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Smestad JA, Maher LJ. Relationships between putative G-quadruplex-forming sequences, RecQ helicases, and transcription. BMC MEDICAL GENETICS 2015; 16:91. [PMID: 26449372 PMCID: PMC4599794 DOI: 10.1186/s12881-015-0236-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 09/23/2015] [Indexed: 01/11/2023]
Abstract
Background Putative G-quadruplex-forming sequences (PQS) have long been implicated in regulation of transcription, though the actual mechanisms are not well understood. One proposed mechanism involves the activity of PQS-specific helicases belonging to the RecQ helicase family. However, patterns of PQS that correlate with transcriptional sensitivity to RecQ helicases are not well studied, and no adequate transcriptional model exists to account for PQS effects. Methods To better understand PQS transcriptional effects, we analyze PQS motifs in genes differentially-transcribed in Bloom Syndrome (BS) and Werner Syndrome (WS), two disorders resulting in loss of PQS-interacting RecQ helicases. We also correlate PQS genome-wide with transcription in multiple human cells lines while controlling for epigenetic status. Finally, we perform neural network clustering of PQS motifs to assess whether certain motifs are over-represented in genes sensitive to RecQ helicase loss. Results By analyzing PQS motifs in promoters of genes differentially-transcribed in BS and WS, we demonstrate that abundance of promoter PQS is generally higher in down-regulated genes and lower in up-regulated genes, and show that these effects are position-dependent. To interpret these correlations we determined genome-wide PQS correlations with transcription while controlling for epigenetic status. Our results identify multiple discrete transcription start site-proximal positions where PQS are correlated with either increased or decreased transcription. Finally, we report neural network clustering analysis of PQS motifs demonstrating that genes differentially-expressed in BS and WS are significantly biased in PQS motif composition. Conclusions Our findings unveil unappreciated detail in the relationship between PQS, RecQ helicases, and transcription. We show that promoter PQS are generally correlated with reduced gene expression, and that this effect is relieved by RecQ helicases. We also show that PQS at certain positions on the downstream sense strand are correlated with increased transcription. We therefore propose a new transcriptional model in which promoter PQS have at least two distinct types of transcriptional regulatory effects. Electronic supplementary material The online version of this article (doi:10.1186/s12881-015-0236-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- John A Smestad
- Mayo Clinic Medical Scientist Training Program, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN, 55905, USA.
| | - L James Maher
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 200 First St. SW, Rochester, MN, 55905, USA.
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52
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Liu JQ, Xiao S, Hao YH, Tan Z. Strand-Biased Formation of G-Quadruplexes in DNA Duplexes Transcribed with T7 RNA Polymerase. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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53
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G-quadruplex forming structural motifs in the genome of Deinococcus radiodurans and their regulatory roles in promoter functions. Appl Microbiol Biotechnol 2015. [PMID: 26201493 DOI: 10.1007/s00253-015-6808-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Deinococcus radiodurans displays compromised radioresistance in the presence of guanine quadruplex (G4)-binding drugs (G4 drugs). Genome-wide scanning showed islands of guanine runs (G-motif) in the upstream regions of coding sequences as well as in the structural regions of many genes, indicating a role for G4 DNA in the regulation of genome functions in this bacterium. G-motifs present upstream to some of the DNA damage-responsive genes like lexA, pprI, recF, recQ, mutL and radA were synthesized, and the formation of G4 DNA structures was probed in vitro. The G-motifs present at the 67th position upstream to recQ and at the 121st position upstream to mutL produced parallel and mixed G4 DNA structures, respectively. Expression of β-galactosidase under recQ and mutL promoters containing respective G-motifs was inhibited by G4 drugs under normal growth conditions in D. radiodurans. However, when such cells were exposed to γ radiation, mutL promoter activity was stimulated while recQ promoter activity was inhibited in the presence of G4 drugs. Deletion of the G-motif from the recQ promoter could relax it from G4 drug repression. D. radiodurans cells treated with G4 drug showed reduction in recQ expression and γ radiation resistance, indicating an involvement of G4 DNA in the radioresistance of this bacterium. These results suggest that G-motifs from D. radiodurans genome form different types of G4 DNA structures at least in vitro, and the recQ and mutL promoters seem to be differentially regulated at the levels of G4 DNA structures.
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54
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Liu JQ, Xiao S, Hao YH, Tan Z. Strand-Biased Formation of G-Quadruplexes in DNA Duplexes Transcribed with T7 RNA Polymerase. Angew Chem Int Ed Engl 2015; 54:8992-6. [PMID: 26074352 DOI: 10.1002/anie.201503648] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Indexed: 11/07/2022]
Abstract
G-quadruplex-forming sequences are enriched near transcription start sites (TSSs) in animal genes. They readily form G-quadruplexes in transcription, which in turn regulate transcription. Therefore, the control of G-quadruplex formation is important for their functionality. It is now shown that G-quadruplexes form efficiently on the non-template, but hardly on the template DNA strand in the downstream vicinity of TSSs in DNA duplexes when they are transcribed by the T7 RNA polymerase (RNAP). Structural analysis reveals that the T7 RNAP causes distortion in a DNA duplex both inside and in front of the enzyme. This structural distortion leads to strand-biased G-quadruplex formation when a G-quadruplex-forming sequence is partially fed into the T7 RNAP to a position about seven nucleotides away from the front of RNA synthesis. Based on these facts, we propose a model for the strand-biased formation of G-quadruplexes in transcribed DNA duplexes.
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Affiliation(s)
- Jia-quan Liu
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 (P. R. China)
| | - Shan Xiao
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 (P. R. China).,Key Laboratory of Zebrafish Modeling and Drug Screening for Human Diseases of Guangdong Higher Education Institutes, Department of Cell Biology, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515 (P. R. China)
| | - Yu-hua Hao
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 (P. R. China)
| | - Zheng Tan
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 (P. R. China).
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55
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Andorf CM, Kopylov M, Dobbs D, Koch KE, Stroupe ME, Lawrence CJ, Bass HW. G-Quadruplex (G4) Motifs in the Maize (Zea mays L.) Genome Are Enriched at Specific Locations in Thousands of Genes Coupled to Energy Status, Hypoxia, Low Sugar, and Nutrient Deprivation. J Genet Genomics 2014; 41:627-47. [DOI: 10.1016/j.jgg.2014.10.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 10/16/2014] [Accepted: 10/24/2014] [Indexed: 02/07/2023]
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56
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Targeting G-quadruplex nucleic acids with heterocyclic alkaloids and their derivatives. Eur J Med Chem 2014; 97:538-51. [PMID: 25466923 DOI: 10.1016/j.ejmech.2014.11.021] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 11/05/2014] [Accepted: 11/11/2014] [Indexed: 01/25/2023]
Abstract
G-Quadruplex nucleic acids or G-quadruplexes (G4s) are four-stranded DNA or RNA secondary structures that are formed in guanine-rich sequences. They are widely distributed in functional regions of the human genome, such as telomeres, ribosomal DNA (rDNA), transcription start sites, promoter regions and untranslated regions of mRNA, suggesting that G-quadruplex structures may play a pivotal role in the control of a variety of cellular processes. G-Quadruplexes are viewed as valid therapeutic targets in human cancer diseases. Small molecules, from naturally occurring to synthetic, are exploited to specifically target G-quadruplexes and have proven to be a new class of anticancer agents. Notably, alkaloids are an important source of G-quadruplex ligands and have significant bioactivities in anticancer therapy. In this review, the authors provide a brief, up-to-date summary of heterocyclic alkaloids and their derivatives targeting G-quadruplexes.
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57
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Ramamoorthy S, Garapati HS, Mishra RK. Length and sequence dependent accumulation of simple sequence repeats in vertebrates: Potential role in genome organization and regulation. Gene 2014; 551:167-75. [DOI: 10.1016/j.gene.2014.08.052] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Revised: 08/03/2014] [Accepted: 08/25/2014] [Indexed: 10/24/2022]
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58
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Du X, Gertz EM, Wojtowicz D, Zhabinskaya D, Levens D, Benham CJ, Schäffer AA, Przytycka TM. Potential non-B DNA regions in the human genome are associated with higher rates of nucleotide mutation and expression variation. Nucleic Acids Res 2014; 42:12367-79. [PMID: 25336616 PMCID: PMC4227770 DOI: 10.1093/nar/gku921] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
While individual non-B DNA structures have been shown to impact gene expression, their broad regulatory role remains elusive. We utilized genomic variants and expression quantitative trait loci (eQTL) data to analyze genome-wide variation propensities of potential non-B DNA regions and their relation to gene expression. Independent of genomic location, these regions were enriched in nucleotide variants. Our results are consistent with previously observed mutagenic properties of these regions and counter a previous study concluding that G-quadruplex regions have a reduced frequency of variants. While such mutagenicity might undermine functionality of these elements, we identified in potential non-B DNA regions a signature of negative selection. Yet, we found a depletion of eQTL-associated variants in potential non-B DNA regions, opposite to what might be expected from their proposed regulatory role. However, we also observed that genes downstream of potential non-B DNA regions showed higher expression variation between individuals. This coupling between mutagenicity and tolerance for expression variability of downstream genes may be a result of evolutionary adaptation, which allows reconciling mutagenicity of non-B DNA structures with their location in functionally important regions and their potential regulatory role.
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Affiliation(s)
- Xiangjun Du
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - E Michael Gertz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Damian Wojtowicz
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Dina Zhabinskaya
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David Levens
- UC Davis Genome Center, University of California Davis, Davis, CA 95616, USA
| | - Craig J Benham
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alejandro A Schäffer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Teresa M Przytycka
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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59
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Budhathoki JB, Ray S, Urban V, Janscak P, Yodh JG, Balci H. RecQ-core of BLM unfolds telomeric G-quadruplex in the absence of ATP. Nucleic Acids Res 2014; 42:11528-45. [PMID: 25245947 PMCID: PMC4191421 DOI: 10.1093/nar/gku856] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Various helicases and single-stranded DNA (ssDNA) binding proteins are known to destabilize G-quadruplex (GQ) structures, which otherwise result in genomic instability. Bulk biochemical studies have shown that Bloom helicase (BLM) unfolds both intermolecular and intramolecular GQ in the presence of ATP. Using single molecule FRET, we show that binding of RecQ-core of BLM (will be referred to as BLM) to ssDNA in the vicinity of an intramolecular GQ leads to destabilization and unfolding of the GQ in the absence of ATP. We show that the efficiency of BLM-mediated GQ unfolding correlates with the binding stability of BLM to ssDNA overhang, as modulated by the nucleotide state, ionic conditions, overhang length and overhang directionality. In particular, we observed enhanced GQ unfolding by BLM in the presence of non-hydrolysable ATP analogs, which has implications for the underlying mechanism. We also show that increasing GQ stability, via shorter loops or higher ionic strength, reduces BLM-mediated GQ unfolding. Finally, we show that while WRN has similar activity as BLM, RecQ and RECQ5 helicases do not unfold GQ in the absence of ATP at physiological ionic strength. In summary, our study points to a novel and potentially very common mechanism of GQ destabilization mediated by proteins binding to the vicinity of these structures.
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Affiliation(s)
| | - Sujay Ray
- Department of Physics, Kent State University, Kent, OH 44242, USA
| | - Vaclav Urban
- Institute of Molecular Genetics AS CR, Prague, Czech Republic
| | - Pavel Janscak
- Institute of Molecular Genetics AS CR, Prague, Czech Republic Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Jaya G Yodh
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Hamza Balci
- Department of Physics, Kent State University, Kent, OH 44242, USA
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60
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Ebert G, Steininger A, Weißmann R, Boldt V, Lind-Thomsen A, Grune J, Badelt S, Heßler M, Peiser M, Hitzler M, Jensen LR, Müller I, Hu H, Arndt PF, Kuss AW, Tebel K, Ullmann R. Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7. BMC Genomics 2014; 15:537. [PMID: 24973960 PMCID: PMC4092221 DOI: 10.1186/1471-2164-15-537] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 06/17/2014] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Segmental duplications (SDs) are not evenly distributed along chromosomes. The reasons for this biased susceptibility to SD insertion are poorly understood. Accumulation of SDs is associated with increased genomic instability, which can lead to structural variants and genomic disorders such as the Williams-Beuren syndrome. Despite these adverse effects, SDs have become fixed in the human genome. Focusing on chromosome 7, which is particularly rich in interstitial SDs, we have investigated the distribution of SDs in the context of evolution and the three dimensional organisation of the chromosome in order to gain insights into the mutual relationship of SDs and chromatin topology. RESULTS Intrachromosomal SDs preferentially accumulate in those segments of chromosome 7 that are homologous to marmoset chromosome 2. Although this formerly compact segment has been re-distributed to three different sites during primate evolution, we can show by means of public data on long distance chromatin interactions that these three intervals, and consequently the paralogous SDs mapping to them, have retained their spatial proximity in the nucleus. Focusing on SD clusters implicated in the aetiology of the Williams-Beuren syndrome locus we demonstrate by cross-species comparison that these SDs have inserted at the borders of a topological domain and that they flank regions with distinct DNA conformation. CONCLUSIONS Our study suggests a link of nuclear architecture and the propagation of SDs across chromosome 7, either by promoting regional SD insertion or by contributing to the establishment of higher order chromatin organisation themselves. The latter could compensate for the high risk of structural rearrangements and thus may have contributed to their evolutionary fixation in the human genome.
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Affiliation(s)
- Grit Ebert
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- />Department of Biology, Chemistry and Pharmacy, Free University Berlin, 14195 Berlin, Germany
| | - Anne Steininger
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- />Department of Biology, Chemistry and Pharmacy, Free University Berlin, 14195 Berlin, Germany
| | - Robert Weißmann
- />Department of Human Genetics, University Medicine Greifswald, and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Fleischmannstraße 42-44, 17475 Greifswald, Germany
| | - Vivien Boldt
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- />Department of Biology, Chemistry and Pharmacy, Free University Berlin, 14195 Berlin, Germany
| | - Allan Lind-Thomsen
- />Wilhelm Johannsen Centre for Functional Genome Research, Department of Cellular and Molecular Medicine, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Jana Grune
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Stefan Badelt
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
- />Institute for Theoretical Chemistry, University of Vienna, Waehringer Straße 17, A-1090 Vienna, Austria
| | - Melanie Heßler
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Matthias Peiser
- />Unit Experimental Research, Department of Product Safety, Federal Institute for Bundeswehr Institute of Radiobiology affiliated, the University of Ulm, Neuherbergstraße 11, 80937 Munich, Germany
| | - Manuel Hitzler
- />Unit Experimental Research, Department of Product Safety, Federal Institute for Bundeswehr Institute of Radiobiology affiliated, the University of Ulm, Neuherbergstraße 11, 80937 Munich, Germany
| | - Lars R Jensen
- />Department of Human Genetics, University Medicine Greifswald, and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Fleischmannstraße 42-44, 17475 Greifswald, Germany
| | - Ines Müller
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Hao Hu
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Peter F Arndt
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Andreas W Kuss
- />Department of Human Genetics, University Medicine Greifswald, and Interfaculty Institute of Genetics and Functional Genomics, University of Greifswald, Fleischmannstraße 42-44, 17475 Greifswald, Germany
| | - Katrin Tebel
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
| | - Reinhard Ullmann
- />Max Planck Institute for Molecular Genetics, Ihnestraße 63-73, 14195 Berlin, Germany
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61
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Agarwal T, Roy S, Kumar S, Chakraborty TK, Maiti S. In the Sense of Transcription Regulation by G-Quadruplexes: Asymmetric Effects in Sense and Antisense Strands. Biochemistry 2014; 53:3711-8. [DOI: 10.1021/bi401451q] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Tani Agarwal
- Proteomics and
Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India
| | - Saumya Roy
- CSIR-Indian Institute
of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500 007, India
| | - Santosh Kumar
- Proteomics and
Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India
| | - Tushar Kanti Chakraborty
- CSIR-Indian Institute
of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500 007, India
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Souvik Maiti
- Proteomics and
Structural Biology Unit, CSIR-Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India
- CSIR-National
Chemical Laboratory, Dr. Homi Bhabha
Road, Pune 411008, India
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62
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Chung WH. To peep into Pif1 helicase: multifaceted all the way from genome stability to repair-associated DNA synthesis. J Microbiol 2014; 52:89-98. [PMID: 24500472 DOI: 10.1007/s12275-014-3524-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 10/29/2013] [Indexed: 01/05/2023]
Abstract
Pif1 DNA helicase is the prototypical member of a 5' to 3' helicase superfamily conserved from bacteria to humans. In Saccharomyces cerevisiae, Pif1 and its homologue Rrm3, localize in both mitochondria and nucleus playing multiple roles in the maintenance of genomic homeostasis. They display relatively weak processivities in vitro, but have largely non-overlapping functions on common genomic loci such as mitochondrial DNA, telomeric ends, and many replication forks especially at hard-to-replicate regions including ribosomal DNA and G-quadruplex structures. Recently, emerging evidence shows that Pif1, but not Rrm3, has a significant new role in repair-associated DNA synthesis with Polδ during homologous recombination stimulating D-loop migration for conservative DNA replication. Comparative genetic and biochemical studies on the structure and function of Pif1 family helicases across different biological systems are further needed to elucidate both diversity and specificity of their mechanisms of action that contribute to genome stability.
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Affiliation(s)
- Woo-Hyun Chung
- College of Pharmacy, Duksung Women's University, Seoul, 132-714, Republic of Korea,
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63
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Zhang JY, Zheng KW, Xiao S, Hao YH, Tan Z. Mechanism and manipulation of DNA:RNA hybrid G-quadruplex formation in transcription of G-rich DNA. J Am Chem Soc 2014; 136:1381-90. [PMID: 24392825 DOI: 10.1021/ja4085572] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We recently reported that a DNA:RNA hybrid G-quadruplex (HQ) forms during transcription of DNA that bears two or more tandem guanine tracts (G-tract) on the nontemplate strand. Putative HQ-forming sequences are enriched in the nearby 1000 nt region right downstream of transcription start sites in the nontemplate strand of warm-blooded animals, and HQ regulates transcription under both in vitro and in vivo conditions. Therefore, knowledge of the mechanism of HQ formation is important for understanding the biological function of HQ as well as for manipulating gene expression by targeting HQ. In this work, we studied the mechanism of HQ formation using an in vitro T7 transcription model. We show that RNA synthesis initially produces an R-loop, a DNA:RNA heteroduplex formed by a nascent RNA transcript and the template DNA strand. In the following round of transcription, the RNA in the R-loop is displaced, releasing the RNA in single-stranded form (ssRNA). Then the G-tracts in the RNA can jointly form HQ with those in the nontemplate DNA strand. We demonstrate that the structural cascade R-loop → ssRNA → HQ offers opportunities to intercept HQ formation, which may provide a potential method to manipulate gene expression.
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Affiliation(s)
- Jia-yu Zhang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences , Beijing 100101, People's Republic of China
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64
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Sugimoto N. Noncanonical structures and their thermodynamics of DNA and RNA under molecular crowding: beyond the Watson-Crick double helix. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2014; 307:205-73. [PMID: 24380597 DOI: 10.1016/b978-0-12-800046-5.00008-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
How does molecular crowding affect the stability of nucleic acid structures inside cells? Water is the major solvent component in living cells, and the properties of water in the highly crowded media inside cells differ from that in buffered solution. As it is difficult to measure the thermodynamic behavior of nucleic acids in cells directly and quantitatively, we recently developed a cell-mimicking system using cosolutes as crowding reagents. The influences of molecular crowding on the structures and thermodynamics of various nucleic acid sequences have been reported. In this chapter, we discuss how the structures and thermodynamic properties of nucleic acids differ under various conditions such as highly crowded environments, compartment environments, and in the presence of ionic liquids, and the major determinants of the crowding effects on nucleic acids are discussed. The effects of molecular crowding on the activities of ribozymes and riboswitches on noncanonical structures of DNA- and RNA-like quadruplexes that play important roles in transcription and translation are also described.
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Affiliation(s)
- Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER) and Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, Japan.
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65
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Nakano SI, Miyoshi D, Sugimoto N. Effects of molecular crowding on the structures, interactions, and functions of nucleic acids. Chem Rev 2013; 114:2733-58. [PMID: 24364729 DOI: 10.1021/cr400113m] [Citation(s) in RCA: 369] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Shu-ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) and Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University , 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
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66
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Meier M, Patel TR, Booy EP, Marushchak O, Okun N, Deo S, Howard R, McEleney K, Harding SE, Stetefeld J, McKenna SA. Binding of G-quadruplexes to the N-terminal recognition domain of the RNA helicase associated with AU-rich element (RHAU). J Biol Chem 2013; 288:35014-27. [PMID: 24151078 PMCID: PMC3853254 DOI: 10.1074/jbc.m113.512970] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Revised: 10/16/2013] [Indexed: 12/31/2022] Open
Abstract
Polynucleotides containing consecutive tracts of guanines can adopt an intramolecular G-quadruplex structure where multiple planar tetrads of hydrogen-bound guanines stack on top of each other. Remodeling of G-quadruplexes impacts numerous aspects of nucleotide biology including transcriptional and translational control. RNA helicase associated with AU-rich element (RHAU), a member of the ATP-dependent DEX(H/D) family of RNA helicases, has been established as a major cellular quadruplex resolvase. RHAU contains a core helicase domain responsible for ATP binding/hydrolysis/helicase activity and is flanked on either side by N- and C-terminal extensions. The N-terminal extension is required for quadruplex recognition, and we have previously demonstrated complex formation between this domain and a quadruplex from human telomerase RNA. Here we used an integrated approach that includes small angle x-ray scattering, nuclear magnetic resonance spectroscopy, circular dichroism, and dynamic light scattering methods to demonstrate the recognition of G-quadruplexes by the N-terminal domain of RHAU. Based on our results, we conclude that (i) quadruplex from the human telomerase RNA and its DNA analog both adopt a disc shape in solution, (ii) RHAU53-105 adopts a defined and extended conformation in solution, and (iii) the N-terminal domain mediates an interaction with a guanine tetrad face of quadruplexes. Together, these data form the foundation for understanding the recognition of quadruplexes by the N-terminal domain of RHAU.
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Affiliation(s)
| | | | | | | | | | | | | | - Kevin McEleney
- Manitoba Institute for Materials, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada and
| | - Stephen E. Harding
- National Centre for Macromolecular Hydrodynamics Laboratory, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom
| | - Jörg Stetefeld
- From the Departments of Chemistry and
- Biochemistry and Medical Genetics and
| | - Sean A. McKenna
- From the Departments of Chemistry and
- Biochemistry and Medical Genetics and
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67
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Takahashi S, Sugimoto N. Effect of Pressure on the Stability of G-Quadruplex DNA: Thermodynamics under Crowding Conditions. Angew Chem Int Ed Engl 2013; 52:13774-8. [DOI: 10.1002/anie.201307714] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Indexed: 12/11/2022]
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68
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Effect of Pressure on the Stability of G-Quadruplex DNA: Thermodynamics under Crowding Conditions. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201307714] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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69
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Wilson T, Costa PJ, Félix V, Williamson MP, Thomas JA. Structural studies on dinuclear ruthenium(II) complexes that bind diastereoselectively to an antiparallel folded human telomere sequence. J Med Chem 2013; 56:8674-83. [PMID: 24088028 PMCID: PMC3835060 DOI: 10.1021/jm401119b] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
![]()
We report DNA binding studies of
the dinuclear ruthenium ligand
[{Ru(phen)2}2tpphz]4+ in enantiomerically
pure forms. As expected from previous studies of related complexes,
both isomers bind with similar affinity to B-DNA and have enhanced
luminescence. However, when tested against the G-quadruplex from human
telomeres (which we show to form an antiparallel basket structure
with a diagonal loop across one end), the ΛΛ isomer binds
approximately 40 times more tightly than the ΔΔ, with
a stronger luminescence. NMR studies show that the complex binds at
both ends of the quadruplex. Modeling studies, based on experimentally
derived restraints obtained for the closely related [{Ru(bipy)2}2tpphz]4+, show that the ΛΛ
isomer fits neatly under the diagonal loop, whereas the ΔΔ
isomer is unable to bind here and binds at the lateral loop end. Molecular
dynamics simulations show that the ΔΔ isomer is prevented
from binding under the diagonal loop by the rigidity of the loop.
We thus present a novel enantioselective binding substrate for antiparallel
basket G-quadruplexes, with features that make it a useful tool for
quadruplex studies.
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Affiliation(s)
- Tom Wilson
- Department of Chemistry, University of Sheffield , Dainton Building, Brook Hill, Sheffield S3 7HF, U.K
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70
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Xiao S, Zhang JY, Zheng KW, Hao YH, Tan Z. Bioinformatic analysis reveals an evolutional selection for DNA:RNA hybrid G-quadruplex structures as putative transcription regulatory elements in warm-blooded animals. Nucleic Acids Res 2013; 41:10379-90. [PMID: 23999096 PMCID: PMC3905843 DOI: 10.1093/nar/gkt781] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Recently, we reported the co-transcriptional formation of DNA:RNA hybrid G-quadruplex (HQ) structure by the non-template DNA strand and nascent RNA transcript, which in turn modulates transcription under both in vitro and in vivo conditions. Here we present bioinformatic analysis on putative HQ-forming sequences (PHQS) in the genomes of eukaryotic organisms. Starting from amphibian, PHQS motifs are concentrated in the immediate 1000-nt region downstream of transcription start sites, implying their potential role in transcription regulation. Moreover, their occurrence shows a strong bias toward the non-template versus the template strand. PHQS has become constitutional in genes in warm-blooded animals, and the magnitude of the strand bias correlates with the ability of PHQS to form HQ, suggesting a selection based on HQ formation. This strand bias is reversed in lower species, implying that the selection of PHQS/HQ depended on the living temperature of the organisms. In comparison with the putative intramolecular G-quadruplex-forming sequences (PQS), PHQS motifs are far more prevalent and abundant in the transcribed regions, making them the dominant candidates in the formation of G-quadruplexes in transcription. Collectively, these results suggest that the HQ structures are evolutionally selected to function in transcription and other transcription-mediated processes that involve guanine-rich non-template strand.
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Affiliation(s)
- Shan Xiao
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P. R. China
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71
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Zhang C, Liu HH, Zheng KW, Hao YH, Tan Z. DNA G-quadruplex formation in response to remote downstream transcription activity: long-range sensing and signal transducing in DNA double helix. Nucleic Acids Res 2013; 41:7144-52. [PMID: 23716646 PMCID: PMC3737545 DOI: 10.1093/nar/gkt443] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
G-quadruplexes, four-stranded structures formed by Guanine-rich nucleic acids, are implicated in many physiological and pathological processes. G-quadruplex-forming sequences are abundant in genomic DNA, and G-quadruplexes have recently been shown to exist in the genome of mammalian cells. However, how G-quadruplexes are formed in the genomes remains largely unclear. Here, we show that G-quadruplex formation can be remotely induced by downstream transcription events that are thousands of base pairs away. The induced G-quadruplexes alter protein recognition and cause transcription termination at the local region. These results suggest that a G-quadruplex-forming sequence can serve as a sensor or receiver to sense remote DNA tracking activity in response to the propagation of mechanical torsion in a DNA double helix. We propose that the G-quadruplex formation may provide a mean for long-range sensing and communication between distal genomic locations to coordinate regulatory transactions in genomic DNA.
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Affiliation(s)
- Chao Zhang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China
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72
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Kouzine F, Wojtowicz D, Yamane A, Resch W, Kieffer-Kwon KR, Bandle R, Nelson S, Nakahashi H, Awasthi P, Feigenbaum L, Menoni H, Hoeijmakers J, Vermeulen W, Ge H, Przytycka TM, Levens D, Casellas R. Global regulation of promoter melting in naive lymphocytes. Cell 2013; 153:988-99. [PMID: 23706737 PMCID: PMC3684982 DOI: 10.1016/j.cell.2013.04.033] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 01/31/2013] [Accepted: 04/04/2013] [Indexed: 11/25/2022]
Abstract
Lymphocyte activation is initiated by a global increase in messenger RNA synthesis. However, the mechanisms driving transcriptome amplification during the immune response are unknown. By monitoring single-stranded DNA genome wide, we show that the genome of naive cells is poised for rapid activation. In G0, ∼90% of promoters from genes to be expressed in cycling lymphocytes are polymerase loaded but unmelted and support only basal transcription. Furthermore, the transition from abortive to productive elongation is kinetically limiting, causing polymerases to accumulate nearer to transcription start sites. Resting lymphocytes also limit the expression of the transcription factor IIH complex, including XPB and XPD helicases involved in promoter melting and open complex extension. To date, two rate-limiting steps have been shown to control global gene expression in eukaryotes: preinitiation complex assembly and polymerase pausing. Our studies identify promoter melting as a third key regulatory step and propose that this mechanism ensures a prompt lymphocyte response to invading pathogens.
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Affiliation(s)
- Fedor Kouzine
- Laboratory of Pathology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Damian Wojtowicz
- National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA
- Institute of Informatics, University of Warsaw, 02-098 Warsaw, Poland
| | - Arito Yamane
- Genomics & Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wolfgang Resch
- Genomics & Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | | | - Russell Bandle
- Laboratory of Pathology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steevenson Nelson
- Genomics & Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hirotaka Nakahashi
- Genomics & Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
| | - Parirokh Awasthi
- Science Applications International Corporation, NCI, Frederick, MD 21702, USA
| | - Lionel Feigenbaum
- Science Applications International Corporation, NCI, Frederick, MD 21702, USA
| | - Herve Menoni
- Department of Genetics, Biomedical Science, Erasmus Medical Center, 3015 GE Rotterdam, Netherlands
| | - Jan Hoeijmakers
- Department of Genetics, Biomedical Science, Erasmus Medical Center, 3015 GE Rotterdam, Netherlands
| | - Wim Vermeulen
- Department of Genetics, Biomedical Science, Erasmus Medical Center, 3015 GE Rotterdam, Netherlands
| | - Hui Ge
- Ascentgene, Inc., Rockville, MD 20850, USA
| | - Teresa M. Przytycka
- National Center for Biotechnology Information, NLM, National Institutes of Health, Bethesda, MD 20894, USA
| | - David Levens
- Laboratory of Pathology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Rafael Casellas
- Genomics & Immunity, NIAMS, National Institutes of Health, Bethesda, MD 20892, USA
- Center of Cancer Research, NCI, National Institutes of Health, Bethesda, MD 20892, USA
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73
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Du X, Wojtowicz D, Bowers AA, Levens D, Benham CJ, Przytycka TM. The genome-wide distribution of non-B DNA motifs is shaped by operon structure and suggests the transcriptional importance of non-B DNA structures in Escherichia coli. Nucleic Acids Res 2013; 41:5965-77. [PMID: 23620297 PMCID: PMC3695496 DOI: 10.1093/nar/gkt308] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Although the right-handed double helical B-form DNA is most common under physiological conditions, DNA is dynamic and can adopt a number of alternative structures, such as the four-stranded G-quadruplex, left-handed Z-DNA, cruciform and others. Active transcription necessitates strand separation and can induce such non-canonical forms at susceptible genomic sequences. Therefore, it has been speculated that these non-B DNA motifs can play regulatory roles in gene transcription. Such conjecture has been supported in higher eukaryotes by direct studies of several individual genes, as well as a number of large-scale analyses. However, the role of non-B DNA structures in many lower organisms, in particular proteobacteria, remains poorly understood and incompletely documented. In this study, we performed the first comprehensive study of the occurrence of B DNA-non-B DNA transition-susceptible sites (non-B DNA motifs) within the context of the operon structure of the Escherichia coli genome. We compared the distributions of non-B DNA motifs in the regulatory regions of operons with those from internal regions. We found an enrichment of some non-B DNA motifs in regulatory regions, and we show that this enrichment cannot be simply explained by base composition bias in these regions. We also showed that the distribution of several non-B DNA motifs within intergenic regions separating divergently oriented operons differs from the distribution found between convergent ones. In particular, we found a strong enrichment of cruciforms in the termination region of operons; this enrichment was observed for operons with Rho-dependent, as well as Rho-independent terminators. Finally, a preference for some non-B DNA motifs was observed near transcription factor-binding sites. Overall, the conspicuous enrichment of transition-susceptible sites in these specific regulatory regions suggests that non-B DNA structures may have roles in the transcriptional regulation of specific operons within the E. coli genome.
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Affiliation(s)
- Xiangjun Du
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health 8600 Rockville Pike, Bethesda, MD 20894, USA
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74
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Mukundan VT, Phan AT. Bulges in G-Quadruplexes: Broadening the Definition of G-Quadruplex-Forming Sequences. J Am Chem Soc 2013; 135:5017-28. [DOI: 10.1021/ja310251r] [Citation(s) in RCA: 213] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | - Anh Tuân Phan
- School of
Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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75
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Sawaya S, Bagshaw A, Buschiazzo E, Kumar P, Chowdhury S, Black MA, Gemmell N. Microsatellite tandem repeats are abundant in human promoters and are associated with regulatory elements. PLoS One 2013; 8:e54710. [PMID: 23405090 PMCID: PMC3566118 DOI: 10.1371/journal.pone.0054710] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2012] [Accepted: 12/18/2012] [Indexed: 12/13/2022] Open
Abstract
Tandem repeats are genomic elements that are prone to changes in repeat number and are thus often polymorphic. These sequences are found at a high density at the start of human genes, in the gene’s promoter. Increasing empirical evidence suggests that length variation in these tandem repeats can affect gene regulation. One class of tandem repeats, known as microsatellites, rapidly alter in repeat number. Some of the genetic variation induced by microsatellites is known to result in phenotypic variation. Recently, our group developed a novel method for measuring the evolutionary conservation of microsatellites, and with it we discovered that human microsatellites near transcription start sites are often highly conserved. In this study, we examined the properties of microsatellites found in promoters. We found a high density of microsatellites at the start of genes. We showed that microsatellites are statistically associated with promoters using a wavelet analysis, which allowed us to test for associations on multiple scales and to control for other promoter related elements. Because promoter microsatellites tend to be G/C rich, we hypothesized that G/C rich regulatory elements may drive the association between microsatellites and promoters. Our results indicate that CpG islands, G-quadruplexes (G4) and untranslated regulatory regions have highly significant associations with microsatellites, but controlling for these elements in the analysis does not remove the association between microsatellites and promoters. Due to their intrinsic lability and their overlap with predicted functional elements, these results suggest that many promoter microsatellites have the potential to affect human phenotypes by generating mutations in regulatory elements, which may ultimately result in disease. We discuss the potential functions of human promoter microsatellites in this context.
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Affiliation(s)
- Sterling Sawaya
- Centre for Reproduction and Genomics, Department of Anatomy, and Allan Wilson Centre for Molecular Ecology and Evolution, University of Otago, Dunedin, New Zealand.
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76
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Zhou W, Suntharalingam K, Brand NJ, Barton PJR, Vilar R, Ying L. Possible regulatory roles of promoter g-quadruplexes in cardiac function-related genes - human TnIc as a model. PLoS One 2013; 8:e53137. [PMID: 23326389 PMCID: PMC3541360 DOI: 10.1371/journal.pone.0053137] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2012] [Accepted: 11/23/2012] [Indexed: 12/15/2022] Open
Abstract
G-quadruplexes (G4s) are four-stranded DNA secondary structures, which are involved in a diverse range of biological processes. Although the anti-cancer potential of G4s in oncogene promoters has been thoroughly investigated, the functions of promoter G4s in non-cancer-related genes are not well understood. We have explored the possible regulatory roles of promoter G4s in cardiac function-related genes using both computational and a wide range of experimental approaches. According to our bioinformatics results, it was found that potential G4-forming sequences are particularly enriched in the transcription regulatory regions (TRRs) of cardiac function-related genes. Subsequently, the promoter of human cardiac troponin I (TnIc) was chosen as a model, and G4s found in this region were subjected to biophysical characterisations. The chromosome 19 specific minisatellite G4 sequence (MNSG4) and near transcription start site (TSS) G4 sequence (−80 G4) adopt anti-parallel and parallel structures respectively in 100 mM KCl, with stabilities comparable to those of oncogene G4s. It was also found that TnIc G4s act cooperatively as enhancers in gene expression regulation in HEK293 cells, when stabilised by a synthetic G4-binding ligand. This study provides the first evidence of the biological significance of promoter G4s in cardiac function-related genes. The feasibility of using a single ligand to target multiple G4s in a particular gene has also been discussed.
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Affiliation(s)
- Wenhua Zhou
- Molecular Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | | | - Nigel J. Brand
- Harefield Heart Science Centre, National Heart and Lung Institute, Imperial College London, Middlesex, United Kingdom
| | - Paul J. R. Barton
- Harefield Heart Science Centre, National Heart and Lung Institute, Imperial College London, Middlesex, United Kingdom
- NIHR Cardiovascular Biomedical Research Unit, Royal Brompton and Harefield NHS Trust, London, United Kingdom
| | - Ramon Vilar
- Department of Chemistry, Imperial College London, London, United Kingdom
| | - Liming Ying
- Molecular Medicine, National Heart and Lung Institute, Imperial College London, London, United Kingdom
- * E-mail:
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77
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Beaume N, Pathak R, Yadav VK, Kota S, Misra HS, Gautam HK, Chowdhury S. Genome-wide study predicts promoter-G4 DNA motifs regulate selective functions in bacteria: radioresistance of D. radiodurans involves G4 DNA-mediated regulation. Nucleic Acids Res 2012; 41:76-89. [PMID: 23161683 PMCID: PMC3592403 DOI: 10.1093/nar/gks1071] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
A remarkable number of guanine-rich sequences with potential to adopt non-canonical secondary structures called G-quadruplexes (or G4 DNA) are found within gene promoters. Despite growing interest, regulatory role of quadruplex DNA motifs in intrinsic cellular function remains poorly understood. Herein, we asked whether occurrence of potential G4 (PG4) DNA in promoters is associated with specific function(s) in bacteria. Using a normalized promoter-PG4-content (PG4P) index we analysed >60 000 promoters in 19 well-annotated species for (a) function class(es) and (b) gene(s) with enriched PG4P. Unexpectedly, PG4-associated functional classes were organism specific, suggesting that PG4 motifs may impart specific function to organisms. As a case study, we analysed radioresistance. Interestingly, unsupervised clustering using PG4P of 21 genes, crucial for radioresistance, grouped three radioresistant microorganisms including Deinococcus radiodurans. Based on these predictions we tested and found that in presence of nanomolar amounts of the intracellular quadruplex-binding ligand N-methyl mesoporphyrin (NMM), radioresistance of D. radiodurans was attenuated by ∼60%. In addition, important components of the RecF recombinational repair pathway recA, recF, recO, recR and recQ genes were found to harbour promoter-PG4 motifs and were also down-regulated in presence of NMM. Together these results provide first evidence that radioresistance may involve G4 DNA-mediated regulation and support the rationale that promoter-PG4s influence selective functions.
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Affiliation(s)
- Nicolas Beaume
- GNR Knowledge Centre for Genome Informatics, Division of Comparative Genomics, Institute of Genomics and Integrative Biology, CSIR, Mall Road, Delhi 110 007, India
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78
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Takahashi H, Nakagawa A, Kojima S, Takahashi A, Cha BY, Woo JT, Nagai K, Machida Y, Machida C. Discovery of novel rules for G-quadruplex-forming sequences in plants by using bioinformatics methods. J Biosci Bioeng 2012; 114:570-5. [PMID: 22721688 DOI: 10.1016/j.jbiosc.2012.05.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Revised: 05/23/2012] [Accepted: 05/23/2012] [Indexed: 12/11/2022]
Abstract
The G-quadruplex is one of the most frequently studied secondary DNA structures and consists of 4 guanine residues that interact through Watson-Crick and Hoogsteen pairing. The G-quadruplex formation is thought to be a molecular switch for gene expression. Genome-wide analyses of G-quadruplexes have been published for many species; however, only one genome-wide analysis of G-quadruplexes in plants has been reported. Here, we propose a new approach involving a two-step procedure for identifying G-quadruplex-forming sequences (potential G4 DNA motif regions: G4MRs) and classifying positional relationships between G4MRs and genes. By using this approach, we exhaustively searched for G4MRs in the whole genomes of 8 species: Arabidopsis thaliana, Oryza sativa subsp. japonica, Populus trichocarpa, Vitis vinifera, Homo sapiens, Danio rerio, Drosophila melanogaster, and Caenorhabditis elegans. We classified genes on the basis of their positional relationships to their proximal G4MRs. We identified novel rules for G4MRs in plants, such as G4MR-enrichment in the template strands at transcription start sites (TSSs). Next, we focused on the template strands of TSSs and conducted gene ontology (GO) analysis of genes proximal to G4MRs. We identified GO terms such as chloroplast and nucleosome (or histone) in O. sativa. Although these terms were strongly associated in O. sativa, weak associations were identified in other plants. These results will be helpful for elucidating the functional roles of G4 DNA.
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Affiliation(s)
- Hiro Takahashi
- Plant Biology Research Center, Chubu University, Matsumoto-cho 1200, Kasugai, Aichi 487-8501, Japan.
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79
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Qureshi MH, Ray S, Sewell AL, Basu S, Balci H. Replication protein A unfolds G-quadruplex structures with varying degrees of efficiency. J Phys Chem B 2012; 116:5588-94. [PMID: 22500657 DOI: 10.1021/jp300546u] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Replication protein A (RPA) is known to interact with guanine- (G-) rich sequences that adopt G-quadruplex (GQ) structures. Most studies reported in the literature were performed on GQ formed by homogeneous sequences, such as the human telomeric repeat, and RPA's ability to unfold GQ structures of differing stability is not known. We compared the thermal stability of three potential GQ-forming DNA sequences (PQSs) to their stability against RPA-mediated unfolding using single-molecule fluorescence resonance energy transfer (FRET) and bulk biophysical and biochemical experiments. One of these sequences is the human telomeric repeat and the other two, located in the promoter region of tyrosine hydroxylase gene, are highly heterogeneous sequences that better represent PQSs in the genome. The three GQ constructs have thermal stabilities that differ significantly. Our measurements showed that the most thermally stable structure (Tm = 86 °C) was also the most stable against RPA-mediated unfolding, although the least thermally stable structure (Tm = 69 °C) had at least an order-of-magnitude higher stability against RPA-mediated unfolding than the structure with intermediate thermal stability (Tm = 78 °C). The significance of this observation becomes more evident when considered within the context of the cellular environment where protein-DNA interactions can be an important determinant of GQ viability. Considering these results, we conclude that thermal stability is not necessarily an adequate criterion for predicting the physiological viability of GQ structures. Finally, we measured the time it takes for an RPA molecule to unfold a GQ from a fully folded to a fully unfolded conformation using a single-molecule stopped-flow method. All three GQ structures were unfolded within Δt ≈ 0.30 ± 0.10 s, a surprising result considering that the unfolding time does not correlate with thermal stability or stability against RPA-mediated unfolding. These results suggest that the limiting step in G-quadruplex unfolding by RPA is simply the accessibility of the structure to the RPA protein.
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Affiliation(s)
- Mohammad H Qureshi
- Department of Physics, †Department of Biological Sciences, and ∥Department of Chemistry and Biochemistry, Kent State University , Kent, Ohio 44242, United States
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80
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81
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Halder R, Riou JF, Teulade-Fichou MP, Frickey T, Hartig JS. Bisquinolinium compounds induce quadruplex-specific transcriptome changes in HeLa S3 cell lines. BMC Res Notes 2012; 5:138. [PMID: 22414013 PMCID: PMC3375199 DOI: 10.1186/1756-0500-5-138] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2011] [Accepted: 03/13/2012] [Indexed: 05/02/2023] Open
Abstract
Background Guanosine rich sequences capable of forming G-quadruplex (G4) motifs are enriched near the gene transcription start site (TSS) in the human genome. When probed at the single gene level, G-quadruplex motifs residing in promoter regions show substantial effects on gene transcription. Moreover, further changes in transcription levels are noticed when G4-motifs are targeted with G-quadruplex-specific small molecules. Results Global studies concerning general changes of the transcriptome via targeting promoter-based G-quadruplex motifs are very limited and have so far only been carried out with compounds displaying weak selectivity for quadruplex sequences. Here we utilize two G-quadruplex-specific bisquinolinium derivatives PhenDC3 and 360A and investigate their effects on the expression of the HeLa S3 transcriptome. Our results show wide-spread changes in the transcriptome with specificity for genes with G-quadruplex motifs near their transcription start sites (TSS). Using real-time PCR we further confirmed the specificity of PhenDC3 and 360A as potent molecules to target G-quadruplex-regulated genes. Conclusions Specific effects on quadruplex-containing genes have been observed utilizing whole-transcriptome analysis upon treatment of cultured cells with quadruplex-selective bisquinolinium compounds.
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Affiliation(s)
- Rashi Halder
- Department of Chemistry and Konstanz Research School Chemical Biology (KoRS-CB), University of Konstanz, Universitätsstraße 10, Konstanz, Germany
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82
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Bugaut A, Balasubramanian S. 5'-UTR RNA G-quadruplexes: translation regulation and targeting. Nucleic Acids Res 2012; 40:4727-41. [PMID: 22351747 PMCID: PMC3367173 DOI: 10.1093/nar/gks068] [Citation(s) in RCA: 469] [Impact Index Per Article: 39.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
RNA structures in the untranslated regions (UTRs) of mRNAs influence post-transcriptional regulation of gene expression. Much of the knowledge in this area depends on canonical double-stranded RNA elements. There has been considerable recent advancement of our understanding of guanine(G)-rich nucleic acids sequences that form four-stranded structures, called G-quadruplexes. While much of the research has been focused on DNA G-quadruplexes, there has recently been a rapid emergence of interest in RNA G-quadruplexes, particularly in the 5′-UTRs of mRNAs. Collectively, these studies suggest that RNA G-quadruplexes exist in the 5′-UTRs of many genes, including genes of clinical interest, and that such structural elements can influence translation. This review features the progresses in the study of 5′-UTR RNA G-quadruplex-mediated translational control. It covers computational analysis, cell-free, cell-based and chemical biology studies that have sought to elucidate the roles of RNA G-quadruplexes in both cap-dependent and -independent regulation of mRNA translation. We also discuss protein trans-acting factors that have been implicated and the evidence that such RNA motifs have potential as small molecule target. Finally, we close the review with a perspective on the future challenges in the field of 5′-UTR RNA G-quadruplex-mediated translation regulation.
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Affiliation(s)
- Anthony Bugaut
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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83
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Jain AK, Bhattacharya S. Interaction of G-Quadruplexes with Nonintercalating Duplex-DNA Minor Groove Binding Ligands. Bioconjug Chem 2011; 22:2355-68. [DOI: 10.1021/bc200268a] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Akash K. Jain
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Santanu Bhattacharya
- Department
of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India
- Chemical Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 012, India
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84
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Loop residues of thrombin-binding DNA aptamer impact G-quadruplex stability and thrombin binding. Biochimie 2011; 93:1231-8. [DOI: 10.1016/j.biochi.2011.03.013] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Accepted: 03/31/2011] [Indexed: 01/02/2023]
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85
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Rangannan V, Bansal M. PromBase: a web resource for various genomic features and predicted promoters in prokaryotic genomes. BMC Res Notes 2011; 4:257. [PMID: 21781326 PMCID: PMC3160392 DOI: 10.1186/1756-0500-4-257] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2011] [Accepted: 07/22/2011] [Indexed: 12/19/2022] Open
Abstract
Background As more and more genomes are being sequenced, an overview of their genomic features and annotation of their functional elements, which control the expression of each gene or transcription unit of the genome, is a fundamental challenge in genomics and bioinformatics. Findings Relative stability of DNA sequence has been used to predict promoter regions in 913 microbial genomic sequences with GC-content ranging from 16.6% to 74.9%. Irrespective of the genome GC-content the relative stability based promoter prediction method has already been proven to be robust in terms of recall and precision. The predicted promoter regions for the 913 microbial genomes have been accumulated in a database called PromBase. Promoter search can be carried out in PromBase either by specifying the gene name or the genomic position. Each predicted promoter region has been assigned to a reliability class (low, medium, high, very high and highest) based on the difference between its average free energy and the downstream region. The recall and precision values for each class are shown graphically in PromBase. In addition, PromBase provides detailed information about base composition, CDS and CG/TA skews for each genome and various DNA sequence dependent structural properties (average free energy, curvature and bendability) in the vicinity of all annotated translation start sites (TLS). Conclusion PromBase is a database, which contains predicted promoter regions and detailed analysis of various genomic features for 913 microbial genomes. PromBase can serve as a valuable resource for comparative genomics study and help the experimentalist to rapidly access detailed information on various genomic features and putative promoter regions in any given genome. This database is freely accessible for academic and non- academic users via the worldwide web http://nucleix.mbu.iisc.ernet.in/prombase/.
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Affiliation(s)
- Vetriselvi Rangannan
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore-560 012, India.
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86
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Abstract
G-quadruplexes are four-stranded DNA structures that are over-represented in gene promoter regions and are viewed as emerging therapeutic targets in oncology, as transcriptional repression of oncogenes through stabilization of these structures could be a novel anticancer strategy. Many gene promoter G-quadruplexes have physicochemical properties and structural characteristics that might make them druggable, and their structural diversity suggests that a high degree of selectivity might be possible. Here, we describe the evidence for G-quadruplexes in gene promoters and discuss their potential as therapeutic targets, as well as progress in the development of strategies to harness this potential through intervention with small-molecule ligands.
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87
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Abstract
Opposed to DNA quadruplex sequences, RNA quadruplexes are still less well characterized. On the other hand, RNA quadruplexes are found to be at least as stable as their DNA counterparts. They show the same dependence on metal ions but seem to be much more restricted with respect to the adopted conformations. Other than DNA, which is mostly found to be double-stranded inside cells, RNAs are produced during transcription without its complementary sequence. The absence of a second strand that is able to hybridize and form a duplex makes the folding of RNA quadruplexes a likely event of intramolecular structure formation. Consequently, the formation of RNA quadruplexes in cellular RNAs has recently been suggested and the study of their influence and potential roles in cellular processes has just started. Here we give an overview of the RNA quadruplex field, summarizing issues such as structures, stabilities, and anticipated roles of these interesting four-stranded, guanosine-rich sequences.
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Affiliation(s)
- Kangkan Halder
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, D-78457 Konstanz, Germany
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88
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Zheng KW, Zhang D, Zhang LX, Hao YH, Zhou X, Tan Z. Dissecting the strand folding orientation and formation of G-quadruplexes in single- and double-stranded nucleic acids by ligand-induced photocleavage footprinting. J Am Chem Soc 2011; 133:1475-83. [PMID: 21207997 DOI: 10.1021/ja108972e] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The widespread of G-quadruplex-forming sequences in genomic DNA and their role in regulating gene expression has made G-quadruplex structures attractive therapeutic targets against a variety of diseases, such as cancer. Information on the structure of G-quadruplexes is crucial for understanding their physiological roles and designing effective drugs against them. Resolving the structures of G-quadruplexes, however, remains a challenge especially for those in double-stranded DNA. In this work, we developed a photocleavage footprinting technique to determine the folding orientation of each individual G-tract in intramolecular G-quadruplex formed in both single- and double-stranded nucleic acids. Based on the differential photocleavage induced by a ligand tetrakis(2-trimethylaminoethylethanol) phthalocyaninato zinc tetraiodine (Zn-TTAPc) to the guanines between the two terminal G-quartets in a G-quadruplex, this method identifies the guanines hosted in each terminal G-quartets to reveal G-tract orientation. The method is extremely intuitive, straightforward, and requires little expertise. Besides, it also detects G-quadruplex formation in long single- and double-stranded nucleic acids.
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Affiliation(s)
- Ke-wei Zheng
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, People's Republic of China
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89
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Abstract
Guanine-rich DNA, which is widely distributed in the human genome, can fold into a supramolecular structure called the G-wire. The G-wire possesses promising characteristics as a functional element for various applications in vitro and in vivo. Here, we describe the preparative procedures for the G-wire and signatures of G-wire formation. Procedures for the regulation of G-wire formation by chemical stimuli will be useful for in vivo and in vitro applications.
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Affiliation(s)
- Daisuke Miyoshi
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), and Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan
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90
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EuPathDomains: the divergent domain database for eukaryotic pathogens. INFECTION GENETICS AND EVOLUTION 2010; 11:698-707. [PMID: 20920608 DOI: 10.1016/j.meegid.2010.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2010] [Revised: 09/17/2010] [Accepted: 09/19/2010] [Indexed: 11/22/2022]
Abstract
Eukaryotic pathogens (e.g. Plasmodium, Leishmania, Trypanosomes, etc.) are a major source of morbidity and mortality worldwide. In Africa, one of the most impacted continents, they cause millions of deaths and constitute an immense economic burden. While the genome sequence of several of these organisms is now available, the biological functions of more than half of their proteins are still unknown. This is a serious issue for bringing to the foreground the expected new therapeutic targets. In this context, the identification of protein domains is a key step to improve the functional annotation of the proteins. However, several domains are missed in eukaryotic pathogens because of the high phylogenetic distance of these organisms from the classical eukaryote models. We recently proposed a method, co-occurrence domain detection (CODD), that improves the sensitivity of Pfam domain detection by exploiting the tendency of domains to appear preferentially with a few other favorite domains in a protein. In this paper, we present EuPathDomains (http://www.atgc-montpellier.fr/EuPathDomains/), an extended database of protein domains belonging to ten major eukaryotic human pathogens. EuPathDomains gathers known and new domains detected by CODD, along with the associated confidence measurements and the GO annotations that can be deduced from the new domains. This database significantly extends the Pfam domain coverage of all selected genomes, by proposing new occurrences of domains as well as new domain families that have never been reported before. For example, with a false discovery rate lower than 20%, EuPathDomains increases the number of detected domains by 13% in Toxoplasma gondii genome and up to 28% in Cryptospordium parvum, and the total number of domain families by 10% in Plasmodium falciparum and up to 16% in C. parvum genome. The database can be queried by protein names, domain identifiers, Pfam or Interpro identifiers, or organisms, and should become a valuable resource to decipher the protein functions of eukaryotic pathogens.
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91
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Wang Q, Ma L, Hao YH, Tan Z. Folding equilibrium constants of telomere G-quadruplexes in free state or associated with proteins determined by isothermal differential hybridization. Anal Chem 2010; 82:9469-75. [PMID: 21028832 DOI: 10.1021/ac102168m] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Guanine rich (G-rich) nucleic acids form G-quadruplex structures that are implicated in many biological processes, pharmaceutical applications, and molecular machinery. The folding equilibrium constant (K(F)) of the G-quadruplex not only determines its stability and competition against duplex formation in genomic DNA but also defines its recognition by proteins and drugs and technical specifications. The K(F) is most conveniently derived from thermal melting analysis that has so far yielded extremely diversified results for the human telomere G-quadruplex. Melting analysis cannot be used for nucleic acids associated with proteins, thus has difficulty to study how protein association affects the folding equilibrium of G-quadruplex structure. In this work, we established an isothermal differential hybridization (IDH) method that is able to determine the K(F) of G-quadruplex, either alone or associated with proteins. Using this method, we studied the folding equilibrium of the core sequence G(3)(T(2)AG(3))(3) from vertebrate telomere in K(+) and Na(+) solutions and how it is affected by proteins associated at its adjacent regions. Our results show that the K(F) obtained for the free G-quadruplex is within 1 order of magnitude of most of those obtained by melting analysis and protein binding beside a G-quadruplex can dramatically destabilize the G-quadruplex.
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Affiliation(s)
- Quan Wang
- State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, PR China
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92
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Rangannan V, Bansal M. High-quality annotation of promoter regions for 913 bacterial genomes. ACTA ACUST UNITED AC 2010; 26:3043-50. [PMID: 20956245 DOI: 10.1093/bioinformatics/btq577] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
MOTIVATION The number of bacterial genomes being sequenced is increasing very rapidly and hence, it is crucial to have procedures for rapid and reliable annotation of their functional elements such as promoter regions, which control the expression of each gene or each transcription unit of the genome. The present work addresses this requirement and presents a generic method applicable across organisms. RESULTS Relative stability of the DNA double helical sequences has been used to discriminate promoter regions from non-promoter regions. Based on the difference in stability between neighboring regions, an algorithm has been implemented to predict promoter regions on a large scale over 913 microbial genome sequences. The average free energy values for the promoter regions as well as their downstream regions are found to differ, depending on their GC content. Threshold values to identify promoter regions have been derived using sequences flanking a subset of translation start sites from all microbial genomes and then used to predict promoters over the complete genome sequences. An average recall value of 72% (which indicates the percentage of protein and RNA coding genes with predicted promoter regions assigned to them) and precision of 56% is achieved over the 913 microbial genome dataset. AVAILABILITY The binary executable for 'PromPredict' algorithm (implemented in PERL and supported on Linux and MS Windows) and the predicted promoter data for all 913 microbial genomes are available at http://nucleix.mbu.iisc.ernet.in/prombase/.
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93
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Jain A, Bacolla A, Chakraborty P, Grosse F, Vasquez KM. Human DHX9 helicase unwinds triple-helical DNA structures. Biochemistry 2010; 49:6992-9. [PMID: 20669935 DOI: 10.1021/bi100795m] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Naturally occurring poly(purine.pyrimidine) rich regions in the human genome are prone to adopting non-canonical DNA structures such as intramolecular triplexes (i.e., H-DNA). Such structure-forming sequences are abundant and can regulate the expression of several disease-linked genes. In addition, the use of triplex-forming oligonucleotides (TFOs) to modulate gene structure and function has potential as an approach to targeted gene therapy. Previously, we found that endogenous H-DNA structures can induce DNA double-strand breaks and promote genomic rearrangements. Herein, we find that the DHX9 helicase co-immunoprecipitates with triplex DNA structures in mammalian cells, suggesting a role in the maintenance of genome stability. We tested this postulate by assessing the helicase activity of purified human DHX9 on various duplex and triplex DNA substrates in vitro. DHX9 displaced the third strand from a specific triplex DNA structure and catalyzed the unwinding with a 3' --> 5' polarity with respect to the displaced third strand. Helicase activity required a 3'-single-stranded overhang on the third strand and was dependent on ATP hydrolysis. The reaction kinetics consisted of a pre-steady-state burst phase followed by a linear, steady-state pseudo-zero-order reaction. In contrast, very little if any helicase activity was detected on blunt triplexes, triplexes with 5'-overhangs, blunt duplexes, duplexes with overhangs, or forked duplex substrates. Thus, triplex structures containing a 3'-overhang represent preferred substrates for DHX9, where it removes the strand with Hoogsteen hydrogen-bonded bases. Our results suggest the involvement of DHX9 in maintaining genome integrity by unwinding mutagenic triplex DNA structures.
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Affiliation(s)
- Aklank Jain
- Department of Carcinogenesis, Science Park-Research Division, The University of Texas M. D. Anderson Cancer Center, Smithville, Texas 78957, USA
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94
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Human Pif1 helicase is a G-quadruplex DNA-binding protein with G-quadruplex DNA-unwinding activity. Biochem J 2010; 430:119-28. [PMID: 20524933 DOI: 10.1042/bj20100612] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Pif1 proteins are helicases that in yeast are implicated in the maintenance of genome stability. One activity of Saccharomyces cerevisiae Pif1 is to stabilize DNA sequences that could otherwise form deleterious G4 (G-quadruplex) structures by acting as a G4 resolvase. The present study shows that human Pif1 (hPif1, nuclear form) is a G4 DNA-binding and resolvase protein and that these activities are properties of the conserved helicase domain (amino acids 206-620 of 641, hPifHD). hPif1 preferentially bound synthetic G4 DNA relative to ssDNA (single-stranded DNA), dsDNA (double-stranded DNA) and a partially single-stranded duplex DNA helicase substrate. G4 DNA unwinding, but not binding, required an extended (>10 nucleotide) 5' ssDNA tail, and in competition assays, G4 DNA was an ineffective suppressor of helicase activity compared with ssDNA. These results suggest a distinction between the determinants of G4 DNA binding and the ssDNA interactions required for helicase action and that hPif1 may act on G4 substrates by binding alone or as a resolvase. Human Pif1 could therefore have a role in processing G4 structures that arise in the single-stranded nucleic acid intermediates formed during DNA replication and gene expression.
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95
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Ghosh S, Majumder P, Pradhan SK, Dasgupta D. Mechanism of interaction of small transcription inhibitors with DNA in the context of chromatin and telomere. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:795-809. [PMID: 20638489 DOI: 10.1016/j.bbagrm.2010.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 06/23/2010] [Accepted: 06/30/2010] [Indexed: 01/13/2023]
Abstract
Small molecules from natural and synthetic sources have long been employed as human drugs. The transcription inhibitory potential of one class of these molecules has paved their use as anticancer drugs. The principal mode of action of these molecules is via reversible interaction with genomic DNA, double and multiple stranded. In this article we have revisited the mechanism of the interaction in the context of chromatin and telomere. The established modes of association of these molecules with double helical DNA provide a preliminary mechanism of their transcription inhibitory potential, but the scenario assumes a different dimension when the genomic DNA is associated with proteins in the transcription apparatus of both prokaryotic and eukaryotic organisms. We have discussed this altered scenario as a prelude to understand the chemical biology of their action in the cell. For the telomeric quadruplex DNA, we have reviewed the mechanism of their association with the quadruplex and resultant cellular consequence.
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Affiliation(s)
- Saptaparni Ghosh
- Biophysics Division, Saha Institute of Nuclear Physics, Sector-I, Block-AF, Bidhan Nagar, Kolkata Pin, 700064, India
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96
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Cellular nucleic-acid-binding protein, a transcriptional enhancer of c-Myc, promotes the formation of parallel G-quadruplexes. Biochem J 2010; 428:491-8. [DOI: 10.1042/bj20100038] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
G-rich sequences that contain stretches of tandem guanines can form four-stranded, intramolecular stable DNA structures called G-quadruplexes (termed G4s). Regulation of the equilibrium between single-stranded and G4 DNA in promoter regions is essential for control of gene expression in the cell. G4s are highly stable structures; however, their folding kinetics are slow under physiological conditions. CNBP (cellular nucleic-acid-binding protein) is a nucleic acid chaperone that binds the G4-forming G-rich sequence located within the NHE (nuclease hypersensitivity element) III of the c-Myc proto-oncogene promoter. Several reports have demonstrated that CNBP enhances the transcription of c-Myc in vitro and in vivo; however, none of these reports have assessed the molecular mechanisms responsible for this control. In the present study, by means of Taq polymerase stop assays, electrophoretic mobility-shift assays and CD spectroscopy, we show that CNBP promotes the formation of parallel G4s to the detriment of anti-parallel G4s, and its nucleic acid chaperone activity is required for this effect. These findings are the first to implicate CNBP as a G4-folding modulator and, furthermore, assign CNBP a novel mode-of-action during c-Myc transcriptional regulation.
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97
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Zhao J, Bacolla A, Wang G, Vasquez KM. Non-B DNA structure-induced genetic instability and evolution. Cell Mol Life Sci 2010; 67:43-62. [PMID: 19727556 PMCID: PMC3017512 DOI: 10.1007/s00018-009-0131-2] [Citation(s) in RCA: 310] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2009] [Revised: 07/22/2009] [Accepted: 08/11/2009] [Indexed: 11/26/2022]
Abstract
Repetitive DNA motifs are abundant in the genomes of various species and have the capacity to adopt non-canonical (i.e., non-B) DNA structures. Several non-B DNA structures, including cruciforms, slipped structures, triplexes, G-quadruplexes, and Z-DNA, have been shown to cause mutations, such as deletions, expansions, and translocations in both prokaryotes and eukaryotes. Their distributions in genomes are not random and often co-localize with sites of chromosomal breakage associated with genetic diseases. Current genome-wide sequence analyses suggest that the genomic instabilities induced by non-B DNA structure-forming sequences not only result in predisposition to disease, but also contribute to rapid evolutionary changes, particularly in genes associated with development and regulatory functions. In this review, we describe the occurrence of non-B DNA-forming sequences in various species, the classes of genes enriched in non-B DNA-forming sequences, and recent mechanistic studies on DNA structure-induced genomic instability to highlight their importance in genomes.
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Affiliation(s)
- Junhua Zhao
- Department of Carcinogenesis, Science Park-Research Division, The University of Texas M.D. Anderson Cancer Center, 1808 Park Road 1-C, P.O. Box 389, Smithville, TX 78957 USA
| | - Albino Bacolla
- Department of Carcinogenesis, Science Park-Research Division, The University of Texas M.D. Anderson Cancer Center, 1808 Park Road 1-C, P.O. Box 389, Smithville, TX 78957 USA
| | - Guliang Wang
- Department of Carcinogenesis, Science Park-Research Division, The University of Texas M.D. Anderson Cancer Center, 1808 Park Road 1-C, P.O. Box 389, Smithville, TX 78957 USA
| | - Karen M. Vasquez
- Department of Carcinogenesis, Science Park-Research Division, The University of Texas M.D. Anderson Cancer Center, 1808 Park Road 1-C, P.O. Box 389, Smithville, TX 78957 USA
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98
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Balkwill GD, Derecka K, Garner TP, Hodgman C, Flint APF, Searle MS. Repression of translation of human estrogen receptor alpha by G-quadruplex formation. Biochemistry 2009; 48:11487-95. [PMID: 19860473 DOI: 10.1021/bi901420k] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Tissue-specific expression of the human estrogen receptor alpha gene (ESR1) is achieved through multiple promoter sequences resulting in various mRNA transcripts encoding a common protein but differing in their 5'-untranslated region (5'-UTR). Many cancers are estrogen-sensitive with neoplastic growth stimulated through the estrogen receptor, a transcription factor that regulates developmental genes. We demonstrate that the human ESR1 gene is rich in potential quadruplex-forming sequences with 3 of 20 identified within exonic regions. In particular, we show using CD, UV, and NMR spectroscopy that a stable DNA G-quadruplex motif is formed within the exon C gene sequence. This motif, which PCR shows is transcribed in normal and neoplastic endometrium and in MCF-7 cells, forms a stable RNA quadruplex demonstrable by CD and UV analysis. Cloning the exon C G-quadruplex sequence upstream of a luciferase reporter gene caused a 6-fold reduction of enzymatic activity compared to a mutant sequence. We conclude that the exon C G-quadruplex motif is present in the 5'-UTR of the mRNA transcript, where it modulates the efficiency of translation.
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Affiliation(s)
- Graham D Balkwill
- Centre for Biomolecular Sciences, School of Chemistry, University of Nottingham, University Park, Nottingham NG7 2RD, UK
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99
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Jenjaroenpun P, Kuznetsov VA. TTS mapping: integrative WEB tool for analysis of triplex formation target DNA sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome. BMC Genomics 2009; 10 Suppl 3:S9. [PMID: 19958507 PMCID: PMC2788396 DOI: 10.1186/1471-2164-10-s3-s9] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background DNA triplexes can naturally occur, co-localize and interact with many other regulatory DNA elements (e.g. G-quadruplex (G4) DNA motifs), specific DNA-binding proteins (e.g. transcription factors (TFs)), and micro-RNA (miRNA) precursors. Specific genome localizations of triplex target DNA sites (TTSs) may cause abnormalities in a double-helix DNA structure and can be directly involved in some human diseases. However, genome localization of specific TTSs, their interconnection with regulatory DNA elements and physiological roles in a cell are poor defined. Therefore, it is important to identify comprehensive and reliable catalogue of specific potential TTSs (pTTSs) and their co-localization patterns with other regulatory DNA elements in the human genome. Results "TTS mapping" database is a web-based search engine developed here, which is aimed to find and annotate pTTSs within a region of interest of the human genome. The engine provides descriptive statistics of pTTSs in a given region and its sequence context. Different annotation tracks of TTS-overlapping gene region(s), G4 motifs, CpG Island, miRNA precursors, miRNA targets, transcription factor binding sites (TFBSs), Single Nucleotide Polymorphisms (SNPs), small nucleolar RNAs (snoRNA), and repeat elements are also mapped based onto a sequence location provided by UCSC genome browser, G4 database http://www.quadruplex.org and several other datasets. The results pages provide links to UCSC genome browser annotation tracks and relative DBs. BLASTN program was included to check the uniqueness of a given pTTS in the human genome. Recombination- and mutation-prone genes (e.g. EVI-1, MYC) were found to be significantly enriched by TTSs and multiple co-occurring with our regulatory DNA elements. TTS mapping reveals that a high-complementary and evolutionarily conserved polypurine and polypyrimidine DNA sequence pair linked by a non-conserved short DNA sequence can form miR-483 transcribed from intron 2 of IGF2 gene and bound double-strand nucleic acid TTSs forming natural triplex structures. Conclusion TTS mapping provides comprehensive visual and analytical tools to help users to find pTTSs, G-quadruplets and other regulatory DNA elements in various genome regions. TTS Mapping not only provides sequence visualization and statistical information, but also integrates knowledge about co-localization TTS with various DNA elements and facilitates that data analysis. In particular, TTS Mapping reveals complex structural-functional regulatory module of gene IGF2 including TF MZF1 binding site and ncRNA precursor mir-483 formed by the high-complementary and evolutionarily conserved polypurine- and polypyrimidine-rich DNA pair. Such ncRNAs capable of forming helical triplex structures with a polypurine strand of a nucleic acid duplexes (DNA or RNA) via Hoogsteen or reverse Hoogsteen hydrogen bonds. Our web tool could be used to discover biologically meaningful genome modules and to optimize experimental design of anti-gene treatment.
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Affiliation(s)
- Piroon Jenjaroenpun
- Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, 30 Biopolis str #07-01, Singapore.
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100
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Abstract
The protocol presented here allows for the investigation of the formation of unusual nucleic acid structures in the 5'-untranslated region (UTR) of bacteria by correlating gene expression levels to the in vitro stability of the respective structure. In particular, we describe the introduction of G-quadruplex forming sequences close to the ribosome-binding site (RBS) on the mRNA of a reporter gene and the subsequent read-out of the expression levels. Insertion of a stable secondary structure results in the cloaking of RBS and eventually reduced gene expression levels. The structures and stability of the introduced sequences are further characterized by circular dichroism (CD) spectroscopy and thermal melting experiments. The extent of inhibition is then correlated to the stability of the respective quadruplex structure, allowing judgement of whether factors other than thermodynamic stability affect the formation of a given quadruplex sequence in vivo. Measuring gene expression levels takes 2 d including cloning; CD experiments take 5 hours per experiment.
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