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Wortman MJ, Dagdanova AV, Clark AM, Godfrey EW, Pascal SM, Johnson EM, Daniel DC. A synthetic Pur-based peptide binds and alters G-quadruplex secondary structure present in the expanded RNA repeat of C9orf72 ALS/FTD. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118674. [PMID: 32035967 DOI: 10.1016/j.bbamcr.2020.118674] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/20/2019] [Accepted: 02/02/2020] [Indexed: 12/26/2022]
Abstract
Increased Pur-alpha (Pura) protein levels in animal models alleviate certain cellular symptoms of the disease spectrum amyotrophic lateral sclerosis/frontotemporal dementia (ALS/FTD). Pura is a member of the Pur family of evolutionarily conserved guanine-rich polynucleotide binding proteins containing a repeated signature PUR domain of 60-80 amino acids. Here we have employed a synthetic peptide, TZIP, similar to a Pur domain, but with sequence alterations based on a consensus of evolutionarily conserved Pur family binding domains and having an added transporter sequence. A major familial form of ALS/FTD, C9orf72 (C9), is due to a hexanucleotide repeat expansion (HRE) of (GGGGCC), a Pur binding element. We show by circular dichroism that RNA oligonucleotides containing this purine-rich sequence consist largely of parallel G-quadruplexes. TZIP peptide binds this repeat sequence in both DNA and RNA. It binds the RNA element, including the G-quadruplexes, with a high degree of specificity versus a random oligonucleotide. In addition, TZIP binds both linear and G-quadruplex repeat RNA to form higher order G-quadruplex secondary structures. This change in conformational form by Pur-based peptide represents a new mechanism for regulating G quadruplex secondary structure within the C9 repeat. TZIP modulation of C9 RNA structural configuration may alter interaction of the complex with other proteins. This Pur-based mechanism provides new targets for therapy, and it may help to explain Pura alleviation of certain cellular pathological aspects of ALS/FTD.
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Affiliation(s)
- Margaret J Wortman
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Ayuna V Dagdanova
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Andrea M Clark
- Old Dominion University, Department of Chemistry and Biochemistry, Norfolk, VA 23529, USA
| | - Earl W Godfrey
- School of Health Professions, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Steven M Pascal
- Old Dominion University, Department of Chemistry and Biochemistry, Norfolk, VA 23529, USA
| | - Edward M Johnson
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA
| | - Dianne C Daniel
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, VA 23507, USA.
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52
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Maestroni L, Audry J, Luciano P, Coulon S, Géli V, Corda Y. RPA and Pif1 cooperate to remove G-rich structures at both leading and lagging strand. Cell Stress 2020; 4:48-63. [PMID: 32190820 PMCID: PMC7063842 DOI: 10.15698/cst2020.03.214] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
In Saccharomyces cerevisiae, the absence of Pif1 helicase induces the instability of G4-containing CEB1 minisatellite during leading strand but not lagging strand replication. We report that RPA and Pif1 cooperate to maintain CEB1 stability when the G4 forming strand is either on the leading or lagging strand templates. At the leading strand, RPA acts in the same pathway as Pif1 to maintain CEB1 stability. Consistent with this result, RPA co-precipitates with Pif1. This association between Pif1 and RPA is affected by the rfa1-D228Y mutation that lowers the affinity of RPA in particular for G-rich single-stranded DNA. At the lagging strand, in contrast to pif1Δ, the rfa1-D228Y mutation strongly increases the frequency of CEB1 rearrangements. We explain that Pif1 is dispensable at the lagging strand DNA by the ability of RPA by itself to prevent formation of stable G-rich secondary structures during lagging strand synthesis. Remarkably, overexpression of Pif1 rescues the instability of CEB1 at the lagging strand in the rfa1-D228Y mutant indicating that Pif1 can also act at the lagging strand. We show that the effects of the rfa1-D228Y (rpa1-D223Y in fission yeast) are conserved in Schizosaccharomyces pombe. Finally, we report that RNase H1 interacts in a DNA-dependent manner with RPA in budding yeast, however overexpression of RNase H1 does not rescue CEB1 instability observed in pif1Δ and rfa1-D228Y mutants. Collectively these results add new insights about the general role of RPA in preventing formation of DNA secondary structures and in coordinating the action of factors aimed at resolving them.
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Affiliation(s)
- Laetitia Maestroni
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe Labellisée par la Ligue Nationale contre le Cancer
| | - Julien Audry
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe Labellisée par la Ligue Nationale contre le Cancer
| | - Pierre Luciano
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe Labellisée par la Ligue Nationale contre le Cancer
| | - Stéphane Coulon
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe Labellisée par la Ligue Nationale contre le Cancer
| | - Vincent Géli
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe Labellisée par la Ligue Nationale contre le Cancer
| | - Yves Corda
- Aix-Marseille Univ, Inserm, CNRS, Institut Paoli-Calmettes, CRCM, Marseille, France. Equipe Labellisée par la Ligue Nationale contre le Cancer
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53
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Puig Lombardi E, Londoño-Vallejo A. A guide to computational methods for G-quadruplex prediction. Nucleic Acids Res 2020; 48:1-15. [PMID: 31754698 PMCID: PMC6943126 DOI: 10.1093/nar/gkz1097] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/31/2019] [Accepted: 11/04/2019] [Indexed: 12/31/2022] Open
Abstract
Guanine-rich nucleic acids can fold into the non-B DNA or RNA structures called G-quadruplexes (G4). Recent methodological developments have allowed the characterization of specific G-quadruplex structures in vitro as well as in vivo, and at a much higher throughput, in silico, which has greatly expanded our understanding of G4-associated functions. Typically, the consensus motif G3+N1-7G3+N1-7G3+N1-7G3+ has been used to identify potential G-quadruplexes from primary sequence. Since, various algorithms have been developed to predict the potential formation of quadruplexes directly from DNA or RNA sequences and the number of studies reporting genome-wide G4 exploration across species has rapidly increased. More recently, new methodologies have also appeared, proposing other estimates which consider non-canonical sequences and/or structure propensity and stability. The present review aims at providing an updated overview of the current open-source G-quadruplex prediction algorithms and straightforward examples of their implementation.
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Affiliation(s)
- Emilia Puig Lombardi
- Telomeres and Cancer Laboratory, Institut Curie, PSL Research University, Sorbonne Universités, CNRS UMR3244, 75005 Paris, France
| | - Arturo Londoño-Vallejo
- Telomeres and Cancer Laboratory, Institut Curie, PSL Research University, Sorbonne Universités, CNRS UMR3244, 75005 Paris, France
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Lowran K, Campbell L, Popp P, Wu CG. Assembly of a G-Quadruplex Repair Complex by the FANCJ DNA Helicase and the REV1 Polymerase. Genes (Basel) 2019; 11:E5. [PMID: 31861576 PMCID: PMC7017153 DOI: 10.3390/genes11010005] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 12/17/2019] [Indexed: 12/14/2022] Open
Abstract
The FANCJ helicase unfolds G-quadruplexes (G4s) in human cells to support DNA replication. This action is coupled to the recruitment of REV1 polymerase to synthesize DNA across from a guanine template. The precise mechanisms of these reactions remain unclear. While FANCJ binds to G4s with an AKKQ motif, it is not known whether this site recognizes damaged G4 structures. FANCJ also has a PIP-like (PCNA Interacting Protein) region that may recruit REV1 to G4s either directly or through interactions mediated by PCNA protein. In this work, we measured the affinities of a FANCJ AKKQ peptide for G4s formed by (TTAGGG)4 and (GGGT)4 using fluorescence spectroscopy and biolayer interferometry (BLI). The effects of 8-oxoguanine (8oxoG) on these interactions were tested at different positions. BLI assays were then performed with a FANCJ PIP to examine its recruitment of REV1 and PCNA. FANCJ AKKQ bound tightly to a TTA loop and was sequestered away from the 8oxoG. Reducing the loop length between guanine tetrads increased the affinity of the peptide for 8oxoG4s. FANCJ PIP targeted both REV1 and PCNA but favored interactions with the REV1 polymerase. The impact of these results on the remodeling of damaged G4 DNA is discussed herein.
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Affiliation(s)
- Kaitlin Lowran
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA; (K.L.); (L.C.)
| | - Laura Campbell
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA; (K.L.); (L.C.)
| | - Phillip Popp
- Case Western Reserve University, Cleveland, OH 44106, USA;
| | - Colin G. Wu
- Department of Chemistry, Oakland University, Rochester, MI 48309, USA; (K.L.); (L.C.)
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55
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Moyer CL, Ivanovich J, Gillespie JL, Doberstein R, Radke MR, Richardson ME, Kaufmann SH, Swisher EM, Goodfellow PJ. Rare BRIP1 Missense Alleles Confer Risk for Ovarian and Breast Cancer. Cancer Res 2019; 80:857-867. [PMID: 31822495 DOI: 10.1158/0008-5472.can-19-1991] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 10/25/2019] [Accepted: 12/04/2019] [Indexed: 11/16/2022]
Abstract
Germline loss-of-function mutations in BRCA1 interacting protein C-terminal helicase 1 (BRIP1) are associated with ovarian carcinoma and may also contribute to breast cancer risk, particularly among patients who develop disease at an early age. Normal BRIP1 activity is required for DNA interstrand cross-link (ICL) repair and is thus central to the maintenance of genome stability. Although pathogenic mutations have been identified in BRIP1, genetic testing more often reveals missense variants, for which the impact on molecular function and subsequent roles in cancer risk are uncertain. Next-generation sequencing of germline DNA in 2,160 early-onset breast cancer and 1,199 patients with ovarian cancer revealed nearly 2% of patients carry a very rare missense variant (minor allele frequency < 0.0001) in BRIP1. This is 3-fold higher than the frequency of all rare BRIP1 missense alleles reported in more than 60,000 individuals of the general population (P < 0.0001, χ 2 test). Using CRISPR-Cas9 gene editing technology and rescue assays, we functionally characterized 20 of these missense variants, focusing on the altered protein's ability to repair ICL damage. A total of 75% of the characterized variants rendered the protein hypomorph or null. In a clinical cohort of >117,000 patients with breast and ovarian cancer who underwent panel testing, the combined OR associated with BRIP1 hypomorph or null missense carriers compared with the general population was 2.30 (95% confidence interval, 1.60-3.30; P < 0.0001). These findings suggest that novel missense variants within the helicase domain of BRIP1 may confer risk for both breast and ovarian cancer and highlight the importance of functional testing for additional variants. SIGNIFICANCE: Functional characterization of rare variants of uncertain significance in BRIP1 revealed that 75% demonstrate loss-of-function activity, suggesting rare missense alleles in BRIP1 confer risk for both breast and ovarian cancer.
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Affiliation(s)
- Cassandra L Moyer
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
- Department of Obstetrics and Gynecology, The Ohio State University, Columbus, Ohio
| | - Jennifer Ivanovich
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, Indiana
| | - Jessica L Gillespie
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
- Department of Obstetrics and Gynecology, The Ohio State University, Columbus, Ohio
| | - Rachel Doberstein
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio
- Department of Obstetrics and Gynecology, The Ohio State University, Columbus, Ohio
| | - Marc R Radke
- Division of Gynecologic Oncology, University of Washington, Seattle, Washington
| | - Marcy E Richardson
- Department of Clinical Genomics, Ambry Genetics, Aliso Viejo, California
| | - Scott H Kaufmann
- Division of Oncology Research, Mayo Clinic, Rochester, Minnesota
| | - Elizabeth M Swisher
- Division of Gynecologic Oncology, University of Washington, Seattle, Washington
| | - Paul J Goodfellow
- James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio.
- Department of Obstetrics and Gynecology, The Ohio State University, Columbus, Ohio
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56
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Lansdorp P, van Wietmarschen N. Helicases FANCJ, RTEL1 and BLM Act on Guanine Quadruplex DNA in Vivo. Genes (Basel) 2019; 10:genes10110870. [PMID: 31683575 PMCID: PMC6896191 DOI: 10.3390/genes10110870] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 10/29/2019] [Accepted: 10/29/2019] [Indexed: 02/03/2023] Open
Abstract
Guanine quadruplex (G4) structures are among the most stable secondary DNA structures that can form in vitro, and evidence for their existence in vivo has been steadily accumulating. Originally described mainly for their deleterious effects on genome stability, more recent research has focused on (potential) functions of G4 structures in telomere maintenance, gene expression, and other cellular processes. The combined research on G4 structures has revealed that properly regulating G4 DNA structures in cells is important to prevent genome instability and disruption of normal cell function. In this short review we provide some background and historical context of our work resulting in the identification of FANCJ, RTEL1 and BLM as helicases that act on G4 structures in vivo. Taken together these studies highlight important roles of different G4 DNA structures and specific G4 helicases at selected genomic locations and telomeres in regulating gene expression and maintaining genome stability.
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Affiliation(s)
- Peter Lansdorp
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC V5Z 1L3, Canada.
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada.
- European Research Institute for the Biology of Ageing, University of Groningen, 9713 AV Groningen, The Netherlands.
| | - Niek van Wietmarschen
- European Research Institute for the Biology of Ageing, University of Groningen, 9713 AV Groningen, The Netherlands.
- Laboratory of Genome Integrity, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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57
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Estep KN, Butler TJ, Ding J, Brosh RM. G4-Interacting DNA Helicases and Polymerases: Potential Therapeutic Targets. Curr Med Chem 2019; 26:2881-2897. [PMID: 29149833 DOI: 10.2174/0929867324666171116123345] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 10/16/2017] [Accepted: 10/16/2017] [Indexed: 02/07/2023]
Abstract
BACKGROUND Guanine-rich DNA can fold into highly stable four-stranded DNA structures called G-quadruplexes (G4). In recent years, the G-quadruplex field has blossomed as new evidence strongly suggests that such alternately folded DNA structures are likely to exist in vivo. G4 DNA presents obstacles for the replication machinery, and both eukaryotic DNA helicases and polymerases have evolved to resolve and copy G4 DNA in vivo. In addition, G4-forming sequences are prevalent in gene promoters, suggesting that G4-resolving helicases act to modulate transcription. METHODS We have searched the PubMed database to compile an up-to-date and comprehensive assessment of the field's current knowledge to provide an overview of the molecular interactions of Gquadruplexes with DNA helicases and polymerases implicated in their resolution. RESULTS Novel computational tools and alternative strategies have emerged to detect G4-forming sequences and assess their biological consequences. Specialized DNA helicases and polymerases catalytically act upon G4-forming sequences to maintain normal replication and genomic stability as well as appropriate gene regulation and cellular homeostasis. G4 helicases also resolve telomeric repeats to maintain chromosomal DNA ends. Bypass of many G4-forming sequences is achieved by the action of translesion DNS polymerases or the PrimPol DNA polymerase. While the collective work has supported a role of G4 in nuclear DNA metabolism, an emerging field centers on G4 abundance in the mitochondrial genome. CONCLUSION Discovery of small molecules that specifically bind and modulate DNA helicases and polymerases or interact with the G4 DNA structure itself may be useful for the development of anticancer regimes.
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Affiliation(s)
- Katrina N Estep
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Blvd Baltimore, MD 21224, United States
| | - Thomas J Butler
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Blvd Baltimore, MD 21224, United States
| | - Jun Ding
- Laboratory of Genetics and Genomics, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Blvd Baltimore, MD 21224, United States
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, 251 Bayview Blvd Baltimore, MD 21224, United States
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58
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Feng W, Simpson DA, Carvajal-Garcia J, Price BA, Kumar RJ, Mose LE, Wood RD, Rashid N, Purvis JE, Parker JS, Ramsden DA, Gupta GP. Genetic determinants of cellular addiction to DNA polymerase theta. Nat Commun 2019; 10:4286. [PMID: 31537809 PMCID: PMC6753077 DOI: 10.1038/s41467-019-12234-1] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 08/22/2019] [Indexed: 02/07/2023] Open
Abstract
Polymerase theta (Pol θ, gene name Polq) is a widely conserved DNA polymerase that mediates a microhomology-mediated, error-prone, double strand break (DSB) repair pathway, referred to as Theta Mediated End Joining (TMEJ). Cells with homologous recombination deficiency are reliant on TMEJ for DSB repair. It is unknown whether deficiencies in other components of the DNA damage response (DDR) also result in Pol θ addiction. Here we use a CRISPR genetic screen to uncover 140 Polq synthetic lethal (PolqSL) genes, the majority of which were previously unknown. Functional analyses indicate that Pol θ/TMEJ addiction is associated with increased levels of replication-associated DSBs, regardless of the initial source of damage. We further demonstrate that approximately 30% of TCGA breast cancers have genetic alterations in PolqSL genes and exhibit genomic scars of Pol θ/TMEJ hyperactivity, thereby substantially expanding the subset of human cancers for which Pol θ inhibition represents a promising therapeutic strategy.
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Affiliation(s)
- Wanjuan Feng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Dennis A Simpson
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Juan Carvajal-Garcia
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Brandon A Price
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Rashmi J Kumar
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Lisle E Mose
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Richard D Wood
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX, 78957, USA
| | - Naim Rashid
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jeremy E Purvis
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Joel S Parker
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Dale A Ramsden
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Gaorav P Gupta
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
- Department of Radiation Oncology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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59
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Varizhuk A, Isaakova E, Pozmogova G. DNA G-Quadruplexes (G4s) Modulate Epigenetic (Re)Programming and Chromatin Remodeling: Transient Genomic G4s Assist in the Establishment and Maintenance of Epigenetic Marks, While Persistent G4s May Erase Epigenetic Marks. Bioessays 2019; 41:e1900091. [PMID: 31379012 DOI: 10.1002/bies.201900091] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 07/09/2019] [Indexed: 01/07/2023]
Abstract
Here, the emerging data on DNA G-quadruplexes (G4s) as epigenetic modulators are reviewed and integrated. This concept has appeared and evolved substantially in recent years. First, persistent G4s (e.g., those stabilized by exogenous ligands) were linked to the loss of the histone code. More recently, transient G4s (i.e., those formed upon replication or transcription and unfolded rapidly by helicases) were implicated in CpG island methylation maintenance and de novo CpG methylation control. The most recent data indicate that there are direct interactions between G4s and chromatin remodeling factors. Finally, multiple findings support the indirect participation of G4s in chromatin reshaping via interactions with remodeling-related transcription factors (TFs) or damage responders. Here, the links between the above processes are analyzed; also, how further elucidation of these processes may stimulate the progress of epigenetic therapy is discussed, and the remaining open questions are highlighted.
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Affiliation(s)
- Anna Varizhuk
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Ekaterina Isaakova
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
| | - Galina Pozmogova
- Biophysics Department, Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, 119435, Russia
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60
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Puig Lombardi E, Holmes A, Verga D, Teulade-Fichou MP, Nicolas A, Londoño-Vallejo A. Thermodynamically stable and genetically unstable G-quadruplexes are depleted in genomes across species. Nucleic Acids Res 2019; 47:6098-6113. [PMID: 31114920 PMCID: PMC6614823 DOI: 10.1093/nar/gkz463] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/10/2019] [Accepted: 05/14/2019] [Indexed: 12/29/2022] Open
Abstract
G-quadruplexes play various roles in multiple biological processes, which can be positive when a G4 is involved in the regulation of gene expression or detrimental when the folding of a stable G4 impairs DNA replication promoting genome instability. This duality interrogates the significance of their presence within genomes. To address the potential biased evolution of G4 motifs, we analyzed their occurrence, features and polymorphisms in a large spectrum of species. We found extreme bias of the short-looped G4 motifs, which are the most thermodynamically stable in vitro and thus carry the highest folding potential in vivo. In the human genome, there is an over-representation of single-nucleotide-loop G4 motifs (G4-L1), which are highly conserved among humans and show a striking excess of the thermodynamically least stable G4-L1A (G3AG3AG3AG3) sequences. Functional assays in yeast showed that G4-L1A caused the lowest levels of both spontaneous and G4-ligand-induced instability. Analyses across 600 species revealed the depletion of the most stable G4-L1C/T quadruplexes in most genomes in favor of G4-L1A in vertebrates or G4-L1G in other eukaryotes. We discuss how these trends might be the result of species-specific mutagenic processes associated to a negative selection against the most stable motifs, thus neutralizing their detrimental effects on genome stability while preserving positive G4-associated biological roles.
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Affiliation(s)
| | - Allyson Holmes
- Institut Curie, PSL Research University, UMR3244 CNRS, 75005 Paris, France
| | - Daniela Verga
- Institut Curie, PSL Research University, Sorbonne Universités, UPMC, CNRS, Inserm, UMR9187/U1196, 91495 Orsay, France
| | - Marie-Paule Teulade-Fichou
- Institut Curie, PSL Research University, Sorbonne Universités, UPMC, CNRS, Inserm, UMR9187/U1196, 91495 Orsay, France
| | - Alain Nicolas
- Institut Curie, PSL Research University, UMR3244 CNRS, 75005 Paris, France
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Sequeira-Mendes J, Vergara Z, Peiró R, Morata J, Aragüez I, Costas C, Mendez-Giraldez R, Casacuberta JM, Bastolla U, Gutierrez C. Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins. Genome Res 2019; 29:784-797. [PMID: 30846531 PMCID: PMC6499314 DOI: 10.1101/gr.240986.118] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 02/25/2019] [Indexed: 12/20/2022]
Abstract
Eukaryotic genome replication depends on thousands of DNA replication origins (ORIs). A major challenge is to learn ORI biology in multicellular organisms in the context of growing organs to understand their developmental plasticity. We have identified a set of ORIs of Arabidopsis thaliana and their chromatin landscape at two stages of post-embryonic development. ORIs associate with multiple chromatin signatures including transcription start sites (TSS) but also proximal and distal regulatory regions and heterochromatin, where ORIs colocalize with retrotransposons. In addition, quantitative analysis of ORI activity led us to conclude that strong ORIs have high GC content and clusters of GGN trinucleotides. Development primarily influences ORI firing strength rather than ORI location. ORIs that preferentially fire at early developmental stages colocalize with GC-rich heterochromatin, but at later stages with transcribed genes, perhaps as a consequence of changes in chromatin features associated with developmental processes. Our study provides the set of ORIs active in an organism at the post-embryo stage that should allow us to study ORI biology in response to development, environment, and mutations with a quantitative approach. In a wider scope, the computational strategies developed here can be transferred to other eukaryotic systems.
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Affiliation(s)
- Joana Sequeira-Mendes
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Zaida Vergara
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Ramon Peiró
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Jordi Morata
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus Universitat Autónoma de Barcelona, Bellaterra, Cerdanyola del Valles, 08193 Barcelona, Spain
| | - Irene Aragüez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Celina Costas
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Raul Mendez-Giraldez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Josep M Casacuberta
- Center for Research in Agricultural Genomics, CRAG (CSIC-IRTA-UAB-UB), Campus Universitat Autónoma de Barcelona, Bellaterra, Cerdanyola del Valles, 08193 Barcelona, Spain
| | - Ugo Bastolla
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
| | - Crisanto Gutierrez
- Centro de Biologia Molecular Severo Ochoa, CSIC-UAM, Nicolas Cabrera 1, Cantoblanco, 28049 Madrid, Spain
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Datta A, Brosh RM. Holding All the Cards-How Fanconi Anemia Proteins Deal with Replication Stress and Preserve Genomic Stability. Genes (Basel) 2019; 10:genes10020170. [PMID: 30813363 PMCID: PMC6409899 DOI: 10.3390/genes10020170] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 12/18/2022] Open
Abstract
Fanconi anemia (FA) is a hereditary chromosomal instability disorder often displaying congenital abnormalities and characterized by a predisposition to progressive bone marrow failure (BMF) and cancer. Over the last 25 years since the discovery of the first linkage of genetic mutations to FA, its molecular genetic landscape has expanded tremendously as it became apparent that FA is a disease characterized by a defect in a specific DNA repair pathway responsible for the correction of covalent cross-links between the two complementary strands of the DNA double helix. This pathway has become increasingly complex, with the discovery of now over 20 FA-linked genes implicated in interstrand cross-link (ICL) repair. Moreover, gene products known to be involved in double-strand break (DSB) repair, mismatch repair (MMR), and nucleotide excision repair (NER) play roles in the ICL response and repair of associated DNA damage. While ICL repair is predominantly coupled with DNA replication, it also can occur in non-replicating cells. DNA damage accumulation and hematopoietic stem cell failure are thought to contribute to the increased inflammation and oxidative stress prevalent in FA. Adding to its confounding nature, certain FA gene products are also engaged in the response to replication stress, caused endogenously or by agents other than ICL-inducing drugs. In this review, we discuss the mechanistic aspects of the FA pathway and the molecular defects leading to elevated replication stress believed to underlie the cellular phenotypes and clinical features of FA.
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Affiliation(s)
- Arindam Datta
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, Baltimore, MD 21224, USA.
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, NIH Biomedical Research Center, Baltimore, MD 21224, USA.
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63
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Lerner LK, Sale JE. Replication of G Quadruplex DNA. Genes (Basel) 2019; 10:genes10020095. [PMID: 30700033 PMCID: PMC6409989 DOI: 10.3390/genes10020095] [Citation(s) in RCA: 106] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 01/21/2019] [Accepted: 01/23/2019] [Indexed: 01/03/2023] Open
Abstract
A cursory look at any textbook image of DNA replication might suggest that the complex machine that is the replisome runs smoothly along the chromosomal DNA. However, many DNA sequences can adopt non-B form secondary structures and these have the potential to impede progression of the replisome. A picture is emerging in which the maintenance of processive DNA replication requires the action of a significant number of additional proteins beyond the core replisome to resolve secondary structures in the DNA template. By ensuring that DNA synthesis remains closely coupled to DNA unwinding by the replicative helicase, these factors prevent impediments to the replisome from causing genetic and epigenetic instability. This review considers the circumstances in which DNA forms secondary structures, the potential responses of the eukaryotic replisome to these impediments in the light of recent advances in our understanding of its structure and operation and the mechanisms cells deploy to remove secondary structure from the DNA. To illustrate the principles involved, we focus on one of the best understood DNA secondary structures, G quadruplexes (G4s), and on the helicases that promote their resolution.
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Affiliation(s)
- Leticia Koch Lerner
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
| | - Julian E Sale
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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64
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Developing Novel G-Quadruplex Ligands: from Interaction with Nucleic Acids to Interfering with Nucleic Acid⁻Protein Interaction. Molecules 2019; 24:molecules24030396. [PMID: 30678288 PMCID: PMC6384609 DOI: 10.3390/molecules24030396] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 01/10/2019] [Accepted: 01/22/2019] [Indexed: 12/20/2022] Open
Abstract
G-quadruplex is a special secondary structure of nucleic acids in guanine-rich sequences of genome. G-quadruplexes have been proved to be involved in the regulation of replication, DNA damage repair, and transcription and translation of oncogenes or other cancer-related genes. Therefore, targeting G-quadruplexes has become a novel promising anti-tumor strategy. Different kinds of small molecules targeting the G-quadruplexes have been designed, synthesized, and identified as potential anti-tumor agents, including molecules directly bind to the G-quadruplex and molecules interfering with the binding between the G-quadruplex structures and related binding proteins. This review will explore the feasibility of G-quadruplex ligands acting as anti-tumor drugs, from basis to application. Meanwhile, since helicase is the most well-defined G-quadruplex-related protein, the most extensive research on the relationship between helicase and G-quadruplexes, and its meaning in drug design, is emphasized.
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Abstract
The maintenance of genome stability in eukaryotic cells relies on accurate and efficient replication along each chromosome following every cell division. The terminal position, repetitive sequence, and structural complexities of the telomeric DNA make the telomere an inherently difficult region to replicate within the genome. Thus, despite functioning to protect genome stability mammalian telomeres are also a source of replication stress and have been recognized as common fragile sites within the genome. Telomere fragility is exacerbated at telomeres that rely on the Alternative Lengthening of Telomeres (ALT) pathway. Like common fragile sites, ALT telomeres are prone to chromosome breaks and are frequent sites of recombination suggesting that ALT telomeres are subjected to chronic replication stress. Here, we will review the features of telomeric DNA that challenge the replication machinery and also how the cell overcomes these challenges to maintain telomere stability and ensure the faithful duplication of the human genome.
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Affiliation(s)
- Emily Mason-Osann
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Cancer Center, Boston University School of Medicine, Boston, MA, USA
| | - Himabindu Gali
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
- Department of Medicine, Cancer Center, Boston University School of Medicine, Boston, MA, USA
| | - Rachel Litman Flynn
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA.
- Department of Medicine, Cancer Center, Boston University School of Medicine, Boston, MA, USA.
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66
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Zhang X, Zhao B, Yan T, Hao A, Gao Y, Li D, Sui G. G-quadruplex structures at the promoter of HOXC10 regulate its expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2018; 1861:1018-1028. [DOI: 10.1016/j.bbagrm.2018.09.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 09/09/2018] [Accepted: 09/10/2018] [Indexed: 12/16/2022]
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Degan P, Cappelli E, Longobardi M, Pulliero A, Cuccarolo P, Dufour C, Ravera S, Calzia D, Izzotti A. A Global MicroRNA Profile in Fanconi Anemia: A Pilot Study. Metab Syndr Relat Disord 2018; 17:53-59. [PMID: 30376422 DOI: 10.1089/met.2018.0085] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
PURPOSE Fanconi anemia (FA) is a complex tumor-prone disease defined by an entangled genotype and phenotype. Despite enormous efforts in the last 20 years, a comprehensive and integrated view of the disease is still missing. The aim of this pilot study was to establish whether a global microRNA (miRNA) analysis approach could be helpful in defining aspects in FA phenotype, which might deserve future attention with the perspective to develop miRNA-based therapies. METHODS miRNA array were employed to characterize the global miRNA (miRNoma) profile of FA RNA samples with respect to normal samples. RESULTS We report and compare miRNA profile from two FA established cell lines and three FA patients. This analysis reveals that 36 and 64 miRNAs, respectively, are found differentially expressed (>2-fold variation and P < 0.05) in the samples from FA cell lines and FA patients. Overlap of these data results in 24 miRNAs as shared in the two sample populations. Available bioinformatics methods were used to predict target genes for the differentially expressed miRNAs and to perform pathway enrichment analysis. CONCLUSIONS Seven pathway results associated with the FA phenotype. It is interesting to note that some of these pathways were previously unrelated to FA phenotype. It might be important to focus on these pathways not previously emerged as dysfunctional in FA to better define the pathophysiological context of this disease. This is the first report of a global miRNA analysis in FA.
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Affiliation(s)
- Paolo Degan
- 1 Mutagenesis and Preventive Oncology, Ospedale Policlinico San Martino, Genova, Italy
| | | | | | - Alessandra Pulliero
- 3 Department of Health Sciences, School of Medicine, University of Genoa, Genova, Italy
| | - Paola Cuccarolo
- 1 Mutagenesis and Preventive Oncology, Ospedale Policlinico San Martino, Genova, Italy
| | - Carlo Dufour
- 2 Hematology, Istituto Giannina Gaslini, Genova, Italy
| | - Silvia Ravera
- 4 Department of Pharmacy, Biochemistry Laboratory, University of Genova, Genova, Italy
| | - Daniela Calzia
- 4 Department of Pharmacy, Biochemistry Laboratory, University of Genova, Genova, Italy
| | - Alberto Izzotti
- 1 Mutagenesis and Preventive Oncology, Ospedale Policlinico San Martino, Genova, Italy.,3 Department of Health Sciences, School of Medicine, University of Genoa, Genova, Italy
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68
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Yates M, Maréchal A. Ubiquitylation at the Fork: Making and Breaking Chains to Complete DNA Replication. Int J Mol Sci 2018; 19:E2909. [PMID: 30257459 PMCID: PMC6213728 DOI: 10.3390/ijms19102909] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 12/11/2022] Open
Abstract
The complete and accurate replication of the genome is a crucial aspect of cell proliferation that is often perturbed during oncogenesis. Replication stress arising from a variety of obstacles to replication fork progression and processivity is an important contributor to genome destabilization. Accordingly, cells mount a complex response to this stress that allows the stabilization and restart of stalled replication forks and enables the full duplication of the genetic material. This response articulates itself on three important platforms, Replication Protein A/RPA-coated single-stranded DNA, the DNA polymerase processivity clamp PCNA and the FANCD2/I Fanconi Anemia complex. On these platforms, the recruitment, activation and release of a variety of genome maintenance factors is regulated by post-translational modifications including mono- and poly-ubiquitylation. Here, we review recent insights into the control of replication fork stability and restart by the ubiquitin system during replication stress with a particular focus on human cells. We highlight the roles of E3 ubiquitin ligases, ubiquitin readers and deubiquitylases that provide the required flexibility at stalled forks to select the optimal restart pathways and rescue genome stability during stressful conditions.
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Affiliation(s)
- Maïlyn Yates
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada.
| | - Alexandre Maréchal
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada.
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Brázda V, Červeň J, Bartas M, Mikysková N, Coufal J, Pečinka P. The Amino Acid Composition of Quadruplex Binding Proteins Reveals a Shared Motif and Predicts New Potential Quadruplex Interactors. Molecules 2018; 23:E2341. [PMID: 30216987 PMCID: PMC6225207 DOI: 10.3390/molecules23092341] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Revised: 09/09/2018] [Accepted: 09/12/2018] [Indexed: 12/27/2022] Open
Abstract
The importance of local DNA structures in the regulation of basic cellular processes is an emerging field of research. Amongst local non-B DNA structures, G-quadruplexes are perhaps the most well-characterized to date, and their presence has been demonstrated in many genomes, including that of humans. G-quadruplexes are selectively bound by many regulatory proteins. In this paper, we have analyzed the amino acid composition of all seventy-seven described G-quadruplex binding proteins of Homo sapiens. Our comparison with amino acid frequencies in all human proteins and specific protein subsets (e.g., all nucleic acid binding) revealed unique features of quadruplex binding proteins, with prominent enrichment for glycine (G) and arginine (R). Cluster analysis with bootstrap resampling shows similarities and differences in amino acid composition of particular quadruplex binding proteins. Interestingly, we found that all characterized G-quadruplex binding proteins share a 20 amino acid long motif/domain (RGRGR GRGGG SGGSG GRGRG) which is similar to the previously described RG-rich domain (RRGDG RRRGG GGRGQ GGRGR GGGFKG) of the FRM1 G-quadruplex binding protein. Based on this protein fingerprint, we have predicted a new set of potential G-quadruplex binding proteins sharing this interesting domain rich in glycine and arginine residues.
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Affiliation(s)
- Václav Brázda
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Jiří Červeň
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
| | - Martin Bartas
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
| | - Nikol Mikysková
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
| | - Jan Coufal
- Institute of Biophysics, Academy of Sciences of the Czech Republic v.v.i., Královopolská 135, 612 65 Brno, Czech Republic.
| | - Petr Pečinka
- Department of Biology and Ecology/Institute of Environmental Technologies, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic.
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Schwindt E, Paeschke K. Mms1 is an assistant for regulating G-quadruplex DNA structures. Curr Genet 2018; 64:535-540. [PMID: 29098365 PMCID: PMC5948289 DOI: 10.1007/s00294-017-0773-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 10/24/2017] [Accepted: 10/26/2017] [Indexed: 12/25/2022]
Abstract
The preservation of genome stability is fundamental for every cell. Genomic integrity is constantly challenged. Among those challenges are also non-canonical nucleic acid structures. In recent years, scientists became aware of the impact of G-quadruplex (G4) structures on genome stability. It has been shown that folded G4-DNA structures cause changes in the cell, such as transcriptional up/down-regulation, replication stalling, or enhanced genome instability. Multiple helicases have been identified to regulate G4 structures and by this preserve genome stability. Interestingly, although these helicases are mostly ubiquitous expressed, they show specificity for G4 regulation in certain cellular processes (e.g., DNA replication). To this date, it is not clear how this process and target specificity of helicases are achieved. Recently, Mms1, an ubiquitin ligase complex protein, was identified as a novel G4-DNA-binding protein that supports genome stability by aiding Pif1 helicase binding to these regions. In this perspective review, we discuss the question if G4-DNA interacting proteins are fundamental for helicase function and specificity at G4-DNA structures.
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Affiliation(s)
- Eike Schwindt
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV, Groningen, The Netherlands
| | - Katrin Paeschke
- European Research Institute for the Biology of Ageing (ERIBA), University Medical Center Groningen, University of Groningen, 9713 AV, Groningen, The Netherlands.
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71
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Che R, Zhang J, Nepal M, Han B, Fei P. Multifaceted Fanconi Anemia Signaling. Trends Genet 2018; 34:171-183. [PMID: 29254745 PMCID: PMC5858900 DOI: 10.1016/j.tig.2017.11.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/28/2017] [Indexed: 01/26/2023]
Abstract
In 1927 Guido Fanconi described a hereditary condition presenting panmyelopathy accompanied by short stature and hyperpigmentation, now better known as Fanconi anemia (FA). With this discovery the genetic and molecular basis underlying FA has emerged as a field of great interest. FA signaling is crucial in the DNA damage response (DDR) to mediate the repair of damaged DNA. This has attracted a diverse range of investigators, especially those interested in aging and cancer. However, recent evidence suggests FA signaling also regulates functions outside the DDR, with implications for many other frontiers of research. We discuss here the characteristics of FA functions and expand upon current perspectives regarding the genetics of FA, indicating that FA plays a role in a myriad of molecular and cellular processes.
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Affiliation(s)
- Raymond Che
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, USA; Graduate Program of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, USA
| | - Jun Zhang
- Department of Laboratory Medicine and Pathology, Mayo Clinic Foundation, USA
| | - Manoj Nepal
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, USA; Graduate Program of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, USA
| | - Bing Han
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, USA
| | - Peiwen Fei
- University of Hawaii Cancer Center, University of Hawaii, Honolulu, HI, USA; Graduate Program of Molecular Biosciences and Bioengineering, University of Hawaii, Honolulu, HI, USA.
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72
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Chen WF, Rety S, Guo HL, Dai YX, Wu WQ, Liu NN, Auguin D, Liu QW, Hou XM, Dou SX, Xi XG. Molecular Mechanistic Insights into Drosophila DHX36-Mediated G-Quadruplex Unfolding: A Structure-Based Model. Structure 2018; 26:403-415.e4. [PMID: 29429875 DOI: 10.1016/j.str.2018.01.008] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 12/13/2017] [Accepted: 01/12/2018] [Indexed: 11/29/2022]
Abstract
Helicase DHX36 plays essential roles in cell development and differentiation at least partially by resolving G-quadruplex (G4) structures. Here we report crystal structures of the Drosophila homolog of DHX36 (DmDHX36) in complex with RNA and a series of DNAs. By combining structural, small-angle X-ray scattering, molecular dynamics simulation, and single-molecule fluorescence studies, we revealed that positively charged amino acids in RecA2 and OB-like domains constitute an elaborate structural pocket at the nucleic acid entrance, in which negatively charged G4 DNA is tightly bound and partially destabilized. The G4 DNA is then completely unfolded through the 3'-5' translocation activity of the helicase. Furthermore, crystal structures and DNA binding assays show that G-rich DNA is preferentially recognized and in the presence of ATP, specifically bound by DmDHX36, which may cooperatively enhance the G-rich DNA translocation and G4 unfolding. On the basis of these results, a conceptual G4 DNA-resolving mechanism is proposed.
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Affiliation(s)
- Wei-Fei Chen
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Stephane Rety
- Université Lyon, ENS de Lyon, Université Claude Bernard, CNRS UMR 5239, INSERM U1210, LBMC, 46 allée d'Italie Site Jacques Monod, 69007, Lyon, France
| | - Hai-Lei Guo
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang-Xue Dai
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wen-Qiang Wu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Na-Nv Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Daniel Auguin
- Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d'Orléans, UPRES EA 1207, INRA-USC1328, 45067 Orléans, France
| | - Qian-Wen Liu
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shuo-Xing Dou
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China; School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi 712100, China; LBPA, ENS de Cachan, Université Paris-Saclay, Centre National de la Recherche Scientifique, 61 Avenue du Président Wilson, 94235 Cachan, France.
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73
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Belmonte-Reche E, Martínez-García M, Guédin A, Zuffo M, Arévalo-Ruiz M, Doria F, Campos-Salinas J, Maynadier M, López-Rubio JJ, Freccero M, Mergny JL, Pérez-Victoria JM, Morales JC. G-Quadruplex Identification in the Genome of Protozoan Parasites Points to Naphthalene Diimide Ligands as New Antiparasitic Agents. J Med Chem 2018; 61:1231-1240. [PMID: 29323491 PMCID: PMC6148440 DOI: 10.1021/acs.jmedchem.7b01672] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
![]()
G-quadruplexes
(G4) are DNA secondary structures that take part
in the regulation of gene expression. Putative G4 forming sequences
(PQS) have been reported in mammals, yeast, bacteria, and viruses.
Here, we present PQS searches on the genomes of T. brucei,
L. major, and P. falciparum. We found telomeric
sequences and new PQS motifs. Biophysical experiments showed that
EBR1, a 29 nucleotide long highly repeated PQS in T. brucei, forms a stable G4 structure. G4 ligands based on carbohydrate conjugated
naphthalene diimides (carb-NDIs) that bind G4’s including hTel
could bind EBR1 with selectivity versus dsDNA. These ligands showed
important antiparasitic activity. IC50 values were in the
nanomolar range against T. brucei with high selectivity
against MRC-5 human cells. Confocal microscopy confirmed these ligands
localize in the nucleus and kinetoplast of T. brucei suggesting they can reach their potential G4 targets. Cytotoxicity
and zebrafish toxicity studies revealed sugar conjugation reduces
intrinsic toxicity of NDIs.
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Affiliation(s)
- Efres Belmonte-Reche
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC , PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - Marta Martínez-García
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC , PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - Aurore Guédin
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, Institut Européen de Chimie Biologie (IECB), 2 Rue Robert Escarpit, 33607 Pessac, France
| | - Michela Zuffo
- Department of Chemistry, University of Pavia , Via Taramelli 10, 27100 Pavia, Italy
| | - Matilde Arévalo-Ruiz
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC , PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - Filippo Doria
- Department of Chemistry, University of Pavia , Via Taramelli 10, 27100 Pavia, Italy
| | - Jenny Campos-Salinas
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC , PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - Marjorie Maynadier
- Dynamique des Interactions Membranaires Normales et Pathologiques, CNRS UMR 5235, Université de Montpellier, 34095 Montpellier, France
| | - José Juan López-Rubio
- CNRS, 5290, IRD 224, University of Montpellier (UMR "MiVEGEC"), INSERM, 34394 Montpellier, France
| | - Mauro Freccero
- Department of Chemistry, University of Pavia , Via Taramelli 10, 27100 Pavia, Italy
| | - Jean-Louis Mergny
- ARNA Laboratory, Université de Bordeaux, Inserm U1212, CNRS UMR5320, Institut Européen de Chimie Biologie (IECB), 2 Rue Robert Escarpit, 33607 Pessac, France.,Institute of Biophysics , AS CR, v.v.i. Kralovopolska 135, 612 65 Brno, Czech Republic
| | - José María Pérez-Victoria
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC , PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
| | - Juan Carlos Morales
- Department of Biochemistry and Molecular Pharmacology, Instituto de Parasitología y Biomedicina, CSIC , PTS Granada, Avda. del Conocimiento, 17, 18016 Armilla, Granada, Spain
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74
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van Wietmarschen N, Merzouk S, Halsema N, Spierings DCJ, Guryev V, Lansdorp PM. BLM helicase suppresses recombination at G-quadruplex motifs in transcribed genes. Nat Commun 2018; 9:271. [PMID: 29348659 PMCID: PMC5773480 DOI: 10.1038/s41467-017-02760-1] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/21/2017] [Indexed: 11/16/2022] Open
Abstract
Bloom syndrome is a cancer predisposition disorder caused by mutations in the BLM helicase gene. Cells from persons with Bloom syndrome exhibit striking genomic instability characterized by excessive sister chromatid exchange events (SCEs). We applied single-cell DNA template strand sequencing (Strand-seq) to map the genomic locations of SCEs. Our results show that in the absence of BLM, SCEs in human and murine cells do not occur randomly throughout the genome but are strikingly enriched at coding regions, specifically at sites of guanine quadruplex (G4) motifs in transcribed genes. We propose that BLM protects against genome instability by suppressing recombination at sites of G4 structures, particularly in transcribed regions of the genome. Bloom syndrome is characterized by high levels of sister chromatid exchanges (SCEs). Here, the authors use single-cell DNA template strand-sequencing to map SCEs in patient cells, and propose that the BLM helicase protects the genome against unwanted recombination at sites of G-quadruplex structures.
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Affiliation(s)
- Niek van Wietmarschen
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Sarra Merzouk
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Nancy Halsema
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Diana C J Spierings
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Victor Guryev
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Peter M Lansdorp
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands. .,Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, V5Z 1L3, Canada. .,Department of Medical Genetics, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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75
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RecQ and Fe-S helicases have unique roles in DNA metabolism dictated by their unwinding directionality, substrate specificity, and protein interactions. Biochem Soc Trans 2017; 46:77-95. [PMID: 29273621 DOI: 10.1042/bst20170044] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 11/15/2017] [Accepted: 11/17/2017] [Indexed: 12/11/2022]
Abstract
Helicases are molecular motors that play central roles in nucleic acid metabolism. Mutations in genes encoding DNA helicases of the RecQ and iron-sulfur (Fe-S) helicase families are linked to hereditary disorders characterized by chromosomal instabilities, highlighting the importance of these enzymes. Moreover, mono-allelic RecQ and Fe-S helicase mutations are associated with a broad spectrum of cancers. This review will discuss and contrast the specialized molecular functions and biological roles of RecQ and Fe-S helicases in DNA repair, the replication stress response, and the regulation of gene expression, laying a foundation for continued research in these important areas of study.
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76
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Poulet-Benedetti J, Valton AL, Prioleau MN. [G-quadruplex: key controllers of human genome duplication]. Med Sci (Paris) 2017; 33:1063-1070. [PMID: 29261494 DOI: 10.1051/medsci/20173312013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The correct duplication of the human genome is under the control of a spatiotemporal program that determines where and when replication forks start. This regulation thus mainly operates on replication start sites named replication origins. During the S-phase, about 50 000 origins fire in one human cell. However, the normal or perturbed progression of replication forks also strongly impacts on replication. Recently, several studies have put forward the role of a noncanonical DNA structure, the G-quadruplex, in the control of genome duplication. In this review, we describe the major impact of this structure on starting points and on the progression of replication forks.
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Affiliation(s)
- Jérémy Poulet-Benedetti
- Institut Jacques Monod, CNRS UMR7592, université Paris Diderot, Équipe labellisée ARC (Association pour la recherche sur le cancer), 75013 Paris, France
| | - Anne-Laure Valton
- Howard Hughes Medical Institute, Program in systems biology, Department of biochemistry and molecular pharmacology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605-0103, États-Unis
| | - Marie-Noëlle Prioleau
- Institut Jacques Monod, CNRS UMR7592, université Paris Diderot, Équipe labellisée ARC (Association pour la recherche sur le cancer), 75013 Paris, France
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77
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Javadekar SM, Yadav R, Raghavan SC. DNA structural basis for fragility at peak III of BCL2 major breakpoint region associated with t(14;18) translocation. Biochim Biophys Acta Gen Subj 2017; 1862:649-659. [PMID: 29246583 DOI: 10.1016/j.bbagen.2017.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 11/23/2017] [Accepted: 12/07/2017] [Indexed: 12/23/2022]
Abstract
Maintaining genome integrity is crucial for normal cellular functions. DNA double-strand breaks (DSBs), when unrepaired, can potentiate chromosomal translocations. t(14;18) translocation involving BCL2 gene on chromosome 18 and IgH loci at chromosome 14, could lead to follicular lymphoma. Molecular basis for fragility of translocation breakpoint regions is an active area of investigation. Previously, formation of non-B DNA structures like G-quadruplex, triplex, B/A transition were investigated at peak I of BCL2 major breakpoint region (MBR); however, it is less understood at peak III. In vitro gel shift assays show faster mobility for MBR peak III sequences, unlike controls. CD studies of peak III sequences reveal a spectral pattern different from B-DNA. Although complementary C-rich stretches exhibit single-strandedness, corresponding guanine-rich sequences do not show DMS protection, ruling out G-quadruplex and triplex DNA. Extrachromosomal assay indicates that peak III halts transcription, unlike its mutated version. Taken together, multiple lines of evidence suggest formation of potential cruciform DNA structure at MBR peak III, which was also supported by in silico studies. Thus, our study reveals formation of non-B DNA structure which could be a basis for fragility at BCL2 breakpoint regions, eventually leading to chromosomal translocations.
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Affiliation(s)
- Saniya M Javadekar
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Rakhee Yadav
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India.
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78
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G-quadruplex structure at intron 2 of TFE3 and its role in Xp11.2 translocation and splicing. Biochim Biophys Acta Gen Subj 2017; 1862:630-636. [PMID: 29138008 DOI: 10.1016/j.bbagen.2017.11.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2017] [Revised: 10/16/2017] [Accepted: 11/10/2017] [Indexed: 12/19/2022]
Abstract
Transcription Factor E3 (TFE3) translocation is found in a group of different type of cancers and most of the translocations are located in the 5' region of TFE3 which may be considered as Breakpoint Region (BR). In our In silico study by QGRS mapper and non BdB web servers we found a Potential G-quadruplex forming Sequence (PQS) in the intron 2 of TFE3 gene. In vitro G-quadruplex formation was shown by native PAGE in presence of Pyridostatin(PDS), which with inter molecular secondary structure caused reduced mobility to migrate slower. G-quadruplex formation was mapped at single base resolution by Sanger sequencing and Circular Dichroism showed the formation of parallel G-quadruplex. FRET analysis revealed increased and decreased formation of G-quadruplex in presence of PDS and antisense oligonucleotide respectively. PCR stop assay, transcriptional and translational inhibition by PQS showed stable G-quadruplex formation affecting the biological processes. TFE3 minigene splicing study showed the involvement of this G-quadruplex in TFE3 splicing too. Therefore, G-quadruplex is evident to be the reason behind TFE3 induced oncogenesis executed by translocation and also involved in the mRNA splicing.
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79
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Escherichia coli and Neisseria gonorrhoeae UvrD helicase unwinds G4 DNA structures. Biochem J 2017; 474:3579-3597. [PMID: 28916651 DOI: 10.1042/bcj20170587] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 11/17/2022]
Abstract
G-quadruplex (G4) secondary structures have been implicated in various biological processes, including gene expression, DNA replication and telomere maintenance. However, unresolved G4 structures impede replication progression which can lead to the generation of DNA double-strand breaks and genome instability. Helicases have been shown to resolve G4 structures to facilitate faithful duplication of the genome. Escherichia coli UvrD (EcUvrD) helicase plays a crucial role in nucleotide excision repair, mismatch repair and in the regulation of homologous recombination. Here, we demonstrate a novel role of E. coli and Neisseria gonorrhoeae UvrD in resolving G4 tetraplexes. EcUvrD and Ngonorrhoeae UvrD were proficient in unwinding previously characterized tetramolecular G4 structures. Notably, EcUvrD was equally efficient in resolving tetramolecular and bimolecular G4 DNA that were derived from the potential G4-forming sequences from the genome of E. coli Interestingly, in addition to resolving intermolecular G4 structures, EcUvrD was robust in unwinding intramolecular G4 structures. These data for the first time provide evidence for the role of UvrD in the resolution of G4 structures, which has implications for the in vivo role of UvrD helicase in G4 DNA resolution and genome maintenance.
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80
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Nath S, Somyajit K, Mishra A, Scully R, Nagaraju G. FANCJ helicase controls the balance between short- and long-tract gene conversions between sister chromatids. Nucleic Acids Res 2017; 45:8886-8900. [PMID: 28911102 PMCID: PMC5587752 DOI: 10.1093/nar/gkx586] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 06/28/2017] [Indexed: 01/01/2023] Open
Abstract
The FANCJ DNA helicase is linked to hereditary breast and ovarian cancers as well as bone marrow failure disorder Fanconi anemia (FA). Although FANCJ has been implicated in the repair of DNA double-strand breaks (DSBs) by homologous recombination (HR), the molecular mechanism underlying the tumor suppressor functions of FANCJ remains obscure. Here, we demonstrate that FANCJ deficient human and hamster cells exhibit reduction in the overall gene conversions in response to a site-specific chromosomal DSB induced by I-SceI endonuclease. Strikingly, the gene conversion events were biased in favour of long-tract gene conversions in FANCJ depleted cells. The fine regulation of short- (STGC) and long-tract gene conversions (LTGC) by FANCJ was dependent on its interaction with BRCA1 tumor suppressor. Notably, helicase activity of FANCJ was essential for controlling the overall HR and in terminating the extended repair synthesis during sister chromatid recombination (SCR). Moreover, cells expressing FANCJ pathological mutants exhibited defective SCR with an increased frequency of LTGC. These data unravel the novel function of FANCJ helicase in regulating SCR and SCR associated gene amplification/duplications and imply that these functions of FANCJ are crucial for the genome maintenance and tumor suppression.
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Affiliation(s)
- Sarmi Nath
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Kumar Somyajit
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Anup Mishra
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Ralph Scully
- Beth Israel Deaconess Medical Center and Harvard Medical School, 330 Brookline Avenue, Boston, MA, USA
| | - Ganesh Nagaraju
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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81
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G-quadruplex unwinding helicases and their function in vivo. Biochem Soc Trans 2017; 45:1173-1182. [DOI: 10.1042/bst20170097] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 07/31/2017] [Accepted: 08/10/2017] [Indexed: 12/21/2022]
Abstract
The concept that G-quadruplex (G4) structures can form within DNA or RNA in vitro has been long known and extensively discussed. In recent years, accumulating evidences imply that G-quadruplex structures form in vivo. Initially, inefficient regulation of G-quadruplex structures was mainly associated with genome instability. However, due to the location of G-quadruplex motifs and their evolutionary conservation, different cellular functions of these structures have been postulated (e.g. in telomere maintenance, DNA replication, transcription, and translation). Regardless of their function, efficient and controlled formation and unwinding are very important, because ‘mis’-regulated G-quadruplex structures are detrimental for a given process, causing genome instability and diseases. Several helicases have been shown to target and regulate specific G-quadruplex structures. This mini-review focuses on the biological consequences of G4 disruption by different helicases in vivo.
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82
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The impact of replication stress on replication dynamics and DNA damage in vertebrate cells. Nat Rev Genet 2017; 18:535-550. [DOI: 10.1038/nrg.2017.46] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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83
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Reinhart M, Cardoso MC. A journey through the microscopic ages of DNA replication. PROTOPLASMA 2017; 254:1151-1162. [PMID: 27943022 PMCID: PMC5376393 DOI: 10.1007/s00709-016-1058-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 12/01/2016] [Indexed: 06/06/2023]
Abstract
Scientific discoveries and technological advancements are inseparable but not always take place in a coherent chronological manner. In the next, we will provide a seemingly unconnected and serendipitous series of scientific facts that, in the whole, converged to unveil DNA and its duplication. We will not cover here the many and fundamental contributions from microbial genetics and in vitro biochemistry. Rather, in this journey, we will emphasize the interplay between microscopy development culminating on super resolution fluorescence microscopy (i.e., nanoscopy) and digital image analysis and its impact on our understanding of DNA duplication. We will interlace the journey with landmark concepts and experiments that have brought the cellular DNA replication field to its present state.
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Affiliation(s)
- Marius Reinhart
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287, Darmstadt, Germany
| | - M Cristina Cardoso
- Cell Biology and Epigenetics, Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 10, 64287, Darmstadt, Germany.
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84
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Hoogenboom WS, Klein Douwel D, Knipscheer P. Xenopus egg extract: A powerful tool to study genome maintenance mechanisms. Dev Biol 2017; 428:300-309. [PMID: 28427716 DOI: 10.1016/j.ydbio.2017.03.033] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 03/29/2017] [Accepted: 03/29/2017] [Indexed: 01/09/2023]
Abstract
DNA repair pathways are crucial to maintain the integrity of our genome and prevent genetic diseases such as cancer. There are many different types of DNA damage and specific DNA repair mechanisms have evolved to deal with these lesions. In addition to these repair pathways there is an extensive signaling network that regulates processes important for repair, such as cell cycle control and transcription. Despite extensive research, DNA damage repair and signaling are not fully understood. In vitro systems such as the Xenopus egg extract system, have played, and still play, an important role in deciphering the molecular details of these processes. Xenopus laevis egg extracts contain all factors required to efficiently perform DNA repair outside a cell, using mechanisms conserved in humans. These extracts have been used to study several genome maintenance pathways, including mismatch repair, non-homologous end joining, ICL repair, DNA damage checkpoint activation, and replication fork stability. Here we describe how the Xenopus egg extract system, in combination with specifically designed DNA templates, contributed to our detailed understanding of these pathways.
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Affiliation(s)
- Wouter S Hoogenboom
- Hubrecht Institute - KNAW, University Medical Center Utrecht & Cancer GenomiCs Netherlands, The Netherlands
| | - Daisy Klein Douwel
- Hubrecht Institute - KNAW, University Medical Center Utrecht & Cancer GenomiCs Netherlands, The Netherlands
| | - Puck Knipscheer
- Hubrecht Institute - KNAW, University Medical Center Utrecht & Cancer GenomiCs Netherlands, The Netherlands.
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85
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Gadaleta MC, Noguchi E. Regulation of DNA Replication through Natural Impediments in the Eukaryotic Genome. Genes (Basel) 2017; 8:genes8030098. [PMID: 28272375 PMCID: PMC5368702 DOI: 10.3390/genes8030098] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 03/03/2017] [Indexed: 02/07/2023] Open
Abstract
All living organisms need to duplicate their genetic information while protecting it from unwanted mutations, which can lead to genetic disorders and cancer development. Inaccuracies during DNA replication are the major cause of genomic instability, as replication forks are prone to stalling and collapse, resulting in DNA damage. The presence of exogenous DNA damaging agents as well as endogenous difficult-to-replicate DNA regions containing DNA–protein complexes, repetitive DNA, secondary DNA structures, or transcribing RNA polymerases, increases the risk of genomic instability and thus threatens cell survival. Therefore, understanding the cellular mechanisms required to preserve the genetic information during S phase is of paramount importance. In this review, we will discuss our current understanding of how cells cope with these natural impediments in order to prevent DNA damage and genomic instability during DNA replication.
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Affiliation(s)
- Mariana C Gadaleta
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.
| | - Eishi Noguchi
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA.
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86
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Dolinnaya NG, Ogloblina AM, Yakubovskaya MG. Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery. BIOCHEMISTRY (MOSCOW) 2017; 81:1602-1649. [PMID: 28260487 PMCID: PMC7087716 DOI: 10.1134/s0006297916130034] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
G-quadruplexes (G4s), which are known to have important roles in regulation of key biological processes in both normal and pathological cells, are the most actively studied non-canonical structures of nucleic acids. In this review, we summarize the results of studies published in recent years that change significantly scientific views on various aspects of our understanding of quadruplexes. Modern notions on the polymorphism of DNA quadruplexes, on factors affecting thermodynamics and kinetics of G4 folding–unfolding, on structural organization of multiquadruplex systems, and on conformational features of RNA G4s and hybrid DNA–RNA G4s are discussed. Here we report the data on location of G4 sequence motifs in the genomes of eukaryotes, bacteria, and viruses, characterize G4-specific small-molecule ligands and proteins, as well as the mechanisms of their interactions with quadruplexes. New information on the structure and stability of G4s in telomeric DNA and oncogene promoters is discussed as well as proof being provided on the occurrence of G-quadruplexes in cells. Prominence is given to novel experimental techniques (single molecule manipulations, optical and magnetic tweezers, original chemical approaches, G4 detection in situ, in-cell NMR spectroscopy) that facilitate breakthroughs in the investigation of the structure and functions of G-quadruplexes.
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Affiliation(s)
- N G Dolinnaya
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia.
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87
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88
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Maestroni L, Matmati S, Coulon S. Solving the Telomere Replication Problem. Genes (Basel) 2017; 8:genes8020055. [PMID: 28146113 PMCID: PMC5333044 DOI: 10.3390/genes8020055] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 01/23/2017] [Indexed: 12/12/2022] Open
Abstract
Telomeres are complex nucleoprotein structures that protect the extremities of linear chromosomes. Telomere replication is a major challenge because many obstacles to the progression of the replication fork are concentrated at the ends of the chromosomes. This is known as the telomere replication problem. In this article, different and new aspects of telomere replication, that can threaten the integrity of telomeres, will be reviewed. In particular, we will focus on the functions of shelterin and the replisome for the preservation of telomere integrity.
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Affiliation(s)
- Laetitia Maestroni
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labélisée Ligue Contre le Cancer, 13273 Marseille, France.
| | - Samah Matmati
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labélisée Ligue Contre le Cancer, 13273 Marseille, France.
| | - Stéphane Coulon
- Aix Marseille Univ, CNRS, INSERM, Institut Paoli-Calmettes, CRCM, Equipe labélisée Ligue Contre le Cancer, 13273 Marseille, France.
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89
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Gadgil R, Barthelemy J, Lewis T, Leffak M. Replication stalling and DNA microsatellite instability. Biophys Chem 2016; 225:38-48. [PMID: 27914716 DOI: 10.1016/j.bpc.2016.11.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/05/2016] [Accepted: 11/05/2016] [Indexed: 01/08/2023]
Abstract
Microsatellites are short, tandemly repeated DNA motifs of 1-6 nucleotides, also termed simple sequence repeats (SRSs) or short tandem repeats (STRs). Collectively, these repeats comprise approximately 3% of the human genome Subramanian et al. (2003), Lander and Lander (2001) [1,2], and represent a large reservoir of loci highly prone to mutations Sun et al. (2012), Ellegren (2004) [3,4] that contribute to human evolution and disease. Microsatellites are known to stall and reverse replication forks in model systems Pelletier et al. (2003), Samadashwily et al. (1997), Kerrest et al. (2009) [5-7], and are hotspots of chromosomal double strand breaks (DSBs). We briefly review the relationship of these repeated sequences to replication stalling and genome instability, and present recent data on the impact of replication stress on DNA fragility at microsatellites in vivo.
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Affiliation(s)
- R Gadgil
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - J Barthelemy
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - T Lewis
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - M Leffak
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA.
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90
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Valton AL, Prioleau MN. G-Quadruplexes in DNA Replication: A Problem or a Necessity? Trends Genet 2016; 32:697-706. [DOI: 10.1016/j.tig.2016.09.004] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 09/01/2016] [Indexed: 10/21/2022]
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91
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Getting Ready for the Dance: FANCJ Irons Out DNA Wrinkles. Genes (Basel) 2016; 7:genes7070031. [PMID: 27376332 PMCID: PMC4962001 DOI: 10.3390/genes7070031] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 06/13/2016] [Accepted: 06/27/2016] [Indexed: 12/21/2022] Open
Abstract
Mounting evidence indicates that alternate DNA structures, which deviate from normal double helical DNA, form in vivo and influence cellular processes such as replication and transcription. However, our understanding of how the cellular machinery deals with unusual DNA structures such as G-quadruplexes (G4), triplexes, or hairpins is only beginning to emerge. New advances in the field implicate a direct role of the Fanconi Anemia Group J (FANCJ) helicase, which is linked to a hereditary chromosomal instability disorder and important for cancer suppression, in replication past unusual DNA obstacles. This work sets the stage for significant progress in dissecting the molecular mechanisms whereby replication perturbation by abnormal DNA structures leads to genomic instability. In this review, we focus on FANCJ and its role to enable efficient DNA replication when the fork encounters vastly abundant naturally occurring DNA obstacles, which may have implications for targeting rapidly dividing cancer cells.
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92
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Wu CG, Spies M. G-quadruplex recognition and remodeling by the FANCJ helicase. Nucleic Acids Res 2016; 44:8742-8753. [PMID: 27342280 PMCID: PMC5062972 DOI: 10.1093/nar/gkw574] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 06/15/2016] [Indexed: 12/16/2022] Open
Abstract
Guanine rich nucleic acid sequences can form G-quadruplex (G4) structures that interfere with DNA replication, repair and RNA transcription. The human FANCJ helicase contributes to maintaining genomic integrity by promoting DNA replication through G4-forming DNA regions. Here, we combined single-molecule and ensemble biochemical analysis to show that FANCJ possesses a G4-specific recognition site. Through this interaction, FANCJ targets G4-containing DNA where its helicase and G4-binding activities enable repeated rounds of stepwise G4-unfolding and refolding. In contrast to other G4-remodeling enzymes, FANCJ partially stabilizes the G-quadruplex. This would preserve the substrate for the REV1 translesion DNA synthesis polymerase to incorporate cytosine across from a replication-stalling G-quadruplex. The residues responsible for G-quadruplex recognition also participate in interaction with MLH1 mismatch-repair protein, suggesting that the FANCJ activity supporting replication and its participation in DNA interstrand crosslink repair and/or heteroduplex rejection are mutually exclusive. Our findings not only describe the mechanism by which FANCJ recognizes G-quadruplexes and mediates their stepwise unfolding, but also explain how FANCJ chooses between supporting DNA repair versus promoting DNA replication through G-rich sequences.
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Affiliation(s)
- Colin G Wu
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Rd., 4-532 BSB, Iowa City, IA 52242, USA
| | - Maria Spies
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Rd., 4-532 BSB, Iowa City, IA 52242, USA
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93
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Barthelemy J, Hanenberg H, Leffak M. FANCJ is essential to maintain microsatellite structure genome-wide during replication stress. Nucleic Acids Res 2016; 44:6803-16. [PMID: 27179029 PMCID: PMC5001596 DOI: 10.1093/nar/gkw433] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Accepted: 05/06/2016] [Indexed: 12/15/2022] Open
Abstract
Microsatellite DNAs that form non-B structures are implicated in replication fork stalling, DNA double strand breaks (DSBs) and human disease. Fanconi anemia (FA) is an inherited disorder in which mutations in at least nineteen genes are responsible for the phenotypes of genome instability and cancer predisposition. FA pathway proteins are active in the resolution of non-B DNA structures including interstrand crosslinks, G quadruplexes and DNA triplexes. In FANCJ helicase depleted cells, we show that hydroxyurea or aphidicolin treatment leads to loss of microsatellite polymerase chain reaction signals and to chromosome recombination at an ectopic hairpin forming CTG/CAG repeat in the HeLa genome. Moreover, diverse endogenous microsatellite signals were also lost upon replication stress after FANCJ depletion, and in FANCJ null patient cells. The phenotype of microsatellite signal instability is specific for FANCJ apart from the intact FA pathway, and is consistent with DSBs at microsatellites genome-wide in FANCJ depleted cells following replication stress.
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Affiliation(s)
- Joanna Barthelemy
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
| | - Helmut Hanenberg
- Department of Pediatrics III, University Children's Hospital Essen, University of Duisburg-Essen, 45122 Essen, Germany Department of Otorhinolaryngology & Head/Neck Surgery, Heinrich Heine University, 40225 Duesseldorf, Germany
| | - Michael Leffak
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH 45435, USA
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94
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Michl J, Zimmer J, Tarsounas M. Interplay between Fanconi anemia and homologous recombination pathways in genome integrity. EMBO J 2016; 35:909-23. [PMID: 27037238 PMCID: PMC4865030 DOI: 10.15252/embj.201693860] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/02/2016] [Accepted: 03/08/2016] [Indexed: 12/22/2022] Open
Abstract
The Fanconi anemia (FA) pathway plays a central role in the repair of DNA interstrand crosslinks (ICLs) and regulates cellular responses to replication stress. Homologous recombination (HR), the error-free pathway for double-strand break (DSB) repair, is required during physiological cell cycle progression for the repair of replication-associated DNA damage and protection of stalled replication forks. Substantial crosstalk between the two pathways has recently been unravelled, in that key HR proteins such as the RAD51 recombinase and the tumour suppressors BRCA1 and BRCA2 also play important roles in ICL repair. Consistent with this, rare patient mutations in these HR genes cause FA pathologies and have been assigned FA complementation groups. Here, we focus on the clinical and mechanistic implications of the connection between these two cancer susceptibility syndromes and on how these two molecular pathways of DNA replication and repair interact functionally to prevent genomic instability.
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Affiliation(s)
- Johanna Michl
- Genome Stability and Tumourigenesis Group, Department of Oncology, The CRUK-MRC Oxford Institute for Radiation Oncology University of Oxford, Oxford, UK
| | - Jutta Zimmer
- Genome Stability and Tumourigenesis Group, Department of Oncology, The CRUK-MRC Oxford Institute for Radiation Oncology University of Oxford, Oxford, UK
| | - Madalena Tarsounas
- Genome Stability and Tumourigenesis Group, Department of Oncology, The CRUK-MRC Oxford Institute for Radiation Oncology University of Oxford, Oxford, UK
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95
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Mutational analysis of FANCJ helicase. Methods 2016; 108:118-29. [PMID: 27107905 DOI: 10.1016/j.ymeth.2016.04.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 04/15/2016] [Accepted: 04/19/2016] [Indexed: 11/21/2022] Open
Abstract
FANCJ is a superfamily 2 DNA helicase, which also belongs to the iron-sulfur domain containing helicases that include XPD, ChlR1 (DDX11), and RTEL1. Mutations in FANCJ are genetically linked to Fanconi anemia (FA), breast cancer, and ovarian cancer. FANCJ plays a critical role in genome stability and participates in DNA interstrand crosslink and double-strand break repair. Enormous sequence alterations in exons and introns of FANCJ have been identified in patients, including 15 mutations in the coding region which are linked to breast cancer, 12 to FA, and two to ovarian cancer. We and other groups have characterized several FANCJ missense mutations, including M299I, A349P, R251C, and Q255H. As an increasing number of clinically relevant FANCJ mutations are identified, understanding the mechanism whereby FANCJ mutation leads to diseases is critical. Mutational analysis of FANCJ will help us elucidate the pathogenesis and potentially lead to therapeutic strategies by targeting FANCJ.
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96
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Yeom K, Park CJ. Expression, Purification and Characterization of the BLM binding region of human Fanconi Anemia Group J Protein. JOURNAL OF THE KOREAN MAGNETIC RESONANCE SOCIETY 2016. [DOI: 10.6564/jkmrs.2016.20.1.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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97
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Cantor SB, Nayak S. FANCJ at the FORK. Mutat Res 2016; 788:7-11. [PMID: 26926912 DOI: 10.1016/j.mrfmmm.2016.02.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 01/28/2016] [Accepted: 02/10/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Sharon B Cantor
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, UMASS Memorial Cancer Center, Worcester, Massachusetts 01605, USA.
| | - Sumeet Nayak
- Department of Molecular, Cell, and Cancer Biology, University of Massachusetts Medical School, UMASS Memorial Cancer Center, Worcester, Massachusetts 01605, USA
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98
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Abstract
Quadruplex-forming sequences are widely prevalent in human and other genomes, including bacterial ones. These sequences are over-represented in eukaryotic telomeres, promoters, and 5' untranslated regions. They can form quadruplex structures, which may be transient in many situations in normal cells since they can be effectively resolved by helicase action. Mutated helicases in cancer cells are unable to unwind quadruplexes, which are impediments to transcription, translation, or replication, depending on their location within a particular gene. Small molecules that can stabilize quadruplex structures augment these effects and produce cell and proliferation growth inhibition. This article surveys the chemical biology of quadruplexes. It critically examines the major classes of quadruplex-binding small molecules that have been developed to date and the various approaches to discovering selective agents. The challenges of requiring (and achieving) small-molecule targeted selectivity for a particular quadruplex are discussed in relation to the potential of these small molecules as clinically useful therapeutic agents.
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Affiliation(s)
- Stephen Neidle
- UCL School of Pharmacy, University College London , 29-39 Brunswick Square, London WC1N 1AX, U.K
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99
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Mendoza O, Bourdoncle A, Boulé JB, Brosh RM, Mergny JL. G-quadruplexes and helicases. Nucleic Acids Res 2016; 44:1989-2006. [PMID: 26883636 PMCID: PMC4797304 DOI: 10.1093/nar/gkw079] [Citation(s) in RCA: 317] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 02/01/2016] [Indexed: 12/16/2022] Open
Abstract
Guanine-rich DNA strands can fold in vitro into non-canonical DNA structures called G-quadruplexes. These structures may be very stable under physiological conditions. Evidence suggests that G-quadruplex structures may act as ‘knots’ within genomic DNA, and it has been hypothesized that proteins may have evolved to remove these structures. The first indication of how G-quadruplex structures could be unfolded enzymatically came in the late 1990s with reports that some well-known duplex DNA helicases resolved these structures in vitro. Since then, the number of studies reporting G-quadruplex DNA unfolding by helicase enzymes has rapidly increased. The present review aims to present a general overview of the helicase/G-quadruplex field.
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Affiliation(s)
- Oscar Mendoza
- University of Bordeaux, ARNA Laboratory F-33000 Bordeaux, France INSERM U1212,CNRS UMR 5320, IECB, F-33600 Pessac, France
| | - Anne Bourdoncle
- University of Bordeaux, ARNA Laboratory F-33000 Bordeaux, France INSERM U1212,CNRS UMR 5320, IECB, F-33600 Pessac, France
| | - Jean-Baptiste Boulé
- CNRS UMR 7196, INSERM U1154, MNHN, F-75005 Paris, France Sorbonne Universités, F-75005 Paris, France
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Jean-Louis Mergny
- University of Bordeaux, ARNA Laboratory F-33000 Bordeaux, France INSERM U1212,CNRS UMR 5320, IECB, F-33600 Pessac, France
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100
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Booy EP, McRae EKS, Howard R, Deo SR, Ariyo EO, Dzananovic E, Meier M, Stetefeld J, McKenna SA. RNA Helicase Associated with AU-rich Element (RHAU/DHX36) Interacts with the 3'-Tail of the Long Non-coding RNA BC200 (BCYRN1). J Biol Chem 2016; 291:5355-72. [PMID: 26740632 DOI: 10.1074/jbc.m115.711499] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Indexed: 12/14/2022] Open
Abstract
RNA helicase associated with AU-rich element (RHAU) is an ATP-dependent RNA helicase that demonstrates high affinity for quadruplex structures in DNA and RNA. To elucidate the significance of these quadruplex-RHAU interactions, we have performed RNA co-immunoprecipitation screens to identify novel RNAs bound to RHAU and characterize their function. In the course of this study, we have identified the non-coding RNA BC200 (BCYRN1) as specifically enriched upon RHAU immunoprecipitation. Although BC200 does not adopt a quadruplex structure and does not bind the quadruplex-interacting motif of RHAU, it has direct affinity for RHAU in vitro. Specifically designed BC200 truncations and RNase footprinting assays demonstrate that RHAU binds to an adenosine-rich region near the 3'-end of the RNA. RHAU truncations support binding that is dependent upon a region within the C terminus and is specific to RHAU isoform 1. Tests performed to assess whether BC200 interferes with RHAU helicase activity have demonstrated the ability of BC200 to act as an acceptor of unwound quadruplexes via a cytosine-rich region near the 3'-end of the RNA. Furthermore, an interaction between BC200 and the quadruplex-containing telomerase RNA was confirmed by pull-down assays of the endogenous RNAs. This leads to the possibility that RHAU may direct BC200 to bind and exert regulatory functions at quadruplex-containing RNA or DNA sequences.
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Affiliation(s)
| | | | | | | | | | | | | | - Jörg Stetefeld
- From the Departments of Chemistry and Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Sean A McKenna
- From the Departments of Chemistry and Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
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