151
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Pabis K. Triplex and other DNA motifs show motif-specific associations with mitochondrial DNA deletions and species lifespan. Mech Ageing Dev 2021; 194:111429. [PMID: 33422563 DOI: 10.1016/j.mad.2021.111429] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 01/02/2021] [Accepted: 01/03/2021] [Indexed: 11/20/2022]
Abstract
The "theory of resistant biomolecules" posits that long-lived species show resistance to molecular damage at the level of their biomolecules. Here, we test this hypothesis in the context of mitochondrial DNA (mtDNA) as it implies that predicted mutagenic DNA motifs should be inversely correlated with species maximum lifespan (MLS). First, we confirmed that guanine-quadruplex and direct repeat (DR) motifs are mutagenic, as they associate with mtDNA deletions in the human major arc of mtDNA, while also adding mirror repeat (MR) and intramolecular triplex motifs to a growing list of potentially mutagenic features. What is more, triplex motifs showed disease-specific associations with deletions and an apparent interaction with guanine-quadruplex motifs. Surprisingly, even though DR, MR and guanine-quadruplex motifs were associated with mtDNA deletions, their correlation with MLS was explained by the biased base composition of mtDNA. Only triplex motifs negatively correlated with MLS even after adjusting for body mass, phylogeny, mtDNA base composition and effective number of codons. Taken together, our work highlights the importance of base composition for the comparative biogerontology of mtDNA and suggests that future research on mitochondrial triplex motifs is warranted.
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Affiliation(s)
- Kamil Pabis
- Georg August University of Göttingen, Göttingen, Germany.
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152
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Kotsantis P, Segura-Bayona S, Margalef P, Marzec P, Ruis P, Hewitt G, Bellelli R, Patel H, Goldstone R, Poetsch AR, Boulton SJ. RTEL1 Regulates G4/R-Loops to Avert Replication-Transcription Collisions. Cell Rep 2020; 33:108546. [PMID: 33357438 PMCID: PMC7773548 DOI: 10.1016/j.celrep.2020.108546] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/29/2020] [Accepted: 12/01/2020] [Indexed: 11/21/2022] Open
Abstract
Regulator of telomere length 1 (RTEL1) is an essential helicase that maintains telomere integrity and facilitates DNA replication. The source of replication stress in Rtel1-deficient cells remains unclear. Here, we report that loss of RTEL1 confers extensive transcriptional changes independent of its roles at telomeres. The majority of affected genes in Rtel1-/- cells possess G-quadruplex (G4)-DNA-forming sequences in their promoters and are similarly altered at a transcriptional level in wild-type cells treated with the G4-DNA stabilizer TMPyP4 (5,10,15,20-Tetrakis-(N-methyl-4-pyridyl)porphine). Failure to resolve G4-DNAs formed in the displaced strand of RNA-DNA hybrids in Rtel1-/- cells is suggested by increased R-loops and elevated transcription-replication collisions (TRCs). Moreover, removal of R-loops by RNaseH1 overexpression suppresses TRCs and alleviates the global replication defects observed in Rtel1-/- and Rtel1PIP_box knockin cells and in wild-type cells treated with TMPyP4. We propose that RTEL1 unwinds G4-DNA/R-loops to avert TRCs, which is important to prevent global deregulation in both transcription and DNA replication.
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Affiliation(s)
| | | | - Pol Margalef
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Paulina Marzec
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Phil Ruis
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Graeme Hewitt
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Harshil Patel
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | | | - Anna R Poetsch
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK; UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK
| | - Simon J Boulton
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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153
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Miglietta G, Russo M, Capranico G. G-quadruplex-R-loop interactions and the mechanism of anticancer G-quadruplex binders. Nucleic Acids Res 2020; 48:11942-11957. [PMID: 33137181 PMCID: PMC7708042 DOI: 10.1093/nar/gkaa944] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 10/05/2020] [Accepted: 10/08/2020] [Indexed: 12/17/2022] Open
Abstract
Genomic DNA and cellular RNAs can form a variety of non-B secondary structures, including G-quadruplex (G4) and R-loops. G4s are constituted by stacked guanine tetrads held together by Hoogsteen hydrogen bonds and can form at key regulatory sites of eukaryote genomes and transcripts, including gene promoters, untranslated exon regions and telomeres. R-loops are 3-stranded structures wherein the two strands of a DNA duplex are melted and one of them is annealed to an RNA. Specific G4 binders are intensively investigated to discover new effective anticancer drugs based on a common rationale, i.e.: the selective inhibition of oncogene expression or specific impairment of telomere maintenance. However, despite the high number of known G4 binders, such a selective molecular activity has not been fully established and several published data point to a different mode of action. We will review published data that address the close structural interplay between G4s and R-loops in vitro and in vivo, and how these interactions can have functional consequences in relation to G4 binder activity. We propose that R-loops can play a previously-underestimated role in G4 binder action, in relation to DNA damage induction, telomere maintenance, genome and epigenome instability and alterations of gene expression programs.
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Affiliation(s)
- Giulia Miglietta
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Marco Russo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126 Bologna, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, via Selmi 3, 40126 Bologna, Italy
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154
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Lim G, Hohng S. Single-molecule fluorescence studies on cotranscriptional G-quadruplex formation coupled with R-loop formation. Nucleic Acids Res 2020; 48:9195-9203. [PMID: 32810236 PMCID: PMC7498336 DOI: 10.1093/nar/gkaa695] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/07/2020] [Accepted: 08/11/2020] [Indexed: 01/13/2023] Open
Abstract
G-quadruplex (GQ) is formed at various regions of DNA, including telomeres of chromosomes and regulatory regions of oncogenes. Since GQ is important in both gene regulation and genome instability, the biological and medical implications of this abnormal DNA structure have been intensively studied. Its formation mechanisms, however, are not clearly understood yet. We report single-molecule fluorescence experiments to monitor the cotranscriptional GQ formation coupled with R-loop formation using T7 RNA polymerase. The GQ is formed very rarely per single-round transcription. R-loop formation precedes and facilitates GQ formation. Once formed, some GQs are extremely stable, resistant even to RNase H treatment, and accumulate in multiple-round transcription conditions. On the other hand, GQ existing in the non-template strand promotes the R-loop formation in the next rounds of transcription. Our study clearly shows the existence of a positive feedback mechanism of GQ and R-loop formations, which may possibly contribute to gene regulation and genome instability.
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Affiliation(s)
- Gunhyoung Lim
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul 08826, Republic of Korea
| | - Sungchul Hohng
- Department of Physics and Astronomy, and Institute of Applied Physics, Seoul National University, Seoul 08826, Republic of Korea
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155
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Unoki M, Sharif J, Saito Y, Velasco G, Francastel C, Koseki H, Sasaki H. CDCA7 and HELLS suppress DNA:RNA hybrid-associated DNA damage at pericentromeric repeats. Sci Rep 2020; 10:17865. [PMID: 33082427 PMCID: PMC7576824 DOI: 10.1038/s41598-020-74636-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/30/2020] [Indexed: 12/18/2022] Open
Abstract
Immunodeficiency, centromeric instability, facial anomalies (ICF) syndrome is a rare autosomal recessive disorder that is caused by mutations in either DNMT3B, ZBTB24, CDCA7, HELLS, or yet unidentified gene(s). Previously, we reported that the CDCA7/HELLS chromatin remodeling complex facilitates non-homologous end-joining. Here, we show that the same complex is required for the accumulation of proteins on nascent DNA, including the DNMT1/UHRF1 maintenance DNA methylation complex as well as proteins involved in the resolution or prevention of R-loops composed of DNA:RNA hybrids and ssDNA. Consistent with the hypomethylation state of pericentromeric repeats, the transcription and formation of aberrant DNA:RNA hybrids at the repeats were increased in ICF mutant cells. Furthermore, the ectopic expression of RNASEH1 reduced the accumulation of DNA damage at a broad range of genomic regions including pericentromeric repeats in these cells. Hence, we propose that hypomethylation due to inefficient DNMT1/UHRF1 recruitment at pericentromeric repeats by defects in the CDCA7/HELLS complex could induce pericentromeric instability, which may explain a part of the molecular pathogenesis of ICF syndrome.
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Affiliation(s)
- Motoko Unoki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka, 812-8582, Japan.
| | - Jafar Sharif
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, 230-0045, Japan
| | - Yuichiro Saito
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Mishima, Shizuoka, 411-8540, Japan
| | - Guillaume Velasco
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, 75205, Paris, France
| | - Claire Francastel
- CNRS UMR7216, Epigenetics and Cell Fate, Université Paris Diderot, Sorbonne Paris Cité, 75205, Paris, France
| | - Haruhiko Koseki
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, 230-0045, Japan
| | - Hiroyuki Sasaki
- Division of Epigenomics and Development, Medical Institute of Bioregulation, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka-shi, Fukuoka, 812-8582, Japan
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156
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Schult P, Paeschke K. The DEAH helicase DHX36 and its role in G-quadruplex-dependent processes. Biol Chem 2020; 402:581-591. [PMID: 33021960 DOI: 10.1515/hsz-2020-0292] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 09/24/2020] [Indexed: 02/07/2023]
Abstract
DHX36 is a member of the DExD/H box helicase family, which comprises a large number of proteins involved in various cellular functions. Recently, the function of DHX36 in the regulation of G-quadruplexes (G4s) was demonstrated. G4s are alternative nucleic acid structures, which influence many cellular pathways on a transcriptional and post-transcriptional level. In this review we provide an overview of the current knowledge about DHX36 structure, substrate specificity, and mechanism of action based on the available models and crystal structures. Moreover, we outline its multiple functions in cellular homeostasis, immunity, and disease. Finally, we discuss the open questions and provide potential directions for future research.
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Affiliation(s)
- Philipp Schult
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, D-53127Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, D-53127Bonn, Germany
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157
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RNA-cDNA hybrids mediate transposition via different mechanisms. Sci Rep 2020; 10:16034. [PMID: 32994470 PMCID: PMC7524711 DOI: 10.1038/s41598-020-73018-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 09/04/2020] [Indexed: 11/21/2022] Open
Abstract
Retrotransposons can represent half of eukaryotic genomes. Retrotransposon dysregulation destabilizes genomes and has been linked to various human diseases. Emerging regulators of retromobility include RNA–DNA hybrid-containing structures known as R-loops. Accumulation of these structures at the transposons of yeast 1 (Ty1) elements has been shown to increase Ty1 retromobility through an unknown mechanism. Here, via a targeted genetic screen, we identified the rnh1Δ rad27Δ yeast mutant, which lacked both the Ty1 inhibitor Rad27 and the RNA–DNA hybrid suppressor Rnh1. The mutant exhibited elevated levels of Ty1 cDNA-associated RNA–DNA hybrids that promoted Ty1 mobility. Moreover, in this rnh1Δ rad27Δ mutant, but not in the double RNase H mutant rnh1Δ rnh201Δ, RNA–DNA hybrids preferentially existed as duplex nucleic acid structures and increased Ty1 mobility in a Rad52-dependent manner. The data indicate that in cells lacking RNA–DNA hybrid and Ty1 repressors, elevated levels of RNA-cDNA hybrids, which are associated with duplex nucleic acid structures, boost Ty1 mobility via a Rad52-dependent mechanism. In contrast, in cells lacking RNA–DNA hybrid repressors alone, elevated levels of RNA-cDNA hybrids, which are associated with triplex nucleic acid structures, boost Ty1 mobility via a Rad52-independent process. We propose that duplex and triplex RNA–DNA hybrids promote transposon mobility via Rad52-dependent or -independent mechanisms.
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158
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Masai H, Tanaka T. G-quadruplex DNA and RNA: Their roles in regulation of DNA replication and other biological functions. Biochem Biophys Res Commun 2020; 531:25-38. [PMID: 32826060 DOI: 10.1016/j.bbrc.2020.05.132] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 12/19/2022]
Abstract
G-quadruplex is one of the best-studied non-B type DNA that is now known to be prevalently present in the genomes of almost all the biological species. Recent studies reveal roles of G-quadruplex (G4) structures in various nucleic acids and chromosome transactions. In this short article, we will first describe recent findings on the roles of G4 in regulation of DNA replication. G4 is involved in regulation of spatio-temporal regulation of DNA replication through interaction with a specific binding protein, Rif1. This regulation is at least partially mediated by generation of specific chromatin architecture through Rif1-G4 interactions. We will also describe recent studies showing the potential roles of G4 in initiation of DNA replication. Next, we will present showcases of highly diversified roles of DNA G4 and RNA G4 in regulation of nucleic acid and chromosome functions. Finally, we will discuss how the formation of cellular G4 could be regulated.
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Affiliation(s)
- Hisao Masai
- Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan.
| | - Taku Tanaka
- Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science, 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
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159
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Bryan TM. G-Quadruplexes at Telomeres: Friend or Foe? Molecules 2020; 25:molecules25163686. [PMID: 32823549 PMCID: PMC7464828 DOI: 10.3390/molecules25163686] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/09/2020] [Accepted: 08/10/2020] [Indexed: 12/28/2022] Open
Abstract
Telomeres are DNA-protein complexes that cap and protect the ends of linear chromosomes. In almost all species, telomeric DNA has a G/C strand bias, and the short tandem repeats of the G-rich strand have the capacity to form into secondary structures in vitro, such as four-stranded G-quadruplexes. This has long prompted speculation that G-quadruplexes play a positive role in telomere biology, resulting in selection for G-rich tandem telomere repeats during evolution. There is some evidence that G-quadruplexes at telomeres may play a protective capping role, at least in yeast, and that they may positively affect telomere maintenance by either the enzyme telomerase or by recombination-based mechanisms. On the other hand, G-quadruplex formation in telomeric DNA, as elsewhere in the genome, can form an impediment to DNA replication and a source of genome instability. This review summarizes recent evidence for the in vivo existence of G-quadruplexes at telomeres, with a focus on human telomeres, and highlights some of the many unanswered questions regarding the location, form, and functions of these structures.
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Affiliation(s)
- Tracy M Bryan
- Children's Medical Research Institute, Faculty of Medicine and Health, University of Sydney, Westmead, NSW 2145, Australia
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160
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De Magis A, Götz S, Hajikazemi M, Fekete-Szücs E, Caterino M, Juranek S, Paeschke K. Zuo1 supports G4 structure formation and directs repair toward nucleotide excision repair. Nat Commun 2020; 11:3907. [PMID: 32764578 PMCID: PMC7413387 DOI: 10.1038/s41467-020-17701-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 07/14/2020] [Indexed: 01/02/2023] Open
Abstract
Nucleic acids can fold into G-quadruplex (G4) structures that can fine-tune biological processes. Proteins are required to recognize G4 structures and coordinate their function. Here we identify Zuo1 as a novel G4-binding protein in vitro and in vivo. In vivo in the absence of Zuo1 fewer G4 structures form, cell growth slows and cells become UV sensitive. Subsequent experiments reveal that these cellular changes are due to reduced levels of G4 structures. Zuo1 function at G4 structures results in the recruitment of nucleotide excision repair (NER) factors, which has a positive effect on genome stability. Cells lacking functional NER, as well as Zuo1, accumulate G4 structures, which become accessible to translesion synthesis. Our results suggest a model in which Zuo1 supports NER function and regulates the choice of the DNA repair pathway nearby G4 structures.
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Affiliation(s)
- Alessio De Magis
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Silvia Götz
- Department of Biochemistry, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
- European Research Institute for the Biology of Ageing, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen, the Netherlands
| | - Mona Hajikazemi
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Enikő Fekete-Szücs
- European Research Institute for the Biology of Ageing, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen, the Netherlands
| | - Marco Caterino
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Stefan Juranek
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Venusberg-Campus 1, 53127, Bonn, Germany
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Venusberg-Campus 1, 53127, Bonn, Germany.
- Department of Biochemistry, Biocenter, University of Würzburg, Am Hubland, 97074, Würzburg, Germany.
- European Research Institute for the Biology of Ageing, University of Groningen, A. Deusinglaan 1, 9713 AV, Groningen, the Netherlands.
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161
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Varshney D, Spiegel J, Zyner K, Tannahill D, Balasubramanian S. The regulation and functions of DNA and RNA G-quadruplexes. Nat Rev Mol Cell Biol 2020; 21:459-474. [PMID: 32313204 PMCID: PMC7115845 DOI: 10.1038/s41580-020-0236-x] [Citation(s) in RCA: 583] [Impact Index Per Article: 145.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/11/2020] [Indexed: 02/06/2023]
Abstract
DNA and RNA can adopt various secondary structures. Four-stranded G-quadruplex (G4) structures form through self-recognition of guanines into stacked tetrads, and considerable biophysical and structural evidence exists for G4 formation in vitro. Computational studies and sequencing methods have revealed the prevalence of G4 sequence motifs at gene regulatory regions in various genomes, including in humans. Experiments using chemical, molecular and cell biology methods have demonstrated that G4s exist in chromatin DNA and in RNA, and have linked G4 formation with key biological processes ranging from transcription and translation to genome instability and cancer. In this Review, we first discuss the identification of G4s and evidence for their formation in cells using chemical biology, imaging and genomic technologies. We then discuss possible functions of DNA G4s and their interacting proteins, particularly in transcription, telomere biology and genome instability. Roles of RNA G4s in RNA biology, especially in translation, are also discussed. Furthermore, we consider the emerging relationships of G4s with chromatin and with RNA modifications. Finally, we discuss the connection between G4 formation and synthetic lethality in cancer cells, and recent progress towards considering G4s as therapeutic targets in human diseases.
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Affiliation(s)
- Dhaval Varshney
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Jochen Spiegel
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Katherine Zyner
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - David Tannahill
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK
| | - Shankar Balasubramanian
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Cambridge, UK.
- Department of Chemistry, University of Cambridge, Cambridge, UK.
- School of Clinical Medicine, University of Cambridge, Cambridge, UK.
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162
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Abstract
Several decades elapsed between the first descriptions of G-quadruplex nucleic acid structures (G4s) assembled in vitro and the emergence of experimental findings indicating that such structures can form and function in living systems. A large body of evidence now supports roles for G4s in many aspects of nucleic acid biology, spanning processes from transcription and chromatin structure, mRNA processing, protein translation, DNA replication and genome stability, and telomere and mitochondrial function. Nonetheless, it must be acknowledged that some of this evidence is tentative, which is not surprising given the technical challenges associated with demonstrating G4s in biology. Here I provide an overview of evidence for G4 biology, focusing particularly on the many potential pitfalls that can be encountered in its investigation, and briefly discuss some of broader biological processes that may be impacted by G4s including cancer.
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Affiliation(s)
- F. Brad Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, United States
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163
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R-loop induced G-quadruplex in non-template promotes transcription by successive R-loop formation. Nat Commun 2020; 11:3392. [PMID: 32636376 PMCID: PMC7341879 DOI: 10.1038/s41467-020-17176-7] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 06/17/2020] [Indexed: 01/06/2023] Open
Abstract
G-quadruplex (G4) is a noncanonical secondary structure of DNA or RNA which can enhance or repress gene expression, yet the underlying molecular mechanism remains uncertain. Here we show that when positioned downstream of transcription start site, the orientation of potential G4 forming sequence (PQS), but not the sequence alters transcriptional output. Ensemble in vitro transcription assays indicate that PQS in the non-template increases mRNA production rate and yield. Using sequential single molecule detection stages, we demonstrate that while binding and initiation of T7 RNA polymerase is unchanged, the efficiency of elongation and the final mRNA output is higher when PQS is in the non-template. Strikingly, the enhanced elongation arises from the transcription-induced R-loop formation, which in turn generates G4 structure in the non-template. The G4 stabilized R-loop leads to increased transcription by a mechanism involving successive rounds of R-loop formation. G-quadruplex (G4) forming sequences are highly enriched in the human genome and function as important regulators of diverse range of biological processes. Here the authors show that while G4 structures on template strand block transcription, folding on the non-template strand enhances transcription by means of successive R-loop formation.
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164
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Catching Common Cold Virus with a Net: Pyridostatin Forms Filaments in Tris Buffer That Trap Viruses-A Novel Antiviral Strategy? Viruses 2020; 12:v12070723. [PMID: 32635420 PMCID: PMC7412420 DOI: 10.3390/v12070723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/24/2020] [Accepted: 06/30/2020] [Indexed: 12/19/2022] Open
Abstract
The neutrophil extracellular trap (ET) is a eukaryotic host defense machinery that operates by capturing and concentrating pathogens in a filamentous network manufactured by neutrophils and made of DNA, histones, and many other components. Respiratory virus-induced ETs are involved in tissue damage and impairment of the alveolar-capillary barrier, but they also aid in fending off infection. We found that the small organic compound pyridostatin (PDS) forms somewhat similar fibrillary structures in Tris buffer in a concentration-dependent manner. Common cold viruses promote this process and become entrapped in the network, decreasing their infectivity by about 70% in tissue culture. We propose studying this novel mechanism of virus inhibition for its utility in preventing viral infection.
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165
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Jurikova K, Gajarsky M, Hajikazemi M, Nosek J, Prochazkova K, Paeschke K, Trantirek L, Tomaska L. Role of folding kinetics of secondary structures in telomeric G-overhangs in the regulation of telomere maintenance in Saccharomyces cerevisiae. J Biol Chem 2020; 295:8958-8971. [PMID: 32385108 PMCID: PMC7335780 DOI: 10.1074/jbc.ra120.012914] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/07/2020] [Indexed: 12/15/2022] Open
Abstract
The ends of eukaryotic chromosomes typically contain a 3' ssDNA G-rich protrusion (G-overhang). This overhang must be protected against detrimental activities of nucleases and of the DNA damage response machinery and participates in the regulation of telomerase, a ribonucleoprotein complex that maintains telomere integrity. These functions are mediated by DNA-binding proteins, such as Cdc13 in Saccharomyces cerevisiae, and the propensity of G-rich sequences to form various non-B DNA structures. Using CD and NMR spectroscopies, we show here that G-overhangs of S. cerevisiae form distinct Hoogsteen pairing-based secondary structures, depending on their length. Whereas short telomeric oligonucleotides form a G-hairpin, their longer counterparts form parallel and/or antiparallel G-quadruplexes (G4s). Regardless of their topologies, non-B DNA structures exhibited impaired binding to Cdc13 in vitro as demonstrated by electrophoretic mobility shift assays. Importantly, whereas G4 structures formed relatively quickly, G-hairpins folded extremely slowly, indicating that short G-overhangs, which are typical for most of the cell cycle, are present predominantly as single-stranded oligonucleotides and are suitable substrates for Cdc13. Using ChIP, we show that the occurrence of G4 structures peaks at the late S phase, thus correlating with the accumulation of long G-overhangs. We present a model of how time- and length-dependent formation of non-B DNA structures at chromosomal termini participates in telomere maintenance.
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Affiliation(s)
- Katarina Jurikova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Martin Gajarsky
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Mona Hajikazemi
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Katarina Prochazkova
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Katrin Paeschke
- Department of Oncology, Hematology and Rheumatology, University Hospital Bonn, Bonn, Germany
| | - Lukas Trantirek
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic; Institute of Biophysics, Czech Academy of Sciences, Brno, Czech Republic.
| | - Lubomir Tomaska
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia.
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166
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Mir SM, Samavarchi Tehrani S, Goodarzi G, Jamalpoor Z, Asadi J, Khelghati N, Qujeq D, Maniati M. Shelterin Complex at Telomeres: Implications in Ageing. Clin Interv Aging 2020; 15:827-839. [PMID: 32581523 PMCID: PMC7276337 DOI: 10.2147/cia.s256425] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 05/18/2020] [Indexed: 12/16/2022] Open
Abstract
Different factors influence the development and control of ageing. It is well known that progressive telomere shorting is one of the molecular mechanisms underlying ageing. The shelterin complex consists of six telomere-specific proteins which are involved in the protection of chromosome ends. More particularly, this vital complex protects the telomeres from degradation, prevents from activation of unwanted repair systems, regulates the activity of telomerase, and has a crucial role in cellular senescent and ageing-related pathologies. This review explores the organization and function of telomeric DNA along with the mechanism of telomeres during ageing, followed by a discussion of the critical role of shelterin components and their changes during ageing.
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Affiliation(s)
- Seyed Mostafa Mir
- Trauma Research Center, AJA University of Medical Sciences, Tehran, Iran.,Student Research Committee, Babol University of Medical Sciences, Babol, Iran.,Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Sadra Samavarchi Tehrani
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Golnaz Goodarzi
- Department of Clinical Biochemistry, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Student Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Zahra Jamalpoor
- Trauma Research Center, AJA University of Medical Sciences, Tehran, Iran
| | - Jahanbakhsh Asadi
- Metabolic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Nafiseh Khelghati
- Department of Clinical Biochemistry, School of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Durdi Qujeq
- Student Research Committee, Babol University of Medical Sciences, Babol, Iran.,Cellular and Molecular Biology Research Center, Health Research Institute, Babol University of Medical Sciences, Babol, Iran
| | - Mahmood Maniati
- School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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167
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New insight into the biology of R-loops. Mutat Res 2020; 821:111711. [PMID: 32516653 DOI: 10.1016/j.mrfmmm.2020.111711] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 11/24/2022]
Abstract
R-loops form when RNA hybridizes with its template DNA generating a three-stranded structure leaving a displaced single strand non-template DNA. During transcription negative supercoiling of DNA behind the advancing RNA polymerase will facilitate the formation of R-loops by the nascent RNA as the DNA is under wound to facilitate transcription. In theory R-loops are classified into pathological and non-pathological depending on the context of its formation. R-loop which are formed normally in various physiological events like in gene regulation and at immunoglobulin class switch regions are considered non-pathological, whereas abnormally stable R-loop which leads to genomic instability are considered pathological. Although pathological R-loop formation is a rare event but once formed completely blocks transcription, mRNA export, elevates mutagenesis, and inhibits gene expression. Hence, R-loop either prevents or induces genomic instability indirectly and are potentially an endogenous source of DNA lesion. Although the existence of R-loop has been reported few decades ago, but only recently we have gained knowledge about its formation and resolution in cells due to the availability of reagents. R-loop biology has generated immense interest in past few years since it connects the important biological processes such as transcription, mRNA splicing, DNA replication, recombination and repair. In this review I will focus on the recent progress made about formation and resolution of R-loop, based on the methodologies that are currently available to study R-loop using biochemical, cell biology and molecular biology approaches.
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168
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G-quadruplex, Friend or Foe: The Role of the G-quartet in Anticancer Strategies. Trends Mol Med 2020; 26:848-861. [PMID: 32467069 DOI: 10.1016/j.molmed.2020.05.002] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/13/2020] [Accepted: 05/06/2020] [Indexed: 02/07/2023]
Abstract
The clinical applicability of G-quadruplexes (G4s) as anticancer drugs is currently being evaluated. Several G4 ligands and aptamers are undergoing clinical trials following the notable examples of quarfloxin and AS1411, respectively. In this review, we summarize the latest achievements and breakthroughs in the use of G4 nucleic acids as both therapeutic tools ('friends', as healing anticancer drugs) and targets ('foes', within the harmful cancer cell), particularly using aptamers and quadruplex-targeted ligands, respectively. We explore the recent research on synthetic G4 ligands toward the discovery of anticancer therapeutics and their mechanism of action. Additionally, we highlight recent advances in chemical and structural biology that enable the design of specific G4 aptamers to be used as novel anticancer agents.
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169
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Vydzhak O, Luke B, Schindler N. Non-coding RNAs at the Eukaryotic rDNA Locus: RNA-DNA Hybrids and Beyond. J Mol Biol 2020; 432:4287-4304. [PMID: 32446803 DOI: 10.1016/j.jmb.2020.05.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 05/14/2020] [Accepted: 05/15/2020] [Indexed: 12/12/2022]
Abstract
The human ribosomal DNA (rDNA) locus encodes a variety of long non-coding RNAs (lncRNAs). Among them, the canonical ribosomal RNAs that are the catalytic components of the ribosomes, as well as regulatory lncRNAs including promoter-associated RNAs (pRNA), stress-induced promoter and pre-rRNA antisense RNAs (PAPAS), and different intergenic spacer derived lncRNA species (IGSRNA). In addition, externally encoded lncRNAs are imported into the nucleolus, which orchestrate the complex regulation of the nucleolar state in normal and stress conditions via a plethora of molecular mechanisms. This review focuses on the triplex and R-loop formation aspects of lncRNAs at the rDNA locus in yeast and human cells. We discuss the protein players that regulate R-loops at rDNA and how their misregulation contributes to DNA damage and disease. Furthermore, we speculate how DNA lesions such as rNMPs or 8-oxo-dG might affect RNA-DNA hybrid formation. The transcription of lncRNA from rDNA has been observed in yeast, plants, flies, worms, mouse and human cells. This evolutionary conservation highlights the importance of lncRNAs in rDNA function and maintenance.
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Affiliation(s)
- Olga Vydzhak
- Institute of Molecular Biology (IMB), Johannes Gutenberg-University Mainz, Ackermannweg 4, 55128 Mainz, Germany
| | - Brian Luke
- Institute of Molecular Biology (IMB), Johannes Gutenberg-University Mainz, Ackermannweg 4, 55128 Mainz, Germany; Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-University Mainz, 55128 Mainz, Germany
| | - Natalie Schindler
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-University Mainz, 55128 Mainz, Germany.
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170
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SLX4 interacts with RTEL1 to prevent transcription-mediated DNA replication perturbations. Nat Struct Mol Biol 2020; 27:438-449. [PMID: 32398829 DOI: 10.1038/s41594-020-0419-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 03/17/2020] [Indexed: 12/20/2022]
Abstract
The SLX4 tumor suppressor is a scaffold that plays a pivotal role in several aspects of genome protection, including homologous recombination, interstrand DNA crosslink repair and the maintenance of common fragile sites and telomeres. Here, we unravel an unexpected direct interaction between SLX4 and the DNA helicase RTEL1, which, until now, were viewed as having independent and antagonistic functions. We identify cancer and Hoyeraal-Hreidarsson syndrome-associated mutations in SLX4 and RTEL1, respectively, that abolish SLX4-RTEL1 complex formation. We show that both proteins are recruited to nascent DNA, tightly co-localize with active RNA pol II, and that SLX4, in complex with RTEL1, promotes FANCD2/RNA pol II co-localization. Importantly, disrupting the SLX4-RTEL1 interaction leads to DNA replication defects in unstressed cells, which are rescued by inhibiting transcription. Our data demonstrate that SLX4 and RTEL1 interact to prevent replication-transcription conflicts and provide evidence that this is independent of the nuclease scaffold function of SLX4.
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171
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Amjadi Oskouie A, Abiri A. Refining our methodologies for assessing quadruplex DNA ligands; selectivity or an illusion of selectivity? Anal Biochem 2020; 613:113744. [PMID: 32325085 DOI: 10.1016/j.ab.2020.113744] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 04/11/2020] [Accepted: 04/15/2020] [Indexed: 12/21/2022]
Abstract
Regulation of transcription and replication by the tetrad patterns of DNA has drawn the attention of many scientists. In this perspective article, we discuss some disparaged parameters in the study of G-quadruplex structures (G4-tetrads). Besides, the implication of "destabilization as a side-effect" by these ligands on quadruplexes is explained. The lack of strict control of in vitro cell-free experiments in terms of ionic concentration, pH, epigenetic modifications, (macro)molecular crowding, and solvent effects is evident in many previous studies. The role of these factors in ligands binding and their possible effects in G-quadruplex structures are also represented.
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Affiliation(s)
- Akbar Amjadi Oskouie
- Department of Biology, Ardabil Branch, Islamic Azad University, Ardabil, Iran; Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Ardavan Abiri
- Department of Medicinal Chemistry, Faculty of Pharmacy, Kerman University of Medical Sciences, Kerman, Iran.
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172
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Nakanishi C, Seimiya H. G-quadruplex in cancer biology and drug discovery. Biochem Biophys Res Commun 2020; 531:45-50. [PMID: 32312519 DOI: 10.1016/j.bbrc.2020.03.178] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 03/30/2020] [Indexed: 12/19/2022]
Abstract
G-quadruplex (G4) is a non-canonical nucleic acid structure formed in guanine-rich DNA or RNA. G4s are formed not only in vitro but also in vivo and are attracting considerable interest owing to their potential involvement in biological processes, including replication, transcription, mRNA splicing, translation and epigenetic regulation of the genome. In this review, we outline the functions of G4 in cellular biology and their implication in human pathogenesis, especially in cancer. Furthermore, we describe the properties of G4-stabilizing chemical compounds, G4 ligands, and their application for cancer therapeutics.
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Affiliation(s)
- Chuya Nakanishi
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Seimiya
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ku, Tokyo, 135-8550, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan.
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173
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Oh KI, Kim J, Park CJ, Lee JH. Dynamics Studies of DNA with Non-canonical Structure Using NMR Spectroscopy. Int J Mol Sci 2020; 21:E2673. [PMID: 32290457 PMCID: PMC7216225 DOI: 10.3390/ijms21082673] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/07/2020] [Accepted: 04/09/2020] [Indexed: 12/11/2022] Open
Abstract
The non-canonical structures of nucleic acids are essential for their diverse functions during various biological processes. These non-canonical structures can undergo conformational exchange among multiple structural states. Data on their dynamics can illustrate conformational transitions that play important roles in folding, stability, and biological function. Here, we discuss several examples of the non-canonical structures of DNA focusing on their dynamic characterization by NMR spectroscopy: (1) G-quadruplex structures and their complexes with target proteins; (2) i-motif structures and their complexes with proteins; (3) triplex structures; (4) left-handed Z-DNAs and their complexes with various Z-DNA binding proteins. This review provides insight into how the dynamic features of non-canonical DNA structures contribute to essential biological processes.
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Affiliation(s)
- Kwang-Im Oh
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea;
| | - Jinwoo Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea;
| | - Chin-Ju Park
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Korea;
| | - Joon-Hwa Lee
- Department of Chemistry and RINS, Gyeongsang National University, Gyeongnam 52828, Korea;
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174
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Tan J, Lan L. The DNA secondary structures at telomeres and genome instability. Cell Biosci 2020; 10:47. [PMID: 32257105 PMCID: PMC7104500 DOI: 10.1186/s13578-020-00409-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 03/14/2020] [Indexed: 01/09/2023] Open
Abstract
Telomeric DNA are TTAGGG tandem repeats, which are susceptible for oxidative DNA damage and hotspot regions for formation of DNA secondary structures such as t-loop, D-loop, G-quadruplexes (G4), and R-loop. In the past two decades, unique DNA or RNA secondary structures at telomeres or some specific regions of genome have become promising therapeutic targets. G-quadruplex and R-loops at telomeres or transcribed regions of genome have been considered as the potential targets for cancer therapy. Here we discuss the potentials to target the secondary structures (G4s and R-loops) in genome as therapy approaches.
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Affiliation(s)
- Jun Tan
- Harvard Medical School, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129 USA
- Department of Radiation Oncology, Harvard Medical School, Massachusetts General Hospital, Boston, MA 02115 USA
| | - Li Lan
- Harvard Medical School, Massachusetts General Hospital Cancer Center, Charlestown, MA 02129 USA
- Department of Radiation Oncology, Harvard Medical School, Massachusetts General Hospital, Boston, MA 02115 USA
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175
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Amato J, Miglietta G, Morigi R, Iaccarino N, Locatelli A, Leoni A, Novellino E, Pagano B, Capranico G, Randazzo A. Monohydrazone Based G-Quadruplex Selective Ligands Induce DNA Damage and Genome Instability in Human Cancer Cells. J Med Chem 2020; 63:3090-3103. [PMID: 32142285 PMCID: PMC7997572 DOI: 10.1021/acs.jmedchem.9b01866] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
![]()
Targeting
G-quadruplex structures is currently viewed as a promising
anticancer strategy. Searching for potent and selective G-quadruplex
binders, here we describe a small series of new monohydrazone derivatives
designed as analogues of a lead which was proved to stabilize G-quadruplex
structures and increase R loop levels in human cancer cells. To investigate
the G-quadruplex binding properties of the new molecules, in vitro biophysical studies were performed employing both
telomeric and oncogene promoter G-quadruplex-forming sequences. The
obtained results allowed the identification of a highly selective
G-quadruplex ligand that, when studied in human cancer cells, proved
to be able to stabilize both G-quadruplexes and R loops and showed
a potent cell killing activity associated with the formation of micronuclei,
a clear sign of genome instability.
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Affiliation(s)
- Jussara Amato
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Giulia Miglietta
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, 40126 Bologna, Italy
| | - Rita Morigi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, 40126 Bologna, Italy
| | - Nunzia Iaccarino
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Alessandra Locatelli
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, 40126 Bologna, Italy
| | - Alberto Leoni
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, 40126 Bologna, Italy
| | - Ettore Novellino
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, 40126 Bologna, Italy
| | - Antonio Randazzo
- Department of Pharmacy, University of Naples Federico II, via D. Montesano 49, 80131 Naples, Italy
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176
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Chedin F, Benham CJ. Emerging roles for R-loop structures in the management of topological stress. J Biol Chem 2020; 295:4684-4695. [PMID: 32107311 DOI: 10.1074/jbc.rev119.006364] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
R-loop structures are a prevalent class of alternative non-B DNA structures that form during transcription upon invasion of the DNA template by the nascent RNA. R-loops form universally in the genomes of organisms ranging from bacteriophages, bacteria, and yeasts to plants and animals, including mammals. A growing body of work has linked these structures to both physiological and pathological processes, in particular to genome instability. The rising interest in R-loops is placing new emphasis on understanding the fundamental physicochemical forces driving their formation and stability. Pioneering work in Escherichia coli revealed that DNA topology, in particular negative DNA superhelicity, plays a key role in driving R-loops. A clear role for DNA sequence was later uncovered. Here, we review and synthesize available evidence on the roles of DNA sequence and DNA topology in controlling R-loop formation and stability. Factoring in recent developments in R-loop modeling and single-molecule profiling, we propose a coherent model accounting for the interplay between DNA sequence and DNA topology in driving R-loop structure formation. This model reveals R-loops in a new light as powerful and reversible topological stress relievers, an insight that significantly expands the repertoire of R-loops' potential biological roles under both normal and aberrant conditions.
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Affiliation(s)
- Frederic Chedin
- Department of Molecular and Cellular Biology, University of California, Davis, California 95616 .,Genome Center, University of California, Davis, California 95616
| | - Craig J Benham
- Genome Center, University of California, Davis, California 95616 .,Departments of Mathematics and Biomedical Engineering, University of California, Davis, California 95616
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177
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From R-Loops to G-Quadruplexes: Emerging New Threats for the Replication Fork. Int J Mol Sci 2020; 21:ijms21041506. [PMID: 32098397 PMCID: PMC7073102 DOI: 10.3390/ijms21041506] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022] Open
Abstract
Replicating the entire genome is one of the most complex tasks for all organisms. Research carried out in the last few years has provided us with a clearer picture on how cells preserve genomic information from the numerous insults that may endanger its stability. Different DNA repair pathways, coping with exogenous or endogenous threat, have been dissected at the molecular level. More recently, there has been an increasing interest towards intrinsic obstacles to genome replication, paving the way to a novel view on genomic stability. Indeed, in some cases, the movement of the replication fork can be hindered by the presence of stable DNA: RNA hybrids (R-loops), the folding of G-rich sequences into G-quadruplex structures (G4s) or repetitive elements present at Common Fragile Sites (CFS). Although differing in their nature and in the way they affect the replication fork, all of these obstacles are a source of replication stress. Replication stress is one of the main hallmarks of cancer and its prevention is becoming increasingly important as a target for future chemotherapeutics. Here we will try to summarize how these three obstacles are generated and how the cells handle replication stress upon their encounter. Finally, we will consider their role in cancer and their exploitation in current chemotherapeutic approaches.
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178
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Tan J, Wang X, Phoon L, Yang H, Lan L. Resolution of ROS‐induced G‐quadruplexes and R‐loops at transcriptionally active sites is dependent on BLM helicase. FEBS Lett 2020; 594:1359-1367. [DOI: 10.1002/1873-3468.13738] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/23/2019] [Accepted: 01/15/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Jun Tan
- Massachusetts General Hospital Cancer Center Harvard Medical School Charlestown MA USA
- Department of Radiation Oncology Harvard Medical School Massachusetts General Hospital Boston MA USA
| | - Xiangyu Wang
- Massachusetts General Hospital Cancer Center Harvard Medical School Charlestown MA USA
- Department of Radiation Oncology Harvard Medical School Massachusetts General Hospital Boston MA USA
| | - Laiyee Phoon
- Massachusetts General Hospital Cancer Center Harvard Medical School Charlestown MA USA
- Department of Radiation Oncology Harvard Medical School Massachusetts General Hospital Boston MA USA
| | - Haibo Yang
- Massachusetts General Hospital Cancer Center Harvard Medical School Charlestown MA USA
- Department of Radiation Oncology Harvard Medical School Massachusetts General Hospital Boston MA USA
| | - Li Lan
- Massachusetts General Hospital Cancer Center Harvard Medical School Charlestown MA USA
- Department of Radiation Oncology Harvard Medical School Massachusetts General Hospital Boston MA USA
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179
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Regulatory R-loops as facilitators of gene expression and genome stability. Nat Rev Mol Cell Biol 2020; 21:167-178. [PMID: 32005969 DOI: 10.1038/s41580-019-0206-3] [Citation(s) in RCA: 258] [Impact Index Per Article: 64.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/17/2019] [Indexed: 12/23/2022]
Abstract
R-loops are three-stranded structures that harbour an RNA-DNA hybrid and frequently form during transcription. R-loop misregulation is associated with DNA damage, transcription elongation defects, hyper-recombination and genome instability. In contrast to such 'unscheduled' R-loops, evidence is mounting that cells harness the presence of RNA-DNA hybrids in scheduled, 'regulatory' R-loops to promote DNA transactions, including transcription termination and other steps of gene regulation, telomere stability and DNA repair. R-loops formed by cellular RNAs can regulate histone post-translational modification and may be recognized by dedicated reader proteins. The two-faced nature of R-loops implies that their formation, location and timely removal must be tightly regulated. In this Perspective, we discuss the cellular processes that regulatory R-loops modulate, the regulation of R-loops and the potential differences that may exist between regulatory R-loops and unscheduled R-loops.
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180
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Localized Inhibition of Protein Phosphatase 1 by NUAK1 Promotes Spliceosome Activity and Reveals a MYC-Sensitive Feedback Control of Transcription. Mol Cell 2020; 77:1322-1339.e11. [PMID: 32006464 PMCID: PMC7086158 DOI: 10.1016/j.molcel.2020.01.008] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 12/09/2019] [Accepted: 01/07/2020] [Indexed: 01/19/2023]
Abstract
Deregulated expression of MYC induces a dependence on the NUAK1 kinase, but the molecular mechanisms underlying this dependence have not been fully clarified. Here, we show that NUAK1 is a predominantly nuclear protein that associates with a network of nuclear protein phosphatase 1 (PP1) interactors and that PNUTS, a nuclear regulatory subunit of PP1, is phosphorylated by NUAK1. Both NUAK1 and PNUTS associate with the splicing machinery. Inhibition of NUAK1 abolishes chromatin association of PNUTS, reduces spliceosome activity, and suppresses nascent RNA synthesis. Activation of MYC does not bypass the requirement for NUAK1 for spliceosome activity but significantly attenuates transcription inhibition. Consequently, NUAK1 inhibition in MYC-transformed cells induces global accumulation of RNAPII both at the pause site and at the first exon-intron boundary but does not increase mRNA synthesis. We suggest that NUAK1 inhibition in the presence of deregulated MYC traps non-productive RNAPII because of the absence of correctly assembled spliceosomes. Nuclear NUAK1 associates with PP1 and phosphorylates its targeting subunit PNUTS NUAK1, PP1, and PNUTS form a trimer that associates with the splicing machinery Inhibition of NUAK1 reduces spliceosome activity and nascent RNA synthesis When MYC is deregulated, NUAK1 inhibition traps RNAPII at the intron-exon boundary
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181
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Carrasco-Salas Y, Malapert A, Sulthana S, Molcrette B, Chazot-Franguiadakis L, Bernard P, Chédin F, Faivre-Moskalenko C, Vanoosthuyse V. The extruded non-template strand determines the architecture of R-loops. Nucleic Acids Res 2020; 47:6783-6795. [PMID: 31066439 PMCID: PMC6648340 DOI: 10.1093/nar/gkz341] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 04/16/2019] [Accepted: 04/26/2019] [Indexed: 01/05/2023] Open
Abstract
Three-stranded R-loop structures have been associated with genomic instability phenotypes. What underlies their wide-ranging effects on genome stability remains poorly understood. Here we combined biochemical and atomic force microscopy approaches with single molecule R-loop footprinting to demonstrate that R-loops formed at the model Airn locus in vitro adopt a defined set of three-dimensional conformations characterized by distinct shapes and volumes, which we call R-loop objects. Interestingly, we show that these R-loop objects impose specific physical constraints on the DNA, as revealed by the presence of stereotypical angles in the surrounding DNA. Biochemical probing and mutagenesis experiments revealed that the formation of R-loop objects at Airn is dictated by the extruded non-template strand, suggesting that R-loops possess intrinsic sequence-driven properties. Consistent with this, we show that R-loops formed at the fission yeast gene sum3 do not form detectable R-loop objects. Our results reveal that R-loops differ by their architectures and that the organization of the non-template strand is a fundamental characteristic of R-loops, which could explain that only a subset of R-loops is associated with replication-dependent DNA breaks.
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Affiliation(s)
- Yeraldinne Carrasco-Salas
- Université de Lyon, ENSL, UCBL, CNRS, Laboratoire de Physique, 46 Allée d'Italie, 69007 Lyon, France
| | - Amélie Malapert
- Université de Lyon, ENSL, UCBL, CNRS, Laboratory of Biology and Modelling of the Cell (LBMC), 46 Allée d'Italie, 69007 Lyon, France
| | - Shaheen Sulthana
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | - Bastien Molcrette
- Université de Lyon, ENSL, UCBL, CNRS, Laboratoire de Physique, 46 Allée d'Italie, 69007 Lyon, France
| | - Léa Chazot-Franguiadakis
- Université de Lyon, ENSL, UCBL, CNRS, Laboratoire de Physique, 46 Allée d'Italie, 69007 Lyon, France
| | - Pascal Bernard
- Université de Lyon, ENSL, UCBL, CNRS, Laboratory of Biology and Modelling of the Cell (LBMC), 46 Allée d'Italie, 69007 Lyon, France
| | - Frédéric Chédin
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA
| | | | - Vincent Vanoosthuyse
- Université de Lyon, ENSL, UCBL, CNRS, Laboratory of Biology and Modelling of the Cell (LBMC), 46 Allée d'Italie, 69007 Lyon, France
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182
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Meeting report: Seventh International Meeting on Quadruplex Nucleic Acids (Changchun, P.R. China, September 6–9, 2019). Biochimie 2020; 168:100-109. [DOI: 10.1016/j.biochi.2019.10.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Accepted: 10/31/2019] [Indexed: 12/24/2022]
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183
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Duskova K, Lejault P, Benchimol É, Guillot R, Britton S, Granzhan A, Monchaud D. DNA Junction Ligands Trigger DNA Damage and Are Synthetic Lethal with DNA Repair Inhibitors in Cancer Cells. J Am Chem Soc 2019; 142:424-435. [PMID: 31833764 DOI: 10.1021/jacs.9b11150] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Translocation of DNA and RNA polymerases along their duplex substrates results in DNA supercoiling. This torsional stress promotes the formation of plectonemic structures, including three-way DNA junction (TWJ), which can block DNA transactions and lead to DNA damage. While cells have evolved multiple mechanisms to prevent the accumulation of such structures, stabilizing TWJ through ad hoc ligands offer an opportunity to trigger DNA damage in cells with high levels of transcription and replication, such as cancer cells. Here, we develop a series of azacryptand-based TWJ ligands, we thoroughly characterize their TWJ-interacting properties in vitro and demonstrate their capacity to trigger DNA damage in rapidly dividing human cancer cells. We also demonstrate that TWJ ligands are amenable to chemically induced synthetic lethality strategies upon association with inhibitors of DNA repair, thus paving the way toward innovative drug combinations to fight cancers.
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Affiliation(s)
- Katerina Duskova
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), CNRS UMR 6302 , UBFC Dijon , 21078 Dijon , France
| | - Pauline Lejault
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), CNRS UMR 6302 , UBFC Dijon , 21078 Dijon , France
| | - Élie Benchimol
- Institut Curie, CNRS UMR 9187, INSERM U1196 , PSL Research University , 91405 Orsay , France.,Université Paris Saclay, CNRS UMR 9187, INSERM U1196 , Université Paris-Sud , 91405 Orsay , France
| | - Régis Guillot
- Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO), CNRS UMR 8182, Université Paris-Sud , Université Paris Saclay , 91405 Orsay , France
| | - Sébastien Britton
- Institut de Pharmacologie et de Biologie Structurale (IPBS), CNRS UMR 5089, Université de Toulouse , UPS , Equipe labellisée la Ligue Contre le Cancer , 31077 Toulouse , France
| | - Anton Granzhan
- Institut Curie, CNRS UMR 9187, INSERM U1196 , PSL Research University , 91405 Orsay , France.,Université Paris Saclay, CNRS UMR 9187, INSERM U1196 , Université Paris-Sud , 91405 Orsay , France
| | - David Monchaud
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), CNRS UMR 6302 , UBFC Dijon , 21078 Dijon , France
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184
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Paul R, Das T, Debnath M, Chauhan A, Dash J. G-Quadruplex-Binding Small Molecule Induces Synthetic Lethality in Breast Cancer Cells by Inhibiting c-MYC and BCL2 Expression. Chembiochem 2019; 21:963-970. [PMID: 31621996 DOI: 10.1002/cbic.201900534] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Indexed: 12/21/2022]
Abstract
Herein, a prolinamide-derived peptidomimetic that preferentially binds to c-MYC and BCL2 G-quadruplexes present in the promoter regions of apoptosis-related genes (c-MYC and BCL2) over other DNA quadruplexes are described. Biological assays, such as real-time quantitative reverse transcription, western blot, dual luciferase, and small interfering RNA knockdown assays, indicate that the ligand triggers a synthetic lethal interaction by simultaneously inhibiting the expression of c-MYC and BCL2 genes through their promoter G-quadruplexes. The ligand shows antiproliferative activity in MCF-7 cells that overexpress both MYC and BCL2 genes, in comparison to cells that overexpress either of the two. Moreover, the ligand induces S-phase cell-cycle arrest, DNA damage, and apoptosis in MCF-7 cells.
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Affiliation(s)
- Rakesh Paul
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Tania Das
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Manish Debnath
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Ajay Chauhan
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
| | - Jyotirmayee Dash
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, 700 032, India
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185
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Drugging the R-loop interactome: RNA-DNA hybrid binding proteins as targets for cancer therapy. DNA Repair (Amst) 2019; 84:102642. [DOI: 10.1016/j.dnarep.2019.102642] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2019] [Revised: 05/16/2019] [Accepted: 07/02/2019] [Indexed: 02/07/2023]
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186
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Chappidi N, Nascakova Z, Boleslavska B, Zellweger R, Isik E, Andrs M, Menon S, Dobrovolna J, Balbo Pogliano C, Matos J, Porro A, Lopes M, Janscak P. Fork Cleavage-Religation Cycle and Active Transcription Mediate Replication Restart after Fork Stalling at Co-transcriptional R-Loops. Mol Cell 2019; 77:528-541.e8. [PMID: 31759821 DOI: 10.1016/j.molcel.2019.10.026] [Citation(s) in RCA: 85] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 07/03/2019] [Accepted: 10/16/2019] [Indexed: 01/08/2023]
Abstract
Formation of co-transcriptional R-loops underlies replication fork stalling upon head-on transcription-replication encounters. Here, we demonstrate that RAD51-dependent replication fork reversal induced by R-loops is followed by the restart of semiconservative DNA replication mediated by RECQ1 and RECQ5 helicases, MUS81/EME1 endonuclease, RAD52 strand-annealing factor, the DNA ligase IV (LIG4)/XRCC4 complex, and the non-catalytic subunit of DNA polymerase δ, POLD3. RECQ5 disrupts RAD51 filaments assembled on stalled forks after RECQ1-mediated reverse branch migration, preventing a new round of fork reversal and facilitating fork cleavage by MUS81/EME1. MUS81-dependent DNA breaks accumulate in cells lacking RAD52 or LIG4 upon induction of R-loop formation, suggesting that RAD52 acts in concert with LIG4/XRCC4 to catalyze fork religation, thereby mediating replication restart. The resumption of DNA synthesis after R-loop-associated fork stalling also requires active transcription, the restoration of which depends on MUS81, RAD52, LIG4, and the transcription elongation factor ELL. These findings provide mechanistic insights into transcription-replication conflict resolution.
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Affiliation(s)
- Nagaraja Chappidi
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Zuzana Nascakova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Barbora Boleslavska
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Ralph Zellweger
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Esin Isik
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Andrs
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Shruti Menon
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jana Dobrovolna
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | | | - Joao Matos
- Institute of Biochemistry, ETH Zurich, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Antonio Porro
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Pavel Janscak
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic.
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187
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Wells JP, White J, Stirling PC. R Loops and Their Composite Cancer Connections. Trends Cancer 2019; 5:619-631. [DOI: 10.1016/j.trecan.2019.08.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 08/29/2019] [Accepted: 08/30/2019] [Indexed: 12/19/2022]
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188
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Pompili L, Maresca C, Dello Stritto A, Biroccio A, Salvati E. BRCA2 Deletion Induces Alternative Lengthening of Telomeres in Telomerase Positive Colon Cancer Cells. Genes (Basel) 2019; 10:genes10090697. [PMID: 31510074 PMCID: PMC6771010 DOI: 10.3390/genes10090697] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/16/2019] [Accepted: 09/03/2019] [Indexed: 11/25/2022] Open
Abstract
BRCA1/2 are tumor suppressor genes controlling genomic stability also at telomeric and subtelomeric loci. Their mutation confers a predisposition to different human cancers but also sensitivity to antitumor drugs including poly(ADP-ribose) polymerase (PARP) inhibitors and G-quadruplex stabilizers. Here we demonstrate that BRCA2 deletion triggers TERRA hyperexpression and alternative lengthening mechanisms (ALT) in colon cancer cells in presence of telomerase activity. This finding opens the question if cancer patients bearing BRCA2 germline or sporadic mutation are suitable for anti-telomerase therapies, or how ALT activation could influence the short or long-term response to anti-PARP inhibitors or anti-G-quadruplex therapies.
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Affiliation(s)
- Luca Pompili
- Oncogenomic and Epigenetic Unit, IRCSS Regina Elena National Cancer Institute, Via Elio Chianesi, 53-00144 Rome, Italy.
| | - Carmen Maresca
- Oncogenomic and Epigenetic Unit, IRCSS Regina Elena National Cancer Institute, Via Elio Chianesi, 53-00144 Rome, Italy.
| | - Angela Dello Stritto
- Biology and Biotechnology Department "Charles Darwin", Sapienza University of Rome, Piazzale Aldo Moro, 5-00185 Rome, Italy.
| | - Annamaria Biroccio
- Oncogenomic and Epigenetic Unit, IRCSS Regina Elena National Cancer Institute, Via Elio Chianesi, 53-00144 Rome, Italy.
| | - Erica Salvati
- Oncogenomic and Epigenetic Unit, IRCSS Regina Elena National Cancer Institute, Via Elio Chianesi, 53-00144 Rome, Italy.
- Institute of Molecular Biology and Pathology, CNR, Via degli Apuli, 4-00185 Rome, Italy.
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189
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Russo M, De Lucca B, Flati T, Gioiosa S, Chillemi G, Capranico G. DROPA: DRIP-seq optimized peak annotator. BMC Bioinformatics 2019; 20:414. [PMID: 31387525 PMCID: PMC6685255 DOI: 10.1186/s12859-019-3009-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 07/29/2019] [Indexed: 11/18/2022] Open
Abstract
Background R-loops are three-stranded nucleic acid structures that usually form during transcription and that may lead to gene regulation or genome instability. DRIP (DNA:RNA Immunoprecipitation)-seq techniques are widely used to map R-loops genome-wide providing insights into R-loop biology. However, annotation of DRIP-seq peaks to genes can be a tricky step, due to the lack of strand information when using the common basic DRIP technique. Results Here, we introduce DRIP-seq Optimized Peak Annotator (DROPA), a new tool for gene annotation of R-loop peaks based on gene expression information. DROPA allows a full customization of annotation options, ranging from the choice of reference datasets to gene feature definitions. DROPA allows to assign R-loop peaks to the DNA template strand in gene body with a false positive rate of less than 7%. A comparison of DROPA performance with three widely used annotation tools show that it identifies less false positive annotations than the others. Conclusions DROPA is a fully customizable peak-annotation tool optimized for co-transcriptional DRIP-seq peaks, which allows a finest gene annotation based on gene expression information. Its output can easily be integrated into pipelines to perform downstream analyses, while useful and informative summary plots and statistical enrichment tests can be produced. Electronic supplementary material The online version of this article (10.1186/s12859-019-3009-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marco Russo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Bruno De Lucca
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy
| | - Tiziano Flati
- National Council of Research, CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy.,SCAI-Super Computing Applications and Innovation Department, CINECA, Rome, Italy
| | - Silvia Gioiosa
- National Council of Research, CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy.,SCAI-Super Computing Applications and Innovation Department, CINECA, Rome, Italy
| | - Giovanni Chillemi
- National Council of Research, CNR, Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, Bari, Italy.,Department for Innovation in Biological, Agro-food and Forest systems (DIBAF), University of Tuscia, Viterbo, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, Italy.
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190
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Goffová I, Vágnerová R, Peška V, Franek M, Havlová K, Holá M, Zachová D, Fojtová M, Cuming A, Kamisugi Y, Angelis KJ, Fajkus J. Roles of RAD51 and RTEL1 in telomere and rDNA stability in Physcomitrella patens. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 98:1090-1105. [PMID: 30834585 DOI: 10.1111/tpj.14304] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 02/21/2019] [Accepted: 02/27/2019] [Indexed: 05/11/2023]
Abstract
Telomeres and ribosomal RNA genes (rDNA) are essential for cell survival and particularly sensitive to factors affecting genome stability. Here, we examine the role of RAD51 and its antagonist, RTEL1, in the moss Physcomitrella patens. In corresponding mutants, we analyse their sensitivity to DNA damage, the maintenance of telomeres and rDNA, and repair of double-stranded breaks (DSBs) induced by genotoxins with various modes of action. While the loss of RTEL1 results in rapid telomere shortening, concurrent loss of both RAD51 genes has no effect on telomere lengths. We further demonstrate here the linked arrangement of 5S and 45S rRNA genes in P. patens. The spacer between 5S and 18S rRNA genes, especially the region downstream from the transcription start site, shows conspicuous clustering of sites with a high propensity to form quadruplex (G4) structures. Copy numbers of 5S and 18S rDNA are reduced moderately in the pprtel1 mutant, and significantly in the double pprad51-1-2 mutant, with no progression during subsequent cultivation. While reductions in 45S rDNA copy numbers observed in pprtel1 and pprad51-1-2 plants apply also to 5S rDNA, changes in transcript levels are different for 45S and 5S rRNA, indicating their independent transcription by RNA polymerase I and III, respectively. The loss of SOL (Sog One-Like), a transcription factor regulating numerous genes involved in DSB repair, increases the rate of DSB repair in dividing as well as differentiated tissue, and through deactivation of G2/M cell-cycle checkpoint allows the cell-cycle progression manifested as a phenotype resistant to bleomycin.
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Affiliation(s)
- Ivana Goffová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Radka Vágnerová
- The Czech Academy of Sciences, Institute of Experimental Botany, Na Karlovce 1, CZ-16000, Prague, Czech Republic
| | - Vratislav Peška
- The Czech Academy of Sciences, Institute of Biophysics, Královopolská 135, 612 65, Brno, Czech Republic
| | - Michal Franek
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Kateřina Havlová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Marcela Holá
- The Czech Academy of Sciences, Institute of Experimental Botany, Na Karlovce 1, CZ-16000, Prague, Czech Republic
| | - Dagmar Zachová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Miloslava Fojtová
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
| | - Andrew Cuming
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Yasuko Kamisugi
- Centre for Plant Sciences, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Karel J Angelis
- The Czech Academy of Sciences, Institute of Experimental Botany, Na Karlovce 1, CZ-16000, Prague, Czech Republic
| | - Jiří Fajkus
- Laboratory of Functional Genomics and Proteomics, National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlářská 2, CZ-61137, Brno, Czech Republic
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500, Brno, Czech Republic
- The Czech Academy of Sciences, Institute of Biophysics, Královopolská 135, 612 65, Brno, Czech Republic
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191
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Burger K, Schlackow M, Gullerova M. Tyrosine kinase c-Abl couples RNA polymerase II transcription to DNA double-strand breaks. Nucleic Acids Res 2019; 47:3467-3484. [PMID: 30668775 PMCID: PMC6468493 DOI: 10.1093/nar/gkz024] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/08/2019] [Accepted: 01/10/2019] [Indexed: 12/23/2022] Open
Abstract
DNA is constantly exposed to endogenous and exogenous damage. Various types of DNA repair counteract highly toxic DNA double-strand breaks (DSBs) to maintain genome stability. Recent findings suggest that the human DNA damage response (DDR) utilizes small RNA species, which are produced as long non-coding (nc)RNA precursors and promote recognition of DSBs. However, regulatory principles that control production of such transcripts remain largely elusive. Here we show that the Abelson tyrosine kinase c-Abl/ABL1 causes formation of RNA polymerase II (RNAPII) foci, predominantly phosphorylated at carboxy-terminal domain (CTD) residue Tyr1, at DSBs. CTD Tyr1-phosphorylated RNAPII (CTD Y1P) synthetizes strand-specific, damage-responsive transcripts (DARTs), which trigger formation of double-stranded (ds)RNA intermediates via DNA-RNA hybrid intermediates to promote recruitment of p53-binding protein 1 (53BP1) and Mediator of DNA damage checkpoint 1 (MDC1) to endogenous DSBs. Interference with transcription, c-Abl activity, DNA-RNA hybrid formation or dsRNA processing impairs CTD Y1P foci formation, attenuates DART synthesis and delays recruitment of DDR factors and DSB signalling. Collectively, our data provide novel insight in RNA-dependent DDR by coupling DSB-induced c-Abl activity on RNAPII to generate DARTs for consequent DSB recognition.
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Affiliation(s)
- Kaspar Burger
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Margarita Schlackow
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
| | - Monika Gullerova
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
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