1
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Cooper SL, Lucius AL, Schneider DA. Quantifying the impact of initial RNA primer length on nucleotide addition by RNA polymerase I. Biophys Chem 2024; 305:107151. [PMID: 38088007 DOI: 10.1016/j.bpc.2023.107151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/30/2023] [Accepted: 12/04/2023] [Indexed: 01/03/2024]
Abstract
Transient state kinetic studies of eukaryotic DNA-dependent RNA polymerases (Pols) in vitro provide quantitative characterization of enzyme activity at the level of individual nucleotide addition events. Previous work revealed heterogeneity in the rate constants governing nucleotide addition by yeast RNA polymerase I (Pol I) for each position on a template DNA. In contrast, the rate constants that described nucleotide addition by yeast RNA polymerase II (Pol II) were more homogeneous. This observation led to the question, what drives the variability of rate constants governing RNA synthesis by Pol I? Are the kinetics of nucleotide addition dictated by the position of the nascent RNA within the polymerase or by the identity of the next encoded nucleotide? In this study, we examine the impact of nucleotide position (i.e. nascent RNA primer length) on the rate constants governing nine sequential nucleotide addition events catalyzed by Pol I. The results reveal a conserved trend in the observed rate constants at each position for all primer lengths used, and highlight that the 9-nucleotide, or 9-mer, RNA primer provides the fastest observed rate constants. These findings suggest that the observed heterogeneity of rate constants for RNA synthesis by Pol I in vitro is driven primarily by the template sequence.
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Affiliation(s)
- Stephanie L Cooper
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Aaron L Lucius
- Department of Chemistry, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
| | - David A Schneider
- Department of Biochemistry and Molecular Genetics, Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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2
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Burlet D, Huber AL, Tissier A, Petrilli V. Crosstalk between inflammasome sensors and DNA damage response pathways. FEBS J 2024. [PMID: 38273453 DOI: 10.1111/febs.17060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/04/2023] [Accepted: 01/10/2024] [Indexed: 01/27/2024]
Abstract
Eukaryotic cells encounter diverse threats jeopardizing their integrity, prompting the development of defense mechanisms against these stressors. Among these mechanisms, inflammasomes are well-known for their roles in coordinating the inflammatory response against infections. Extensive research has unveiled their multifaceted involvement in cellular processes beyond inflammation. Recent studies emphasize the intricate relationship between the inflammasome and the DNA damage response (DDR). They highlight how the DDR participates in inflammasome activation and the reciprocal impact of inflammasome on DDR and genome integrity preservation. Moreover, novel functions of inflammasome sensors in DDR pathways have emerged, broadening our understanding of their roles. Finally, this review delves into identifying common signals that drive the activation of inflammasome sensors alongside activation cues for the DNA damage response, offering potential insights into shared regulatory pathways between these critical cellular processes.
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Affiliation(s)
- Delphine Burlet
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, France
- Université de Lyon, Université Lyon 1, France
- Centre Léon Bérard, Lyon, France
| | - Anne-Laure Huber
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, France
- Université de Lyon, Université Lyon 1, France
- Centre Léon Bérard, Lyon, France
| | - Agnès Tissier
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, France
- Université de Lyon, Université Lyon 1, France
- Centre Léon Bérard, Lyon, France
| | - Virginie Petrilli
- INSERM U1052, Centre de Recherche en Cancérologie de Lyon, France
- CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, France
- Université de Lyon, Université Lyon 1, France
- Centre Léon Bérard, Lyon, France
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3
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Thompson VF, Wieland DR, Mendoza-Leon V, Janis HI, Lay MA, Harrell LM, Schwartz JC. Binding of the nuclear ribonucleoprotein family member FUS to RNA prevents R-loop RNA:DNA hybrid structures. J Biol Chem 2023; 299:105237. [PMID: 37690693 PMCID: PMC10556777 DOI: 10.1016/j.jbc.2023.105237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/17/2023] [Accepted: 08/25/2023] [Indexed: 09/12/2023] Open
Abstract
The protein FUS (FUSed in sarcoma) is a metazoan RNA-binding protein that influences RNA production by all three nuclear polymerases. FUS also binds nascent transcripts, RNA processing factors, RNA polymerases, and transcription machinery. Here, we explored the role of FUS binding interactions for activity during transcription. In vitro run-off transcription assays revealed FUS-enhanced RNA produced by a non-eukaryote polymerase. The activity also reduced the formation of R-loops between RNA products and their DNA template. Analysis by domain mutation and deletion indicated RNA-binding was required for activity. We interpret that FUS binds and sequesters nascent transcripts to prevent R-loops from forming with nearby DNA. DRIP-seq analysis showed that a knockdown of FUS increased R-loop enrichment near expressed genes. Prevention of R-loops by FUS binding to nascent transcripts has the potential to affect transcription by any RNA polymerase, highlighting the broad impact FUS can have on RNA metabolism in cells and disease.
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Affiliation(s)
- Valery F Thompson
- Department of Pharmacology, University of Arizona, Tucson, Arizona, USA; University of Arizona Cancer Center, Tucson, Arizona, USA
| | - Daniel R Wieland
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Vivian Mendoza-Leon
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Helen I Janis
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Michelle A Lay
- Department of Pharmacology, University of Arizona, Tucson, Arizona, USA; University of Arizona Cancer Center, Tucson, Arizona, USA; Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Lucas M Harrell
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, USA
| | - Jacob C Schwartz
- Department of Pharmacology, University of Arizona, Tucson, Arizona, USA; University of Arizona Cancer Center, Tucson, Arizona, USA.
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4
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Gong Y, Liu Y. R-Loops at Chromosome Ends: From Formation, Regulation, and Cellular Consequence. Cancers (Basel) 2023; 15:cancers15072178. [PMID: 37046839 PMCID: PMC10093737 DOI: 10.3390/cancers15072178] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/14/2023] Open
Abstract
Telomeric repeat containing RNA (TERRA) is transcribed from subtelomeric regions to telomeres. TERRA RNA can invade telomeric dsDNA and form telomeric R-loop structures. A growing body of evidence suggests that TERRA-mediated R-loops are critical players in telomere length homeostasis. Here, we will review current knowledge on the regulation of R-loop levels at telomeres. In particular, we will discuss how the central player TERRA and its binding proteins modulate R-loop levels through various mechanisms. We will further provide an overview of the consequences of TERRA-mediated persistent or unscheduled R-loops at telomeres in human ALT cancers and other organisms, with a focus on telomere length regulation after replication interference-induced damage and DNA homologous recombination-mediated repair.
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Affiliation(s)
- Yi Gong
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Yie Liu
- Laboratory of Genetics and Genomics, National Institute on Aging/National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
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5
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Dey A, Prakash J, Das R, Shelar S, Saini A, Cherian S, Patel SC, Hassan PA, Khandekar A, Dasgupta K, Misra HS, Uppal S. Development of a rapid and ultra-sensitive RNA:DNA hybrid immunocapture based biosensor for visual detection of SARS-CoV-2 RNA. PNAS Nexus 2023; 2:pgad031. [PMID: 36909823 PMCID: PMC9998032 DOI: 10.1093/pnasnexus/pgad031] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 12/23/2022] [Accepted: 01/24/2023] [Indexed: 02/04/2023]
Abstract
The Development of reliable and field-compatible detection methods is essential to monitoring and controlling the spread of any global pandemic. We herein report a novel anti-RNA:DNA hybrid (anti-RDH) antibody-based biosensor for visual, colorimetric lateral flow assay, using gold nanoparticles, coupled with transcription-mediated-isothermal-RNA-amplification (TMIRA) for specific and sensitive detection of viral RNA. We have demonstrated its utility for SARS-CoV-2 RNA detection. This technique, which we have named RDH-LFA (anti-RNA:DNA hybrid antibody-based lateral flow assay), exploits anti-RDH antibody for immunocapture of viral RNA hybridized with specific DNA probes in lateral flow assay. This method uses biotinylated-oligonucleotides (DNAB) specific to SARS-CoV-2 RNA (vRNA) to generate a vRNA-DNAB hybrid. The biotin-tagged vRNA-DNAB hybrid molecules bind to streptavidin conjugated with gold nanoparticles. This hybrid complex is trapped by the anti-RDH antibody immobilized on the nitrocellulose membrane resulting in pink color signal leading to visual naked-eye detection in 1 minute. Combining RDH-LFA with isothermal RNA amplification (TMIRA) significantly improves the sensitivity (LOD:10 copies/µl) with a total turnaround time of an hour. More importantly, RDH-LFA coupled with the TMIRA method showed 96.6% sensitivity and 100% specificity for clinical samples when compared to a commercial gold standard reverse-transcription quantitative polymerase-chain-reaction assay. Thus, the present study reports a rapid, sensitive, specific, and simple method for visual detection of viral RNA, which can be used at the point-of-care without requiring sophisticated instrumentation.
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Affiliation(s)
- Anusree Dey
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Jyoti Prakash
- Materials Group, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Rituparna Das
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Sandeep Shelar
- Chemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - Ajay Saini
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Susan Cherian
- Medical Division, Bhabha Atomic Research Centre, Anushakti Nagar, Mumbai, 400094, India
| | - Sofia C Patel
- Medical Division, Bhabha Atomic Research Centre, Anushakti Nagar, Mumbai, 400094, India
| | - Puthusserickal A Hassan
- Chemistry Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Ashwini Khandekar
- Medical Division, Bhabha Atomic Research Centre, Anushakti Nagar, Mumbai, 400094, India
| | - Kinshuk Dasgupta
- Materials Group, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Hari Sharan Misra
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Sheetal Uppal
- Molecular Biology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
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6
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Audoynaud C, Schirmeisen K, Ait Saada A, Gesnik A, Fernández-Varela P, Boucherit V, Ropars V, Chaudhuri A, Fréon K, Charbonnier JB, Lambert SAE. RNA:DNA hybrids from Okazaki fragments contribute to establish the Ku-mediated barrier to replication-fork degradation. Mol Cell 2023:S1097-2765(23)00106-5. [PMID: 36868227 DOI: 10.1016/j.molcel.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/09/2022] [Accepted: 02/04/2023] [Indexed: 03/05/2023]
Abstract
Nonhomologous end-joining (NHEJ) factors act in replication-fork protection, restart, and repair. Here, we identified a mechanism related to RNA:DNA hybrids to establish the NHEJ factor Ku-mediated barrier to nascent strand degradation in fission yeast. RNase H activities promote nascent strand degradation and replication restart, with a prominent role of RNase H2 in processing RNA:DNA hybrids to overcome the Ku barrier to nascent strand degradation. RNase H2 cooperates with the MRN-Ctp1 axis to sustain cell resistance to replication stress in a Ku-dependent manner. Mechanistically, the need of RNaseH2 in nascent strand degradation requires the primase activity that allows establishing the Ku barrier to Exo1, whereas impairing Okazaki fragment maturation reinforces the Ku barrier. Finally, replication stress induces Ku foci in a primase-dependent manner and favors Ku binding to RNA:DNA hybrids. We propose a function for the RNA:DNA hybrid originating from Okazaki fragments in controlling the Ku barrier specifying nuclease requirement to engage fork resection.
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7
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Yang H, Lan L. Immunostaining and Protein Pull-Down of Methyl-5-Cytosine-Marked RNA:DNA Hybrids. Methods Mol Biol 2022; 2528:271-276. [PMID: 35704197 DOI: 10.1007/978-1-0716-2477-7_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
RNA:DNA hybrids not only function in various physiological cellular processes but also represent a threat to genome integrity. The methyl-5-cytosine (m5C) marked RNA:DNA hybrids containing the m5C modified RNA strand add another layer of regulation to the R-loop structure. Here we describe the detection of m5C modifications in the context of RNA:DNA hybrids using immunostaining, and identification of specific binding partners of m5C marked RNA:DNA hybrids using pull-down method.
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Affiliation(s)
- Haibo Yang
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Li Lan
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA, USA.
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
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8
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Achar YJ, Foiani M. Topology of RNA:DNA Hybrids and R-Loops in Yeast. Methods Mol Biol 2022; 2528:317-328. [PMID: 35704201 DOI: 10.1007/978-1-0716-2477-7_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
RNA:DNA hybrids are generated naturally behind the elongating RNA polymerase as a transcriptional intermediate. However, prolonged persistence of these structures challenges the integrity of the genome by creating R-loops and by interfering with DNA replication and other chromatin related processes. Precise mapping and characterization of their distribution across the genome has been a major challenge to understand the genesis of RNA:DNA hybrids and their conversion into genotoxic intermediates. Here we provide the detailed protocol for mapping RNA:DNA hybrid across the Saccharomyces cerevisiae genome.
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Affiliation(s)
- Yathish Jagadheesh Achar
- IFOM (Fondazione Istituto FIRC di Oncologia Molecolare), Milan, Italy.
- Centre for DNA Fingerprinting and Diagnostics, Hyderabad, Telangana, India.
| | - Marco Foiani
- IFOM (Fondazione Istituto FIRC di Oncologia Molecolare), Milan, Italy
- Università degli Studi di Milano, Milan, Italy
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9
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Nair L, Zhang W, Laffleur B, Jha MK, Lim J, Lee H, Wu L, Alvarez NS, Liu ZP, Munteanu EL, Swayne T, Hanna JH, Ding L, Rothschild G, Basu U. Mechanism of noncoding RNA-associated N 6-methyladenosine recognition by an RNA processing complex during IgH DNA recombination. Mol Cell 2021; 81:3949-3964.e7. [PMID: 34450044 PMCID: PMC8571800 DOI: 10.1016/j.molcel.2021.07.037] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 03/04/2021] [Accepted: 07/28/2021] [Indexed: 01/13/2023]
Abstract
Immunoglobulin heavy chain (IgH) locus-associated G-rich long noncoding RNA (SμGLT) is important for physiological and pathological B cell DNA recombination. We demonstrate that the METTL3 enzyme-catalyzed N6-methyladenosine (m6A) RNA modification drives recognition and 3' end processing of SμGLT by the RNA exosome, promoting class switch recombination (CSR) and suppressing chromosomal translocations. The recognition is driven by interaction of the MPP6 adaptor protein with nuclear m6A reader YTHDC1. MPP6 and YTHDC1 promote CSR by recruiting AID and the RNA exosome to actively transcribe SμGLT. Direct suppression of m6A modification of SμGLT or of m6A reader YTHDC1 reduces CSR. Moreover, METTL3, an essential gene for B cell development in the bone marrow and germinal center, suppresses IgH-associated aberrant DNA breaks and prevents genomic instability. Taken together, we propose coordinated and central roles for MPP6, m6A modification, and m6A reader proteins in controlling long noncoding RNA processing, DNA recombination, and development in B cells.
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Affiliation(s)
- Lekha Nair
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Wanwei Zhang
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Brice Laffleur
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Mukesh K Jha
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Junghyun Lim
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Heather Lee
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Department of Rehabilitation and Regenerative Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Lijing Wu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Nehemiah S Alvarez
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, KS 66160, USA
| | - Zhi-Ping Liu
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan 250061, Shandong, China
| | - Emilia L Munteanu
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Theresa Swayne
- Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Jacob H Hanna
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Lei Ding
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA; Department of Rehabilitation and Regenerative Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA
| | - Gerson Rothschild
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
| | - Uttiya Basu
- Department of Microbiology and Immunology, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA.
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10
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Mitchell BP, Hsu RV, Medrano MA, Zewde NT, Narkhede YB, Palermo G. Spontaneous Embedding of DNA Mismatches Within the RNA:DNA Hybrid of CRISPR-Cas9. Front Mol Biosci 2020; 7:39. [PMID: 32258048 PMCID: PMC7093078 DOI: 10.3389/fmolb.2020.00039] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 02/19/2020] [Indexed: 12/15/2022] Open
Abstract
CRISPR-Cas9 is the forefront technology for editing the genome. In this system, the Cas9 protein is programmed with guide RNAs to process DNA sequences that match the guide RNA forming an RNA:DNA hybrid structure. However, the binding of DNA sequences that do not fully match the guide RNA can limit the applicability of CRISPR-Cas9 for genome editing, resulting in the so-called off-target effects. Here, molecular dynamics is used to probe the effect of DNA base pair mismatches within the RNA:DNA hybrid in CRISPR-Cas9. Molecular simulations revealed that the presence of mismatched pairs in the DNA at distal sites with respect to the Protospacer Adjacent Motif (PAM) recognition sequence induces an extended opening of the RNA:DNA hybrid, leading to novel interactions established by the unwound nucleic acids and the protein counterpart. On the contrary, mismatched pairs upstream of the RNA:DNA hybrid are rapidly incorporated within the heteroduplex, with minor effect on the protein-nucleic acid interactions. As a result, mismatched pairs at PAM distal ends interfere with the activation of the catalytic HNH domain, while mismatches fully embedded in the RNA:DNA do not affect the HNH dynamics and enable its activation to cleave the DNA. These findings provide a mechanistic understanding to the intriguing experimental evidence that PAM distal mismatches hamper a proper function of HNH, explaining also why mismatches within the heteroduplex are much more tolerated. This constitutes a step forward in understanding off-target effects in CRISPR-Cas9, which encourages novel structure-based engineering efforts aimed at preventing the onset of off-target effects.
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Affiliation(s)
- Brandon P. Mitchell
- Department of Bioengineering, University of California, Riverside, Riverside, CA, United States
| | - Rohaine V. Hsu
- Department of Bioengineering, University of California, Riverside, Riverside, CA, United States
| | - Marco A. Medrano
- Department of Bioengineering, University of California, Riverside, Riverside, CA, United States
| | - Nehemiah T. Zewde
- Department of Bioengineering, University of California, Riverside, Riverside, CA, United States
| | - Yogesh B. Narkhede
- Department of Bioengineering, University of California, Riverside, Riverside, CA, United States
| | - Giulia Palermo
- Department of Bioengineering, University of California, Riverside, Riverside, CA, United States
- Department of Chemistry, University of California, Riverside, Riverside, CA, United States
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11
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Puget N, Miller KM, Legube G. Non-canonical DNA/RNA structures during Transcription-Coupled Double-Strand Break Repair: Roadblocks or Bona fide repair intermediates? DNA Repair (Amst) 2019; 81:102661. [PMID: 31331819 DOI: 10.1016/j.dnarep.2019.102661] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Although long overlooked, it is now well understood that DNA does not systematically assemble into a canonical double helix, known as B-DNA, throughout the entire genome but can also accommodate other structures including DNA hairpins, G-quadruplexes and RNA:DNA hybrids. Notably, these non-canonical DNA structures form preferentially at transcriptionally active loci. Acting as replication roadblocks and being targeted by multiple machineries, these structures weaken the genome and render it prone to damage, including DNA double-strand breaks (DSB). In addition, secondary structures also further accumulate upon DSB formation. Here we discuss the potential functions of pre-existing or de novo formed nucleic acid structures, as bona fide repair intermediates or repair roadblocks, especially during Transcription-Coupled DNA Double-Strand Break repair (TC-DSBR), and provide an update on the specialized protein complexes displaying the ability to remove these structures to safeguard genome integrity.
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12
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Kumari D, Gazy I, Usdin K. Pharmacological Reactivation of the Silenced FMR1 Gene as a Targeted Therapeutic Approach for Fragile X Syndrome. Brain Sci 2019; 9:brainsci9020039. [PMID: 30759772 PMCID: PMC6406686 DOI: 10.3390/brainsci9020039] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Revised: 02/07/2019] [Accepted: 02/08/2019] [Indexed: 12/22/2022] Open
Abstract
More than ~200 CGG repeats in the 5′ untranslated region of the FMR1 gene results in transcriptional silencing and the absence of the FMR1 encoded protein, FMRP. FMRP is an RNA-binding protein that regulates the transport and translation of a variety of brain mRNAs in an activity-dependent manner. The loss of FMRP causes dysregulation of many neuronal pathways and results in an intellectual disability disorder, fragile X syndrome (FXS). Currently, there is no effective treatment for FXS. In this review, we discuss reactivation of the FMR1 gene as a potential approach for FXS treatment with an emphasis on the use of small molecules to inhibit the pathways important for gene silencing.
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Affiliation(s)
- Daman Kumari
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Inbal Gazy
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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13
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Soslau G. Circular RNA (circRNA) was an important bridge in the switch from the RNA world to the DNA world. J Theor Biol 2018; 447:32-40. [PMID: 29567323 DOI: 10.1016/j.jtbi.2018.03.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 03/10/2018] [Accepted: 03/14/2018] [Indexed: 12/01/2022]
Abstract
The concept that life on Earth began as an RNA world has been built upon extensive experimentation demonstrating that many of the building blocks required for living cells could be synthesized in the laboratory under conditions approximating our primordial world. Many of the building blocks for life have also been found in meteorites indicating that meteors may have been a source for these molecules, or more likely, that they represent the chemical library present in most/all bodies in the universe after the big bang. Perhaps the most important support for the concept comes from the fact that some RNA species possess catalytic activity, ribozymes, and that RNA could be reverse transcribe to DNA. The thrust of numerous papers on this topic has been to explore how the available molecules on Earth, at its birth, gave rise to life as we know it today. This paper focuses more on a reverse view of the topic. The "how" molecular building blocks were synthesized is not addressed nor how the "first" RNA molecules were synthesized. We can clearly speculate on the variable environmental conditions and chemistry available on Earth billions of years ago. However, we can never truly replicate the changing conditions or know the chemical composition of Earth at the beginning of time. We can, however, confirm that over millions, perhaps billions of years the basic building blocks for life accumulated sufficiently to initiate evolution to an RNA world followed by our RNA/DNA world. Here we are attempting to take the information from our current knowledge of biology and by inference and extrapolation work backward to hypothesize biological events in the march forward from RNA to DNA. It is proposed that the primordial replicating RNA cell, the ribocyte, evolved from liposomes encompassing required reactants and products for "life" and that ribonucleopeptide complexes formed membrane pores to support bidirectional ion and molecular transport to maintain biological functions and osmolarity. Circular RNA, circRNA, is proposed as a critical stable RNA molecule that served as the genetic precursor for the switch to DNA and the replication of circRNA by a rolling circle mechanism gave rise to the RNA complexity required for the genetic functions of the cell. The replicating ribocyte would have required protein synthesis as well as RNA replication and a model for non-coded and primordial coded protein synthesis is proposed. Finally, the switch from the RNA to the DNA world would have involved the synthesis of an RNA:DNA hybrid prior to the formation of dsDNA. If the hybrid was a circular molecule that ultimately yielded a circular dsDNA molecule, it could predict that the primordial DNA cell would evolve into a bacterial cell with a single circular chromosome. One would hope that continued speculation of the origin of life will spur new directions of research that may never fully answer the questions of the past but add to our ability to regulate potentially harmful biological events in the present and in the future.
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Affiliation(s)
- Gerald Soslau
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, 245 N 15th ST, Philadelphia, PA 19102, United States.
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Abstract
The division of prokaryotic and eukaryotic cells produces two cells that inherit a perfect copy of the genetic material originally derived from the mother cell. The initiation of canonical DNA replication must be coordinated to the cell cycle to ensure the accuracy of genome duplication. Controlled replication initiation depends on a complex interplay of cis-acting DNA sequences, the so-called origins of replication (ori), with trans-acting factors involved in the onset of DNA synthesis. The interplay of cis-acting elements and trans-acting factors ensures that cells initiate replication at sequence-specific sites only once, and in a timely order, to avoid chromosomal endoreplication. However, chromosome breakage and excessive RNA:DNA hybrid formation can cause break-induced (BIR) or transcription-initiated replication (TIR), respectively. These non-canonical replication events are expected to affect eukaryotic genome function and maintenance, and could be important for genome evolution and disease development. In this review, we describe the difference between canonical and non-canonical DNA replication, and focus on mechanistic differences and common features between BIR and TIR. Finally, we discuss open issues on the factors and molecular mechanisms involved in TIR.
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Affiliation(s)
- Bazilė Ravoitytė
- Nature Research Centre, Akademijos g. 2, LT-08412 Vilnius, Lithuania.
| | - Ralf Erik Wellinger
- CABIMER-Universidad de Sevilla, Avd Americo Vespucio sn, 41092 Sevilla, Spain.
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15
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Nadel J, Athanasiadou R, Lemetre C, Wijetunga NA, Ó Broin P, Sato H, Zhang Z, Jeddeloh J, Montagna C, Golden A, Seoighe C, Greally JM. RNA:DNA hybrids in the human genome have distinctive nucleotide characteristics, chromatin composition, and transcriptional relationships. Epigenetics Chromatin 2015; 8:46. [PMID: 26579211 PMCID: PMC4647656 DOI: 10.1186/s13072-015-0040-6] [Citation(s) in RCA: 114] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 10/29/2015] [Indexed: 01/01/2023] Open
Abstract
Background RNA:DNA hybrids represent a non-canonical nucleic acid structure that has been associated with a range of human diseases and potential transcriptional regulatory functions. Mapping of RNA:DNA hybrids in human cells reveals them to have a number of characteristics that give insights into their functions. Results We find RNA:DNA hybrids to occupy millions of base pairs in the human genome. A directional sequencing approach shows the RNA component of the RNA:DNA hybrid to be purine-rich, indicating a thermodynamic contribution to their in vivo stability. The RNA:DNA hybrids are enriched at loci with decreased DNA methylation and increased DNase hypersensitivity, and within larger domains with characteristics of heterochromatin formation, indicating potential transcriptional regulatory properties. Mass spectrometry studies of chromatin at RNA:DNA hybrids shows the presence of the ILF2 and ILF3 transcription factors, supporting a model of certain transcription factors binding preferentially to the RNA:DNA conformation. Conclusions Overall, there is little to indicate a dependence for RNA:DNA hybrids forming co-transcriptionally, with results from the ribosomal DNA repeat unit instead supporting the intriguing model of RNA generating these structures intrans. The results of the study indicate heterogeneous functions of these genomic elements and new insights into their formation and stability in vivo. Electronic supplementary material The online version of this article (doi:10.1186/s13072-015-0040-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julie Nadel
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Rodoniki Athanasiadou
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA ; Department of Biology, Center for Genomics and Systems Biology, New York University, 12 Waverly Place, New York, NY 10003 USA
| | - Christophe Lemetre
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA ; Integrated Genomics Operation, Memorial Sloan-Kettering Cancer Center, New York, NY 10065 USA
| | - N Ari Wijetunga
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Pilib Ó Broin
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Hanae Sato
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Zhengdong Zhang
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | | | - Cristina Montagna
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Aaron Golden
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA
| | - Cathal Seoighe
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland Galway, Galway, Ireland
| | - John M Greally
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY 10461 USA ; Department of Genetics, Center for Epigenomics and Division of Computational Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461 USA
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16
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Zhang ZZ, Pannunzio NR, Lu Z, Hsu E, Yu K, Lieber MR. The repetitive portion of the Xenopus IgH Mu switch region mediates orientation-dependent class switch recombination. Mol Immunol 2015; 67:524-31. [PMID: 26277278 DOI: 10.1016/j.molimm.2015.07.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Revised: 07/29/2015] [Accepted: 07/30/2015] [Indexed: 11/26/2022]
Abstract
Vertebrates developed immunoglobulin heavy chain (IgH) class switch recombination (CSR) to express different IgH constant regions. Most double-strand breaks for Ig CSR occur within the repetitive portion of the switch regions located upstream of each set of constant domain exons for the Igγ, Igα or Igϵ heavy chain. Unlike mammalian switch regions, Xenopus switch regions do not have a high G-density on the non-template DNA strand. In previous studies, when Xenopus Sμ DNA was moved to the genome of mice, it is able to support substantial CSR when it is used to replace the murine Sγ1 region. Here, we tested both the 2kb repetitive portion and the 4.6 kb full-length portions of the Xenopus Sμ in both their natural (forward) orientation relative to the constant domain exons, as well as the opposite (reverse) orientation. Consistent with previous work, we find that the 4.6 kb full-length Sμ mediates similar levels of CSR in both the forward and reverse orientations. Whereas, the forward orientation of the 2kb portion can restore the majority of the CSR level of the 4.6 kb full-length Sμ, the reverse orientation poorly supports R-looping and no CSR. The forward orientation of the 2kb repetitive portion has more GG dinucleotides on the non-template strand than the reverse orientation. The correlation of R-loop formation with CSR efficiency, as demonstrated in the 2kb repetitive fragment of the Xenopus switch region, confirms a role played by R-looping in CSR that appears to be conserved through evolution.
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Affiliation(s)
- Zheng Z Zhang
- USC Norris Comprehensive Cancer Ctr. Molecular and Computational Biology Program, Department of Biological Sciences, Departments of Pathology, Biochemistry & Molecular Biology, Molecular Microbiology & Immunology, Urology, University of Southern California Keck School of Medicine, 1441 Eastlake Ave., Rm, 5428, Los Angeles, CA 90089-9176, United States
| | - Nicholas R Pannunzio
- USC Norris Comprehensive Cancer Ctr. Molecular and Computational Biology Program, Department of Biological Sciences, Departments of Pathology, Biochemistry & Molecular Biology, Molecular Microbiology & Immunology, Urology, University of Southern California Keck School of Medicine, 1441 Eastlake Ave., Rm, 5428, Los Angeles, CA 90089-9176, United States
| | - Zhengfei Lu
- USC Norris Comprehensive Cancer Ctr. Molecular and Computational Biology Program, Department of Biological Sciences, Departments of Pathology, Biochemistry & Molecular Biology, Molecular Microbiology & Immunology, Urology, University of Southern California Keck School of Medicine, 1441 Eastlake Ave., Rm, 5428, Los Angeles, CA 90089-9176, United States
| | - Ellen Hsu
- Department of Physiology and Pharmacology, State University of New York Downstate Medical Center, New York, NY 11203, United States
| | - Kefei Yu
- Department of Microbiology and Molecular Genetics, Michigan State University, 5175 Biomedical Physical Sciences, East Lansing, MI 48824, United States
| | - Michael R Lieber
- USC Norris Comprehensive Cancer Ctr. Molecular and Computational Biology Program, Department of Biological Sciences, Departments of Pathology, Biochemistry & Molecular Biology, Molecular Microbiology & Immunology, Urology, University of Southern California Keck School of Medicine, 1441 Eastlake Ave., Rm, 5428, Los Angeles, CA 90089-9176, United States
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17
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Molodtsov V, Anikin M, McAllister WT. The presence of an RNA:DNA hybrid that is prone to slippage promotes termination by T7 RNA polymerase. J Mol Biol 2014; 426:3095-3107. [PMID: 24976131 DOI: 10.1016/j.jmb.2014.06.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Revised: 06/20/2014] [Accepted: 06/23/2014] [Indexed: 11/17/2022]
Abstract
Intrinsic termination signals for multisubunit bacterial RNA polymerases (RNAPs) encode a GC-rich stem-loop structure followed by a polyuridine [poly(U)] tract, and it has been proposed that steric clash of the stem-loop with the exit pore of the RNAP imposes a shearing force on the RNA in the downstream RNA:DNA hybrid, resulting in misalignment of the active site. The structurally unrelated T7 RNAP terminates at a similar type of signal (TΦ), suggesting a common mechanism for termination. In the absence of a hairpin (passive conditions), T7 RNAP slips efficiently in both homopolymeric A and U tracts, and we have found that replacement of the U tract in TΦ with a slippage-prone A tract still allows efficient termination. Under passive conditions, incorporation of a single G residue following a poly(U) tract (which is the situation during termination at TΦ) results in a "locked" complex that is unable to extend the transcript. Our results support a model in which transmission of the shearing force generated by steric clash of the hairpin with the exit pore is promoted by the presence of a slippery tracts downstream, resulting in alterations in the active site and the formation of a locked complex that represents an early step in the termination pathway.
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Affiliation(s)
- Vadim Molodtsov
- Graduate Program in Cell and Molecular Biology, Rowan University School of Osteopathic Medicine, 42 East Laurel Road, UDP 2200, Stratford, NJ 08084, USA; Department of Cell Biology, Rowan University School of Osteopathic Medicine, 42 East Laurel Road, UDP 2200, Stratford, NJ 08084, USA
| | - Michael Anikin
- Department of Cell Biology, Rowan University School of Osteopathic Medicine, 42 East Laurel Road, UDP 2200, Stratford, NJ 08084, USA
| | - William T McAllister
- Department of Cell Biology, Rowan University School of Osteopathic Medicine, 42 East Laurel Road, UDP 2200, Stratford, NJ 08084, USA.
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