | - Harry Mahtani
- Department of Neurology, University of AlabamaBirmingham, AL 35295, USA
- Birmingham Veterans Affairs Medical CenterBirmingham, AL 35295, USA
| | - Peter H. King
- Department of Neurology, University of AlabamaBirmingham, AL 35295, USA
- Department of Physiology and Biophysics, University of AlabamaBirmingham, AL 35295, USA
- Birmingham Veterans Affairs Medical CenterBirmingham, AL 35295, USA
- To whom correspondence should be addressed. Tel: +1 205 975 8116; Fax: +1 205 934 0928;
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Osada K, Yamasaki Y, Katayose S, Kataoka K. A Synthetic Block Copolymer Regulates S1 Nuclease Fragmentation of Supercoiled Plasmid DNA. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200500201] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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21
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Osada K, Yamasaki Y, Katayose S, Kataoka K. A Synthetic Block Copolymer Regulates S1 Nuclease Fragmentation of Supercoiled Plasmid DNA. Angew Chem Int Ed Engl 2005; 44:3544-8. [PMID: 15880738 DOI: 10.1002/anie.200500201] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Kensuke Osada
- Department of Materials Science and Engineering, Graduate School of Engineering, The University of Tokyo, Hongo 7-3-1, Bunkyo, Tokyo 113-8655, Japan
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22
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Etzioni S, Yafe A, Khateb S, Weisman-Shomer P, Bengal E, Fry M. Homodimeric MyoD preferentially binds tetraplex structures of regulatory sequences of muscle-specific genes. J Biol Chem 2005; 280:26805-12. [PMID: 15923190 DOI: 10.1074/jbc.m500820200] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Myogenic transcription is activated by the binding of heterodimers of the basic helix-loop-helix proteins MyoD and E12 or E47 to a consensus E-box sequence, d(CANNTG), in promoter or enhancer regions of muscle-specific genes. Homodimers of MyoD bind E-box less tightly and are less efficient activators of transcription. Recent results from our laboratory (Yafe, A., Etzioni, S., Weisman-Shomer, P., and Fry, M. (2005) Nucleic Acids Res. 33, 2887-2900) indicate that regulatory sequences of several muscle-specific genes contain a disproportionate high content of guanine clusters that readily form hairpin and parallel-stranded unimolecular and bimolecular tetraplex structures. Here we have shown that homodimers of full-length recombinant MyoD formed complexes with bimolecular tetraplex structures of muscle-specific regulatory sequences but not with their double-stranded, hairpin, or unimolecular tetraplex forms. Preferential binding of homodimeric MyoD to bimolecular tetraplex DNA structures over E-box DNA was reflected by the 18.7-39.9-fold lower dissociation constants, Kd, of the MyoD-tetraplex DNA complexes. Conversely, MyoD-E47 heterodimers formed tighter complexes with E-box as indicated by their 6.8-19.0-fold lower Kd relative to complexes with bimolecular tetraplex DNA structures. Similarly, homodimers of the 60-amino acid basic helix-loop-helix domain of MyoD bound E-box more efficiently and tetraplex DNA less efficiently than homodimers of full-length MyoD. It might be that the favored binding of MyoD homodimers to tetraplex DNA structures lowers their ability to activate muscle-specific gene transcription, whereas the formation of MyoD-E47 heterodimers and their preferential binding to E-box DNA enhance transcription.
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Affiliation(s)
- Shulamit Etzioni
- Department of Biochemistry, Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, P. O. Box 9649 Bat Galim, Haifa 31096, Israel
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23
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Yagil G. The over-representation of binary DNA tracts in seven sequenced chromosomes. BMC Genomics 2004; 5:19. [PMID: 15113401 PMCID: PMC407849 DOI: 10.1186/1471-2164-5-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2003] [Accepted: 03/03/2004] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA tracts composed of only two bases are possible in six combinations: A+G (purines, R), C+T (pyrimidines, Y), G+T (Keto, K), A+C (Imino, M), A+T (Weak, W) and G+C (Strong, S). It is long known that all-pyrimidine tracts, complemented by all-purines tracts ("R.Y tracts"), are excessively present in analyzed DNA. We have previously shown that R.Y tracts are in vast excess in yeast promoters, and brought evidence for their role in gene regulation. Here we report the systematic mapping of all six binary combinations on the level of complete sequenced chromosomes, as well as in their different subregions. RESULTS DNA tracts composed of the above binary base combinations have been mapped in seven sequenced chromosomes: Human chromosomes 21 and 22 (the major contigs); Drosophila melanogaster chr. 2R; Caenorhabditis elegans chr. I; Arabidopsis thaliana chr. II; Saccharomyces cerevisiae chr. IV and M. jannaschii. A huge over-representation, reaching million-folds, has been found for very long tracts of all binary motifs except S, in each of the seven organisms. Long R.Y tracts are the most excessive, except in D. melanogaster, where the K.M motif predominates. S (G, C rich) tracts are in excess mainly in CpG islands; the W motif predominates in bacteria. Many excessively long W tracts are nevertheless found also in the archeon and in the eukaryotes. The survey of complete chromosomes enables us, for the first time, to map systematically the intergenic regions. In human and other chromosomes we find the highest over-representation of the binary DNA tracts in the intergenic regions. These over-representations are only partly explainable by the presence of interspersed elements. CONCLUSIONS The over-representation of long DNA tracts composed of five of the above motifs is the largest deviation from randomness so far established for DNA, and this in a wide range of eukaryotic and archeal chromosomes. A propensity for ready DNA unwinding is proposed as the functional role, explaining the evolutionary conservation of the huge excesses observed.
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Affiliation(s)
- Gad Yagil
- Dept of Molecular Cell Biology, The Weizmann Institute of Biology, Rehovot, Israel 76100.
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24
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Abstract
MUC1 is a tumor antigen, overexpressed in approximately 90% of human breast cancers. In normal glandular epithelia, MUC1 is expressed at the apical surface; however, in carcinomas an aberrantly glycosylated form of MUC1 is upregulated and expressed around the entire surface of the cell. Previously, we have shown that a lack of Muc1 significantly delays tumor progression and/or onset in MMTV-PyV-mT and MMTV-Wnt-1 transgenic mice. Here we show that, unlike the models mentioned above, a loss of Muc1 in MMTV-c-Neu mice (MMTV-c-Neu/Muc1(-/-)) altered neither mammary tumor onset nor progression. Moreover, characterization of MMTV-c-Neu/Muc1(+/+) tumors revealed that Muc1 expression was repressed at the level of transcription. In contrast, normal mammary gland tissue adjacent to tumor tissue expressed Muc1 and pregnant mammary glands from c-Neu transgenic animals expressed high levels of Muc1. We found that transient transfection of activated ErbB2 into human embryonic kidney 293/MUC1 cells resulted in the repression of MUC1 expression. Further, transient transfection of activated ErbB2 resulted in the inhibition of Muc1 transcriptional activation in luciferase reporter assays. These data suggest that the activation of ErbB2, which only occurs in c-Neu tumors, selectively inhibits Muc1 expression.
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Affiliation(s)
- Melissa C Adriance
- Tumor Biology Program, Mayo Medical/Graduate School, Mayo Clinic Scottsdale, Scottsdale, AZ 85259, USA
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25
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Gal M, Katz T, Ovadia A, Yagil G. TRACTS: A program to map oligopurine.oligopyrimidine and other binary DNA tracts. Nucleic Acids Res 2003; 31:3682-5. [PMID: 12824393 PMCID: PMC169031 DOI: 10.1093/nar/gkg625] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A program to map the locations and frequencies of DNA tracts composed of only two bases ('Binary DNA') is described. The program, TRACTS (URL http://bioportal.weizmann.ac.il/tracts/tracts.html and/or http://bip.weizmann.ac.il/miwbin/servers/tracts) is of interest because long tracts composed of only two bases are highly over-represented in most genomes. In eukaryotes, oligopurine.oligopyrimidine tracts ('R.Y tracts') are found in the highest excess. In prokaryotes, W tracts predominate (A,T 'rich'). A pre-program, ANEX, parses database annotation files of GenBank and EMBL, to produce a convenient one-line list of every gene (exon, intron) in a genome. The main unit lists and analyzes tracts of the three possible binary pairs (R.Y, K.M and S;W). As an example, the results of R.Y tract mapping of mammalian gene p53 is described.
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Affiliation(s)
- Moshe Gal
- BioMining Ltd, POB 2526, Kadima, Israel.
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26
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Maiti AK, Brahmachari SK. Poly purine.pyrimidine sequences upstream of the beta-galactosidase gene affect gene expression in Saccharomyces cerevisiae. BMC Mol Biol 2001; 2:11. [PMID: 11696239 PMCID: PMC59624 DOI: 10.1186/1471-2199-2-11] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2001] [Accepted: 10/08/2001] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Poly purine.pyrimidine sequences have the potential to adopt intramolecular triplex structures and are overrepresented upstream of genes in eukaryotes. These sequences may regulate gene expression by modulating the interaction of transcription factors with DNA sequences upstream of genes. RESULTS A poly purine.pyrimidine sequence with the potential to adopt an intramolecular triplex DNA structure was designed. The sequence was inserted within a nucleosome positioned upstream of the beta-galactosidase gene in yeast, Saccharomyces cerevisiae, between the cycl promoter and gal 10 Upstream Activating Sequences (UASg). Upon derepression with galactose, beta-galactosidase gene expression is reduced 12-fold in cells carrying single copy poly purine.pyrimidine sequences. This reduction in expression is correlated with reduced transcription. Furthermore, we show that plasmids carrying a poly purine.pyrimidine sequence are not specifically lost from yeast cells. CONCLUSION We propose that a poly purine.pyrimidine sequence upstream of a gene affects transcription. Plasmids carrying this sequence are not specifically lost from cells and thus no additional effort is needed for the replication of these sequences in eukaryotic cells.
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Affiliation(s)
- Amit K Maiti
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
| | - Samir K Brahmachari
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560012, India
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27
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Borges K, Dingledine R. Functional organization of the GluR1 glutamate receptor promoter. J Biol Chem 2001; 276:25929-38. [PMID: 11340067 DOI: 10.1074/jbc.m009105200] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The GluR1 glutamate receptor subunit is expressed in most brain areas and plays a major role in excitatory synaptic transmission. We cloned and sequenced 5 kilobase pairs of the rat GluR1 promoter and identified multiple transcriptional start sites between -295 and -202 (relative to the first ATG). Similar to other glutamate receptor subunit promoters, the GluR1 promoter lacks TATA and CAAT elements in that region but binds Sp1 proteins at two sites. Promoter activity of GluR1 fragments cloned into pGL3 was assessed by immunocytochemistry and by measuring luciferase activity after transfection into primary cultures of rat cortical neurons and glia. GluR1 promoter activity was stronger in neurons, with neuronal specificity appearing to reside mainly within the neuronal expression-enhancing regions, -1395 to -743 and -253 to -48. The latter region contains 4 sites that bound recombinant cAMP-response element-binding proteins and a glial silencing region between -253 and -202. In both neurons and glia, promoter activity was increased by a 64-base pair GA repeat upstream of the initiation sites and reduced by a 57-base pair region that contained an N box. In contrast to the GluR2 promoter the regulatory regions are mainly located outside of the GluR1 initiation region.
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Affiliation(s)
- K Borges
- Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia 30322, USA.
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28
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Stankunas K, Graef IA, Neilson JR, Park SH, Crabtree GR. Signaling through calcium, calcineurin, and NF-AT in lymphocyte activation and development. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2001; 64:505-16. [PMID: 11232327 DOI: 10.1101/sqb.1999.64.505] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- K Stankunas
- Department of Developmental Biology and Department of Pathology, Howard Hughes Medical Institute, Stanford University Medical School, Stanford, California 94305, USA
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29
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Ko JL, Loh HH. Single-stranded DNA-binding complex involved in transcriptional regulation of mouse mu-opioid receptor gene. J Biol Chem 2001; 276:788-95. [PMID: 11027679 DOI: 10.1074/jbc.m004279200] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Previously, we reported the presence of dual (distal and proximal) promoters in mouse mu-opioid receptor (mor) gene, with mor transcription in mouse brain predominantly initiated by the proximal promoter. Sp factors, bound to double-stranded (ds) cis-regulatory elements, are critical for proximal promoter activity. Here, we further report that a single-stranded (ss) cis-regulatory element and trans-acting protein factor are also important for proximal promoter activity. A 26-bp mor polypyrimidine/polypurine region (PPy/u) can adopt ss DNA conformation, as demonstrated by S1 nuclease sensitivity. Using electrophoretic mobility shift analysis with nuclear extracts from mor-expressing SH-SY5Y cells, we demonstrate that the sense strand of PPy/u interacts with a major nuclear protein, termed mor polypyrimidine-binding protein (mPy), which is not related to Sp factors. Southwestern blot analysis indicated that mPy protein is approximately 25 kDa in size. Functional analysis suggests that mPy protein can trans-activate mor promoter as well as a heterologous promoter. Moreover, combinatorial activation of ss (mPy) and ds (Sps) DNA binding factors, interacting with an overlapping DNA (PPy/u) region, is necessary for proximal promoter activation. Thus our results suggest that transcription of mouse mor gene is regulated by an interplay of ss and ds DNA binding factors.
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Affiliation(s)
- J L Ko
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota 55455, USA.
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30
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Ashley C, Lee JS. A triplex-mediated knot between separated polypurine-polypyrimidine tracts in circular DNA blocks transcription by Escherichia coli RNA polymerase. DNA Cell Biol 2000; 19:235-41. [PMID: 10798447 DOI: 10.1089/104454900314500] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Polypurine-polypyrimidine tracts are overrepresented in eukaryotes and many have the potential to form triplex DNA. Transmolecular triplexes form between separated but complementary polypurine-polypyrimidine tracts in duplex DNA. Transmolecular triplexes (T-loops) were studied previously using a circular plasmid containing a pair of separated polypurine-polypyrimidine tracts designed to able to form a triplex with each other. T-Loops formed when the nicked plasmid was incubated at low pH in the presence of spermine. When the pH was raised to 8, the T-loops were constrained by a hydrogen-bonded knot composed of multistranded and single-stranded regions. The present experiments used T-loops as a model system to investigate the influence of transmolecular triplex formation on transcription. T-Loops and control open circular, linear, and supercoiled plasmid forms were isolated from bands on agarose gels. Transcription assays were carried out with the isolated plasmid forms and Escherichia coli RNA polymerase holoenzyme and the core enzyme, which lacked sigma70. Transcription was significantly inhibited in T-loop forms compared with control plasmid forms. There was no evidence that the single-stranded regions of T-loops facilitated nonspecific initiation of transcription. Instead, the multistranded component of the hydrogen-bonded knot at the root of the T-loop structure inhibited transcription.
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Affiliation(s)
- C Ashley
- Department of Biochemistry, University of Saskatchewan, Saskatoon, Canada
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31
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Takaku H, Ushijima K, Ishibashi T, Tsukahara S, Takai K. Inhibition of Restriction Endonuclease Cleavage by Triplex Formation with Oligo-2'-O-methyl-ribonucleotides Containing 8-Oxo-2'-O-methyladenosine in Place of Cytidine. HETEROCYCLES 2000. [DOI: 10.3987/com-99-s38] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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32
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Shomer B, Yagil G. Long W tracts are over-represented in the Escherichia coli and Haemophilus influenzae genomes. Nucleic Acids Res 1999; 27:4491-500. [PMID: 10536160 PMCID: PMC148734 DOI: 10.1093/nar/27.22.4491] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The occurrence of DNA tracts of the three binary base combinations: R.Y, K.M and W;S has been mapped in the complete genomes of Haemophilus influenzae and Escherichia coli. A highly significant over-representation of W tracts is observed in both bacteria. The excess of W tracts is particularly striking in the 10% intercoding regions. Subdivision of intercoding regions into divergent (promoting), convergent (terminating) and sequential subregions shows that the excess of W tracts is most concentrated in the promoter regions. A particularly high excess of W tracts is observed in the first 200 bases 5' upstream of coding start sites. The data suggest that W tracts have a role in promoter function. A function as unwinding centers, analogous to the role of R.Y tracts in eukaryotes, is proposed. R.Y and K.M tracts are only modestly over-represented in the two bacteria.
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Affiliation(s)
- B Shomer
- The European Bioinformatics Institute, Hinxton, Cambridge, UK
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33
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Benazzouz A, Duprey P. The vimentin promoter as a tool to analyze the early events of retinoic acid-induced differentiation of cultured embryonal carcinoma cells. Differentiation 1999; 65:171-80. [PMID: 10631814 DOI: 10.1046/j.1432-0436.1999.6530171.x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The vimentin gene encodes an intermediate filament protein expressed in the parietal endoderm, mesodermal, and early neural cells in vivo but by most in vitro-cultured cells regardless of their embryonic origin. Here we show that the vimentin gene promoter is very active in F9 embryonal carcinoma cells and increases in activity during differentiation. Using a series of 5'-deletion mutants, we provide evidence that the regions of the promoter involved in F9 cell activity are different from those previously demonstrated to be active in differentiated cell lines. Furthermore, we show that in differentiating F9 cells the activities of two different regions of the promoter are significantly enhanced. A distal region (-1710/-957) appears to contain functional binding sites for the murine Hox-A5 homeoprotein as demonstrated by band shift and footprinting experiments. A proximal region (-140/-78) contains a 30-bp repetitive sequence found in other genes activated during differentiation of F9 cells. Using band shift assays and methylation interference, we present evidence that a sequence-specific single-stranded DNA-binding protein(s) specifically interacts with the minus strand of the 30-bp sequence.
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34
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Exploring the Structural Repertoire of Guanine-Rich DNA Sequences: Computer Modelling Studies. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s1380-7323(99)80083-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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35
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Abstract
The capacity of promoter DNA of two yeast genes to be unwound was studied. Both promoters, those of the CYC1 and DED1 genes, contain long oligopurine.oligopyrimidine (R.Y) tracts. The two promoters were cloned into negatively supercoiled plasmids, and their sensitivity to single-strand specific nuclease P1 was examined. Extensive P1 cleavage was located within the R.Y tracts, and cleavage sites were mapped. The extent of cleavage was only slightly dependent on P1 concentration, indicating a slow conversion of an intermediate form of DNA into the P1 reactive state. The cleavage required negative supercoiling and was suppressed by NaCl, MgCl2 and spermine. Two-dimensional topoisomer analysis showed that six superhelical turns were opened in the plasmids examined. The results indicate that at sufficient torsional stress, the R.Y tracts can intermittently undergo a transition into an unwound, ready-to-separate state. The oligopurine.oligopyrimidine tracts may thus serve as DNA unwinding centers in the gene promoters where they reside.
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Affiliation(s)
- G Yagil
- Department of Molecular Cell Biology, The Weizmann Institute of Science, Rehovot, Israel.
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36
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Van Raay TJ, Burn TC, Connors TD, Petry LR, Germino GG, Klinger KW, Landes GM. A 2.5 kb polypyrimidine tract in the PKD1 gene contains at least 23 H-DNA-forming sequences. MICROBIAL & COMPARATIVE GENOMICS 1998; 1:317-27. [PMID: 9689215 DOI: 10.1089/mcg.1996.1.317] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
A pyrimidine-rich element (PyRE), present in the 21st intron of the PKD1 gene, posed a significant obstacle in determining the primary structure of the gene. Only cycle sequencing of nested, single-stranded phage templates of the CT-rich strand enabled complete and accurate sequence data. Similar attempts on the GA-rich strand were unsuccessful. The resulting primary structure showed the 3 kb 21st intron to contain a 2.5 kb PyRE, whose sense-strand is 97% C + T. The PKD1 PyRE does not appear to be polymorphic based on RFLP analysis of DNA from 6 unrelated individuals digested with 9 different restriction enzymes. This is the largest pyrimidine tract sequenced to date, being over twice as large as those previously identified and shows little homology to other polypyrimidine tracts. Additional analysis of this PyRE revealed the presence of 23 mirror repeats with stem lengths of at least 10 nucleotides. The 23 H-DNA-forming sequences in the PKD1 PyRE exceed the cumulative total of 22 found in 157 human genes that have been completely sequenced. The mirror repeats confer this region of the PKD1 gene with a strong probability of forming H-DNA or triplex structures under appropriate conditions. Based on studies with PyRE found in other eukaryotic genes, the PKD1 PyRE may play a role in regulating PKD1 expression, and its potential for forming an extended triplex structure may explain some of the observed instability in the PKD1 locus.
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Affiliation(s)
- T J Van Raay
- Department of Human Genetics, Genzyme Genetics, Inc., Framingham, Massachusetts, USA
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37
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Bemark M, Olsson H, Heinegård D, Leanderson T. Purification and characterization of a protein binding to the SP6 kappa promoter. A potential role for CArG-box binding factor-A in kappa transcription. J Biol Chem 1998; 273:18881-90. [PMID: 9668064 DOI: 10.1074/jbc.273.30.18881] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
A protein interacting with an A-T-rich region that is a positive control element within the SP6 kappa promoter was purified and identified as CArG-box binding factor-A. The purified protein was shown to interact specifically with the coding strand of single-stranded DNA and, with lower affinity, with double-stranded DNA. A mutation that inhibited binding of the protein to the A-T-rich region also aborted the transcriptional stimulatory effect of the region. Two Ets proteins, PU.1 and elf-1, that have previously been shown to bind to an adjacent DNA element were shown to physically interact with CArG-box binding factor-A. An antiserum raised against the protein recognized two different forms indicating either that different splice-forms of CArG-box binding factor-A are expressed, or that the protein is subject to post-translational modification.
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Affiliation(s)
- M Bemark
- Immunology, Department of Cellular and Molecular Biology, Lund University, S-220 07 Lund, Sweden
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38
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Abstract
BACKGROUND During reepithelialization keratinocytes show increased expression of the integrin subunit alpha-v. We have investigated the promoter region of the alpha-v integrin subunit to learn more about its regulation. METHODS The promoter region of the human integrin alpha-v gene was cloned into a luciferase reporter vector. Deletional mutants were created using PCR. Computerized sequence analysis was performed using the Wisconsin Package. Gel-shift analysis was performed using keratinocyte nuclear extracts and oligonucleotides spanning th regions of interest. RESULTS Deletion from -522 bp to -235 resulted in no discernible effect on promoter activity. In contrast deletion of the next 22 bp, which included a putative ets binding site, reduced activity by approximately half. Further deletion to -139 bp essentially abolished promoter activity. Computer searching of this region of the integrin alpha-v promoter revealed two tandemly repeated motifs, TCCTCCTCC, that had previously been implicated in the function of the epidermal growth factor receptor (EGFR) promoter. Comparison of the alpha-v integrin promoter to the EGFR promoter revealed an area of high homology in this region. Gel-shift analysis revealed binding of a single-strand specific DNA binding protein to single stranded oligos comprising these motifs, but no binding of factors to the double- stranded oligo containing the ets binding site. CONCLUSIONS In keratinocytes alpha-v integrin expression is controlled by a region of the promoter with high homology to the epidermal growth factor receptor promoter This region binds single-strand specific DNA binding proteins that are likely to be important in controlling transcription.
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Affiliation(s)
- L T Kim
- Department of Surgery, University of Texas Southwestern Medical Center, Dallas, USA
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39
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Swamynathan SK, Nambiar A, Guntaka RV. Role of single-stranded DNA regions and Y-box proteins in transcriptional regulation of viral and cellular genes. FASEB J 1998; 12:515-22. [PMID: 9576478 DOI: 10.1096/fasebj.12.7.515] [Citation(s) in RCA: 81] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Single-stranded regions, known to be important for optimal rates of transcription, have been observed in the promoters of several cellular genes as well as in the promoters of many pathogenic viruses. Several host-encoded, single-stranded DNA binding proteins capable of binding these regions have been purified and their genes isolated. In this review, information available about single-stranded regions present within various promoters and the interaction of a novel class of single-stranded DNA binding transcription factors belonging to the Y-box family of proteins is reviewed. Mechanisms by which these proteins influence transcription of both cellular and viral genes are proposed.
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Affiliation(s)
- S K Swamynathan
- Department of Molecular Microbiology and Immunology, University of Missouri-Columbia, School of Medicine, 65212, USA
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40
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Abstract
A hallmark feature of mitosis is the extinction of bulk cellular transcription. The mechanism by which transcription is abrogated is likely linked to mitotic specific events such as chromosome condensation. Recent studies that probe the structure of genes that can be reactivated rapidly after mitotic repression (early G1) suggest that there are structural distortions in the promoter regions of these genes. These distortions are absent in genes that are typically repressed or reactivated in later phases of the cell cycle (late G1, S, or G2). Such changes in the chromatin structure of these genes may create a transient window for transcription factor binding and rapid reactivation of genes in subsequent phases of the cell cycle.
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Affiliation(s)
- S John
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park 16802-4500, USA
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Magdesian MH, da Silva AR, Ho PL, Furtado MF, Yamane T. Cloning and characterization of a repetitive 1.9 Kb HindIII DNA fragment from Crotalus durissus terrificus genome. Comp Biochem Physiol B Biochem Mol Biol 1997; 118:7-11. [PMID: 9417988 DOI: 10.1016/s0305-0491(97)00004-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Eukaryote genomes are endowed with varying quantities of repeated DNA families. These families show different patterns of conservation among species, copy numbers, chromosomal distribution, and transcription. Characterization of repeated DNA sequences could help to understand the genome anatomy and organization or be used in molecular systematics and molecular evolution studies. We describe here a repetitive DNA sequence of the HindIII family present in the genome of the rattlesnake Crotalus durissus terrificus. In Brazil, the family Crotalus is comprised only by one species durissus, which include several subspecies. The number and distribution of these subspecies are controversial. In the present study, the genomic DNA of a female rattlesnake was digested with HindIII resulting in a strong 1.9 Kb band. A partial genomic library was constructed from the 1.9 Kb DNAs rescued from the agarose gel after HindIII digestion and ligated to the vector pGEM3Zf(+) (Promega). Analysis of 69 clones, 44 hybridized with the 1.9 Kb probe isolated from one of the clones-clone 76, indicating that the DNA isolated from this clone should represent the 1.9 Kb HindIII fragment. This 1.9 Kb HindIII DNA was completely characterized by sequencing.
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Affiliation(s)
- M H Magdesian
- Centro de Biotecnologia, Instituto Butantan, São Paulo-SP, Brazil
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42
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Abstract
We have investigated mitochondrial DNA (mtDNA) mutagenesis in the laboratory mouse. Using a nested PCR method for quantification, the absolute frequency, tissue distribution and rate of increase of mitochondrial deletion mutations was determined. Multiple deletions arise in brain, cardiac muscle and kidney tissues: deletions occur most frequently at regions of directly repeated mtDNA homology. Deletion frequencies rose by 2.5 x 10(5), 6300- and 4000-fold in heart, brain and kidney, respectively, between young and old mice. The rates of mtDNA mutation accumulation in mouse and human hearts are modeled well by exponential equations, with r-values of 0.96 and 0.97, and mutations rose much faster in mouse than human mtDNA per unit time. Thus, maintenance of the human mitochondrial genome is much better than that of mice, consistent with the higher rate and final extent of total DNA repair in humans than mice, that has been observed by others and consistent with the predictions of the disposable soma model of aging. A comparison of mtDNA mutagenesis from cardiocytes vs. whole heart tissue was undertaken. Deletion mutations were observed to be 100-fold lower in DNA prepared from isolated cardiocytes than from whole heart homogenates, consistent with a model of uneven mtDNA mutation accumulation.
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Affiliation(s)
- E Wang
- Department of Molecular Biosciences, University of California, Davis 95616, USA
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43
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Ding Y, Osugi T, Kuo CH, Tanaka H, Do E, Irie Y, Miki N. Characterization of a nuclear factor that enhances DNA binding activity of SSCRE-BP/PUR alpha, a single-stranded DNA binding protein. Neurochem Int 1997; 31:45-54. [PMID: 9185164 DOI: 10.1016/s0197-0186(96)00127-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Pur alpha has been identified as a single-stranded DNA binding protein that specifically binds to the purine-rich strand present in the DNA replication initiation zone of the human c-myc gene. We have previously demonstrated that chronic morphine treatment decreases the DNA binding activity of ssCRE-BP (single-stranded cyclic AMP response element-binding protein), which has been shown to be identical to pur alpha by cDNA cloning, and is abundant in the brain. In this report we identified an activator of ssCRE-BP/pur alpha in the brain and characterized it. Although purified ssCRE-BP/pur alpha or its GST-fusion protein exhibited very low DNA binding activities, they were markedly enhanced by including nuclear extract in the binding assay. The enhanced binding activity is trypsin-sensitive, heat-stable and has a molecular weight of approximately 66 kDa. Casein could substitute for the activator and increased the DNA binding activity of ssCRE-BP/pur alpha by one order. A series of deletion mutants were prepared in order to determine the DNA binding and activator interacting domains, and both of them were found to reside in AA 50-215 of ssCRE-BP/pur alpha. These data suggest that the DNA binding activity of ssCRE-BP/pur alpha is augmented by a nuclear protein, which may modulate the ssCRE-BP/pur alpha activity to develop morphine dependence and tolerance.
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Affiliation(s)
- Y Ding
- Department of Pharmacology 1, Osaka University Medical School, Japan
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44
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Abstract
We address here the question of the in vivo structure of a natural alternating d(TA)n sequence found at the 3' region of the Saccharomyces cerevisiae FBP1 gene. This sequence consists of 13 TA pairs interrupted by a TT dinucleotide in the middle of the tract. Previous experiments with cruciform-specific nucleases S1 and Endonuclease VII demonstrated the presence in vitro of a cruciform in this region. We also showed this region to be part of a nuclease hypersensitive site flanked by nucleosomes in yeast chromatin. Here we demonstrate, by means of S1 in vivo footprinting, that in yeast plasmids also adopts in vivo a non B-DNA structure where is not a cruciform. A theoretical analysis of this region that it contains a site susceptible to superhelical stress duplex destabilization. The locations and conditions under which alternative structures form in the wild-type sequence and in deletion mutants agree with these theoretical predictions, suggesting that some kind of denaturation is the alternative structure adopted by the sequence in vivo. This suggests that negative superhelical stress sufficient for local denaturation exists in nucleosomal DNA. We also demonstrate by micrococcal nuclease digestions that the deletion of the alternating d(TA)n sequence modifies the chromatin hypersensitive site but does not affect nucleosome positioning.
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Affiliation(s)
- A Aranda
- Departamento de Bioquímica y Biología Molecular, Universitat de València and Instituto de Agroquímica y Tecnología de Alimentos, CSIC, Burjassot, Spain
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45
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Tsukahara S, Suzuki J, Ushijima K, Takai K, Takaku H. Nonenzymatic sequence-specific cleavage of duplex DNA via triple-helix formation by homopyrimidine phosphorothioate oligonucleotides. Bioorg Med Chem 1996; 4:2219-24. [PMID: 9022985 DOI: 10.1016/s0968-0896(96)00226-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Phenanthroline was attached covalently to the 5'-terminus of the unmodified and modified (3'-terminal phosphorothioate) oligonucleotide sequences, TTTTTTCTTCTCTTTCC (OP-17 mer) and TTTTTTTCTTCTCTTTCsC (OPRp-17 mer or OPSp-17 mer) via a phosphoramidite bond. Simian virus 40 DNA contains a single target site for these oligonucleotides. In the presence of copper ions, the efficient double-stranded cleavage at 37 degrees C and pH 7.0 was observed by agarose gel electrophoresis. The asymmetric distribution of the cleavage sites on the two strands revealed that the cleavage reaction took place in the minor groove, even though the linker was located in the major groove. Of particular interest are the 3'-terminal phosphorothioate oligonucleotide-phenanthroline derivatives (Rp or Sp), which were found to have cleavage activities of the same order as for the oligonucleotide phenanthroline (OP-17 mer). Furthermore, the OPSp-17 mer was intact after incubation in 10% fetal bovine serum for 24 h, whereas, the OPRp-17 mer was slightly more unstable than the OPSp-17 mer. However, the OP-17 mer was completely degraded. An increased resistance to nucleases has been observed by the introduction of phosphorothioate groups on the 3'-terminus of oligonucleotide-phenanthroline derivatives. This stabilization should help us to design much more efficient chemical recognition enzymes and antisense nucleic acid based anti-viral therapies, which could be used as tools in cellular biology.
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Affiliation(s)
- S Tsukahara
- Department of Industrial Chemistry, Chiba Institute of Technology, Japan
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46
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Xu G, Goodridge AG. Characterization of a polypyrimidine/polypurine tract in the promoter of the gene for chicken malic enzyme. J Biol Chem 1996; 271:16008-19. [PMID: 8663263 DOI: 10.1074/jbc.271.27.16008] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Starvation inhibits and refeeding stimulates transcription of the malic enzyme gene in chick liver. DNA between -320 and +72 base pairs (bp) is DNase I-hypersensitive in hepatic nuclei from fed but not starved chicks (Ma, X. J., and Goodridge, A. G. (1992) Nucleic Acids Res. 20, 4997-5002). A polypyrimidine/polypurine (PPY/PPU) tract lies within the DNase I-hypersensitive region. In hepatocytes transiently transfected with plasmids containing triiodothyronine response elements and a minimal promoter from the malic enzyme gene linked to the chloramphenicol acetyltransferase gene, deletion of the PPY/PPU tract inhibited chloramphenicol acetyltransferase activity by about 90% with or without triiodothyronine. Fine mapping of S1 nuclease-sensitive sites suggests that the PPY/PPU tract can assume different isoforms of non-B-DNA, some of which may be triplex structures. The PPY/PPU tract contains specific binding sites for single- and double-stranded DNA binding proteins and, with 8 bp 3' of the tract, can function as a promoter. A (CT)7 repeat binds single-stranded DNA-binding protein and is essential for promoter activity. Two C-rich elements bind single-stranded DNA-binding proteins and may mediate inhibition of promoter function. The single- and double-stranded DNA-binding proteins that interact with the PPY/PPU tract may regulate transcription of the malic enzyme gene.
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Affiliation(s)
- G Xu
- Department of Biochemistry, University of Iowa, Iowa City, Iowa 52240, USA
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47
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Abstract
Sequence specific regulators of eukaryotic gene expression, axiomatically, act through double stranded DNA targets. Proteins that recognize DNA cis-elements as single strands but for which compelling evidence has been lacking to indicate in vivo involvement in transcription are orphaned in this scheme. We sought to determine whether sequence specific single strand binding proteins can find their cognate elements and modify transcription in vivo by studying heterogeneous nuclear ribonucleoprotein K (hnRNP K), which binds the single stranded sequence (CCCTCCCCA; CT-element) of the human c-myc gene in vitro. To monitor its DNA binding in vivo, the ability of hnRNP K to activate a reporter gene was amplified by fusion with the VP16 transactivation domain. This chimeric protein was found to transactivate circular but not linear CT-element driven reporters, suggesting that hnRNP K recognizes a single strand region generated by negative supercoiling in circular plasmid. When CT-elements were engineered to overlap with lexA operators, addition of lexA protein, either in vivo or in vitro, abrogated hnRNP K binding most likely by preventing single strand formation. These results not only reveal hnRNP K to be a single strand DNA binding protein in vivo, but demonstrate how a segment of DNA may modify the transcriptional activity of an adjacent gene through the interconversion of duplex and single strands.
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Affiliation(s)
- T Tomonaga
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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48
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Potaman VN, Ussery DW, Sinden RR. Formation of a combined H-DNA/open TATA box structure in the promoter sequence of the human Na,K-ATPase alpha2 gene. J Biol Chem 1996; 271:13441-7. [PMID: 8662935 DOI: 10.1074/jbc.271.23.13441] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Structural variation of DNA within the promoter of the human Na, K-ATPase alpha2 gene, which contains a 35-base pair (bp) homopyrimidine.homopurine (Py.Pu) tract adjacent to a TATA box has been studied. The Py.Pu tract contains a 26-bp quasi-mirror repeat sequence with a potential for intramolecular triplex formation. As analyzed by two-dimensional agarose gel electrophoresis, a plasmid containing 151 bp of the promoter sequence including the 35-bp Py.Pu tract undergoes structural transitions under moderately acidic pH. Chemical probing with chloroacetaldehyde, dimethyl sulfate, and potassium permanganate is consistent with the formation of triplex DNA within the Py.Pu tract at native superhelical density as isolated from Escherichia coli. Chemical probing was used to determine a supercoil dependence for the formation of this combined unwound structure. At the superhelical density sufficient to locally unwind DNA, an H-y3 isomer of intermolecular triplex likely forms. However, at higher superhelical tension an H-y5 structure forms in the Py.Pu tract, and with increasing supercoiling the local DNA unwinding extends into the abutting TATA box. The H-y5/open TATA box combination structure might be favorable at higher superhelical densities since it relaxes more supercoils. The possible involvement of the H-y5/open TATA box structure in transcription is discussed.
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Affiliation(s)
- V N Potaman
- Institute of Biosciences and Technology, Texas A&M University, Houston, Texas 77030-3303, USA
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49
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Michelotti GA, Michelotti EF, Pullner A, Duncan RC, Eick D, Levens D. Multiple single-stranded cis elements are associated with activated chromatin of the human c-myc gene in vivo. Mol Cell Biol 1996; 16:2656-69. [PMID: 8649373 PMCID: PMC231256 DOI: 10.1128/mcb.16.6.2656] [Citation(s) in RCA: 176] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Transcription activation and repression of eukaryotic genes are associated with conformational and topological changes of the DNA and chromatin, altering the spectrum of proteins associated with an active gene. Segments of the human c-myc gene possessing non-B structure in vivo located with enzymatic and chemical probes. Sites hypertensive to cleavage with single-strand-specific S1 nuclease or the single-strand-selective agent potassium permanganate included the major promoters P1 and P2 as well as the far upstream sequence element (FUSE) and CT elements, which bind, respectively, the single-strand-specific factors FUSE-binding protein and heterogeneous nuclear ribonucleoprotein K in vitro. Active and inactive c-myc genes yielded different patterns of S1 nuclease and permanganate sensitivity, indicating alternative chromatin configurations of active and silent genes. The melting of specific cis elements of active c-myc genes in vivo suggested that transcriptionally associated torsional strain might assist strand separation and facilitate factor binding. Therefore, the interaction of FUSE-binding protein and heterogeneous nuclear ribonucleoprotein K with supercoiled DNA was studied. Remarkably, both proteins recognize their respective elements torsionally strained but not as liner duplexes. Single-strand- or supercoil-dependent gene regulatory proteins may directly link alterations in DNA conformation and topology with changes in gene expression.
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Affiliation(s)
- G A Michelotti
- Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland 20892, USA
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50
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Michelotti EF, Michelotti GA, Aronsohn AI, Levens D. Heterogeneous nuclear ribonucleoprotein K is a transcription factor. Mol Cell Biol 1996; 16:2350-60. [PMID: 8628302 PMCID: PMC231223 DOI: 10.1128/mcb.16.5.2350] [Citation(s) in RCA: 291] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The CT element is a positively acting homopyrimidine tract upstream of the c-myc gene to which the well-characterized transcription factor Spl and heterogeneous nuclear ribonucleoprotein (hnRNP) K, a less well-characterized protein associated with hnRNP complexes, have previously been shown to bind. The present work demonstrates that both of these molecules contribute to CT element-activated transcription in vitro. The pyrimidine-rich strand of the CT element both bound to hnRNP K and competitively inhibited transcription in vitro, suggesting a role for hnRNP K in activating transcription through this single-stranded sequence. Direct addition of recombinant hnRNP K to reaction mixtures programmed with templates bearing single-stranded CT elements increased specific RNA synthesis. If hnRNP K is a transcription factor, then interactions with the RNA polymerase II transcription apparatus are predicted. Affinity columns charged with recombinant hnRNP K specifically bind a component(s) necessary for transcription activation. The depleted factors were biochemically complemented by a crude TFIID phosphocellulose fraction, indicating that hnRNP K might interact with the TATA-binding protein (TBP)-TBP-associated factor complex. Coimmunoprecipitation of a complex formed in vivo between hnRNP K and epitope-tagged TBP as well as binding in vitro between recombinant proteins demonstrated a protein-protein interaction between TBP and hnRNP K. Furthermore, when the two proteins were overexpressed in vivo, transcription from a CT element-dependent reporter was synergistically activated. These data indicate that hnRNP K binds to a specific cis element, interacts with the RNA polymerase II transcription machinery, and stimulates transcription and thus has all of the properties of a transcription factor.
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Affiliation(s)
- E F Michelotti
- Laboratory of Pathology, National Cancer Institute, National Institute of Health, Bethesda, Maryland 20892, USA
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