1
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Gonzales LR, Blom S, Henriques R, Bachem CWB, Immink RGH. LncRNAs: the art of being influential without protein. TRENDS IN PLANT SCIENCE 2024; 29:770-785. [PMID: 38368122 DOI: 10.1016/j.tplants.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 01/15/2024] [Accepted: 01/23/2024] [Indexed: 02/19/2024]
Abstract
The plant long noncoding (lnc)RNA field is on the brink of transitioning from large-scale identification of lncRNAs to their functional characterization. Due to the cross-kingdom conservation of interaction types and molecular functions, there is much to be learned from mammalian lncRNA research. Here, we discuss the different molecular processes involving lncRNAs from the regulation of chromatin to splicing. Furthermore, we discuss the lncRNA interactome, which includes proteins, other RNAs, and DNA. We explore and discuss how mammalian lncRNA functionalities could be reflected in similar pathways in plants and hypothesize that several breakthroughs in mammalian research could lead to the discovery of novel plant lncRNA molecular functions. Expanding our knowledge of the biological role of lncRNAs and their multiple applications paves the way for future agricultural applications.
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Affiliation(s)
| | - Suze Blom
- Laboratory of Molecular Biology, Wageningen University and Research, Wageningen, The Netherlands; Bioscience, Wageningen University and Research, Wageningen, The Netherlands
| | - Rossana Henriques
- School of Biological, Earth, and Environmental Sciences, University College Cork, Cork, Ireland; Environmental Research Institute, University College Cork, Cork, Ireland
| | - Christian W B Bachem
- Plant Breeding, Wageningen University and Research, Wageningen, The Netherlands.
| | - Richard G H Immink
- Laboratory of Molecular Biology, Wageningen University and Research, Wageningen, The Netherlands; Bioscience, Wageningen University and Research, Wageningen, The Netherlands.
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2
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Leisegang MS, Warwick T, Stötzel J, Brandes RP. RNA-DNA triplexes: molecular mechanisms and functional relevance. Trends Biochem Sci 2024; 49:532-544. [PMID: 38582689 DOI: 10.1016/j.tibs.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/05/2024] [Accepted: 03/18/2024] [Indexed: 04/08/2024]
Abstract
Interactions of RNA with DNA are principles of gene expression control that have recently gained considerable attention. Among RNA-DNA interactions are R-loops and RNA-DNA hybrid G-quadruplexes, as well as RNA-DNA triplexes. It is proposed that RNA-DNA triplexes guide RNA-associated regulatory proteins to specific genomic locations, influencing transcription and epigenetic decision making. Although triplex formation initially was considered solely an in vitro event, recent progress in computational, biochemical, and biophysical methods support in vivo functionality with relevance for gene expression control. Here, we review the central methodology and biology of triplexes, outline paradigms required for triplex function, and provide examples of physiologically important triplex-forming long non-coding RNAs.
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Affiliation(s)
- Matthias S Leisegang
- Institute for Cardiovascular Physiology, Goethe University Frankfurt, Frankfurt, Germany; German Centre of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany.
| | - Timothy Warwick
- Institute for Cardiovascular Physiology, Goethe University Frankfurt, Frankfurt, Germany; German Centre of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Julia Stötzel
- Institute for Cardiovascular Physiology, Goethe University Frankfurt, Frankfurt, Germany; German Centre of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Goethe University Frankfurt, Frankfurt, Germany; German Centre of Cardiovascular Research (DZHK), Partner site RheinMain, Frankfurt, Germany
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3
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Krause NM, Bains JK, Blechar J, Richter C, Bessi I, Grote P, Leisegang MS, Brandes RP, Schwalbe H. Biophysical Investigation of RNA ⋅ DNA : DNA Triple Helix and RNA : DNA Heteroduplex Formation by the lncRNAs MEG3 and Fendrr. Chembiochem 2024; 25:e202400049. [PMID: 38456652 DOI: 10.1002/cbic.202400049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/09/2024]
Abstract
Long non-coding RNAs (lncRNAs) are important regulators of gene expression and can associate with DNA as RNA : DNA heteroduplexes or RNA ⋅ DNA : DNA triple helix structures. Here, we review in vitro biochemical and biophysical experiments including electromobility shift assays (EMSA), circular dichroism (CD) spectroscopy, thermal melting analysis, microscale thermophoresis (MST), single-molecule Förster resonance energy transfer (smFRET) and nuclear magnetic resonance (NMR) spectroscopy to investigate RNA ⋅ DNA : DNA triple helix and RNA : DNA heteroduplex formation. We present the investigations of the antiparallel triplex-forming lncRNA MEG3 targeting the gene TGFB2 and the parallel triplex-forming lncRNA Fendrr with its target gene Emp2. The thermodynamic properties of these oligonucleotides lead to concentration-dependent heterogeneous mixtures, where a DNA duplex, an RNA : DNA heteroduplex and an RNA ⋅ DNA : DNA triplex coexist and their relative populations are modulated in a temperature-dependent manner. The in vitro data provide a reliable readout of triplex structures, as RNA ⋅ DNA : DNA triplexes show distinct features compared to DNA duplexes and RNA : DNA heteroduplexes. Our experimental results can be used to validate computationally predicted triple helix formation between novel disease-relevant lncRNAs and their DNA target genes.
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Affiliation(s)
- Nina M Krause
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße7, 60438, Frankfurt am Main, Germany
| | - Jasleen K Bains
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße7, 60438, Frankfurt am Main, Germany
| | - Julius Blechar
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße7, 60438, Frankfurt am Main, Germany
| | - Christian Richter
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße7, 60438, Frankfurt am Main, Germany
| | - Irene Bessi
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße7, 60438, Frankfurt am Main, Germany
- Institute for Organic Chemistry, Julius-Maximilians-University, Würzburg, Bavaria, 97074, Germany
| | - Phillip Grote
- Institute of Cardiovascular Regeneration, Centre for Molecular Medicine, Frankfurt am Main, Hesse, 60590, Germany
- Georg-Speyer-Haus, Frankfurt am Main, Hesse, 60590, Germany
| | - Matthias S Leisegang
- Institute for Cardiovascular Physiology, Johann Wolfgang Goethe University, Frankfurt, Hesse, 60596, Germany
- German Centre of Cardiovascular Research (DZHK), Partner site Rhine-Main, Frankfurt, Hesse, 60596, Germany
| | - Ralf P Brandes
- Institute for Cardiovascular Physiology, Johann Wolfgang Goethe University, Frankfurt, Hesse, 60596, Germany
- German Centre of Cardiovascular Research (DZHK), Partner site Rhine-Main, Frankfurt, Hesse, 60596, Germany
| | - Harald Schwalbe
- Center for Biomolecular Magnetic Resonance, Institute for Organic Chemistry and Chemical Biology, Johann Wolfgang Goethe University, Max-von-Laue-Straße7, 60438, Frankfurt am Main, Germany
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4
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Lei Y, Li C, Ji X, Sun H, Liu X, Mao Z, Chen W, Qing Z, Liu J. Lowering Entropic Barriers in Triplex DNA Switches Facilitating Biomedical Applications at Physiological pH. Angew Chem Int Ed Engl 2024; 63:e202402123. [PMID: 38453654 DOI: 10.1002/anie.202402123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/29/2024] [Accepted: 03/07/2024] [Indexed: 03/09/2024]
Abstract
Triplex DNA switches are attractive allosteric tools for engineering smart nanodevices, but their poor triplex-forming capacity at physiological conditions limited the practical applications. To address this challenge, we proposed a low-entropy barrier design to facilitate triplex formation by introducing a hairpin duplex linker into the triplex motif, and the resulting triplex switch was termed as CTNSds. Compared to the conventional clamp-like triplex switch, CTNSds increased the triplex-forming ratio from 30 % to 91 % at pH 7.4 and stabilized the triple-helix structure in FBS and cell lysate. CTNSds was also less sensitive to free-energy disturbances, such as lengthening linkers or mismatches in the triple-helix stem. The CTNSds design was utilized to reversibly isolate CTCs from whole blood, achieving high capture efficiencies (>86 %) at pH 7.4 and release efficiencies (>80 %) at pH 8.0. Our approach broadens the potential applications of DNA switches-based switchable nanodevices, showing great promise in biosensing and biomedicine.
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Affiliation(s)
- Yanli Lei
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food and Bioengineering, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Chuangchuang Li
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food and Bioengineering, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Xinyue Ji
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food and Bioengineering, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Haiyan Sun
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food and Bioengineering, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Xiaowen Liu
- Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, 410083, China
| | - Zenghui Mao
- Changsha Hospital for Maternal and Child Health Care Affiliated to Hunan Normal University, Changsha, 410083, China
| | - Weiju Chen
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food and Bioengineering, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Zhihe Qing
- Hunan Provincial Key Laboratory of Cytochemistry, School of Food and Bioengineering, School of Chemistry and Chemical Engineering, Changsha University of Science and Technology, Changsha, 410114, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2 L 3G1, Canada
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5
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Shivakumar KM, Mahendran G, Brown JA. Locked Nucleic Acid Oligonucleotides Facilitate RNA•LNA-RNA Triple-Helix Formation and Reduce MALAT1 Levels. Int J Mol Sci 2024; 25:1630. [PMID: 38338910 PMCID: PMC10855403 DOI: 10.3390/ijms25031630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/25/2024] [Accepted: 01/25/2024] [Indexed: 02/12/2024] Open
Abstract
Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and multiple endocrine neoplasia-β (MENβ) are two long noncoding RNAs upregulated in multiple cancers, marking these RNAs as therapeutic targets. While traditional small-molecule and antisense-based approaches are effective, we report a locked nucleic acid (LNA)-based approach that targets the MALAT1 and MENβ triple helices, structures comprised of a U-rich internal stem-loop and an A-rich tract. Two LNA oligonucleotides resembling the A-rich tract (i.e., A9GCA4) were examined: an LNA (L15) and a phosphorothioate LNA (PS-L15). L15 binds tighter than PS-L15 to the MALAT1 and MENβ stem loops, although both L15 and PS-L15 enable RNA•LNA-RNA triple-helix formation. Based on UV thermal denaturation assays, both LNAs selectively stabilize the Hoogsteen interface by 5-13 °C more than the Watson-Crick interface. Furthermore, we show that L15 and PS-L15 displace the A-rich tract from the MALAT1 and MENβ stem loop and methyltransferase-like protein 16 (METTL16) from the METTL16-MALAT1 triple-helix complex. Human colorectal carcinoma (HCT116) cells transfected with LNAs have 2-fold less MALAT1 and MENβ. This LNA-based approach represents a potential therapeutic strategy for the dual targeting of MALAT1 and MENβ.
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Affiliation(s)
| | | | - Jessica A. Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA; (K.M.S.); (G.M.)
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6
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Trojan A, Lone YC, Briceno I, Trojan J. Anti-Gene IGF-I Vaccines in Cancer Gene Therapy: A Review of a Case of Glioblastoma. Curr Med Chem 2024; 31:1983-2002. [PMID: 38031775 DOI: 10.2174/0109298673237968231106095141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 06/27/2023] [Accepted: 10/10/2023] [Indexed: 12/01/2023]
Abstract
OBJECTIVE Vaccines for the deadliest brain tumor - glioblastoma (GBM) - are generally based on targeting growth factors or their receptors, often using antibodies. The vaccines described in the review were prepared to suppress the principal cancer growth factor - IGF-I, using anti-gene approaches either of antisense (AS) or of triple helix (TH) type. Our objective was to increase the median survival of patients treated with AS and TH cell vaccines. METHODOLOGY The cells were transfected in vitro by both constructed IGF-I AS and IGF-I TH expression episomal vectors; part of these cells was co-cultured with plant phytochemicals, modulating IGF-I expression. Both AS and TH approaches completely suppressed IGF-I expression and induced MHC-1 / B7 immunogenicity related to the IGF-I receptor signal. RESULTS This immunogenicity proved to be stronger in IGF-I TH than in IGF-I AS-prepared cell vaccines, especially in TH / phytochemical cells. The AS and TH vaccines generated an important TCD8+ and TCD8+CD11b- immune response in treated GBM patients and increased the median survival of patients up to 17-18 months, particularly using TH vaccines; in some cases, 2- and 3-year survival was reported. These clinical results were compared with those obtained in therapies targeting other growth factors. CONCLUSION The anti-gene IGF-I vaccines continue to be applied in current GBM personalized medicine. Technical improvements in the preparation of AS and TH vaccines to increase MHC-1 and B7 immunogenicity have, in parallel, allowed to increase in the median survival of patients.
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Affiliation(s)
- Annabelle Trojan
- INSERM UMR 1197, Cancer Center & University of Paris / Saclay, PO Box: 94802 Villejuif, France
- Faculty of Medicine, University of Cartagena, PO Box: 130014 Cartagena de Indias, Colombia
| | - Yu-Chun Lone
- INSERM UMR 1197, Cancer Center & University of Paris / Saclay, PO Box: 94802 Villejuif, France
- CEDEA / ICGT - Center of Oncological Diseases Diagnosis, PO Box: 110231 Bogota, Colombia
| | - Ignacio Briceno
- Faculty of Medicine, University of La Sabana, PO Box: 250008 Chia, Colombia
| | - Jerzy Trojan
- INSERM UMR 1197, Cancer Center & University of Paris / Saclay, PO Box: 94802 Villejuif, France
- CEDEA / ICGT - Center of Oncological Diseases Diagnosis, PO Box: 110231 Bogota, Colombia
- National Academy of Medicine - ANM, PO Box: 75272 Paris, France
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7
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Maldonado R, Längst G. The chromatin - triple helix connection. Biol Chem 2023; 404:1037-1049. [PMID: 37506218 DOI: 10.1515/hsz-2023-0189] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023]
Abstract
Mammalian genomes are extensively transcribed, producing a large number of coding and non-coding transcripts. A large fraction of the nuclear RNAs is physically associated with chromatin, functioning in gene activation and silencing, shaping higher-order genome organisation, such as involvement in long-range enhancer-promoter interactions, transcription hubs, heterochromatin, nuclear bodies and phase transitions. Different mechanisms allow the tethering of these chromatin-associated RNAs (caRNA) to chromosomes, including RNA binding proteins, the RNA polymerases and R-loops. In this review, we focus on the sequence-specific targeting of RNA to DNA by forming triple helical structures and describe its interplay with chromatin. It turns out that nucleosome positioning at triple helix target sites and the nucleosome itself are essential factors in determining the formation and stability of triple helices. The histone H3-tail plays a critical role in triple helix stabilisation, and the role of its epigenetic modifications in this process is discussed.
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Affiliation(s)
- Rodrigo Maldonado
- Institute of Anatomy, Histology, and Pathology, Faculty of Medicine, Universidad Austral de Chile, 5090000 Valdivia, Chile
| | - Gernot Längst
- Regensburg Center for Biochemistry (RCB), University of Regensburg, D-93053 Regensburg, Germany
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8
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Yildiz CB, Kundu T, Gehrmann J, Koesling J, Ravaei A, Wolff P, Kraft F, Maié T, Jakovcevski M, Pensold D, Zimmermann O, Rossetti G, Costa IG, Zimmer-Bensch G. EphrinA5 regulates cell motility by modulating Snhg15/DNA triplex-dependent targeting of DNMT1 to the Ncam1 promoter. Epigenetics Chromatin 2023; 16:42. [PMID: 37880732 PMCID: PMC10601256 DOI: 10.1186/s13072-023-00516-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 10/13/2023] [Indexed: 10/27/2023] Open
Abstract
Cell-cell communication is mediated by membrane receptors and their ligands, such as the Eph/ephrin system, orchestrating cell migration during development and in diverse cancer types. Epigenetic mechanisms are key for integrating external "signals", e.g., from neighboring cells, into the transcriptome in health and disease. Previously, we reported ephrinA5 to trigger transcriptional changes of lncRNAs and protein-coding genes in cerebellar granule cells, a cell model for medulloblastoma. LncRNAs represent important adaptors for epigenetic writers through which they regulate gene expression. Here, we investigate a lncRNA-mediated targeting of DNMT1 to specific gene loci by the combined power of in silico modeling of RNA/DNA interactions and wet lab approaches, in the context of the clinically relevant use case of ephrinA5-dependent regulation of cellular motility of cerebellar granule cells. We provide evidence that Snhg15, a cancer-related lncRNA, recruits DNMT1 to the Ncam1 promoter through RNA/DNA triplex structure formation and the interaction with DNMT1. This mediates DNA methylation-dependent silencing of Ncam1, being abolished by ephrinA5 stimulation-triggered reduction of Snhg15 expression. Hence, we here propose a triple helix recognition mechanism, underlying cell motility regulation via lncRNA-targeted DNA methylation in a clinically relevant context.
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Affiliation(s)
- Can Bora Yildiz
- Institute of Zoology (Biology 2), Division of Neuroepigenetics, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
- Research Training Group 2416 Multi Senses - Multi Scales, RWTH Aachen University, 52074, Aachen, Germany
| | - Tathagata Kundu
- Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Julia Gehrmann
- Institute for Computational Genomics, RWTH Aachen University, Medical Faculty, 52074, Aachen, Germany
| | - Jannis Koesling
- Institute of Zoology (Biology 2), Division of Neuroepigenetics, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Amin Ravaei
- Institute of Zoology (Biology 2), Division of Neuroepigenetics, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
- Department of Neurosciences and Rehabilitation, Section of Medical Biochemistry, Molecular Biology and Genetics, University of Ferrara, Ferrara, Italy
| | - Philip Wolff
- Institute of Zoology (Biology 2), Division of Neuroepigenetics, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Florian Kraft
- Institute for Human Genetics and Genomic Medicine, Medical Faculty, RWTH Aachen University, 52074, Aachen, Germany
| | - Tiago Maié
- Institute for Computational Genomics, RWTH Aachen University, Medical Faculty, 52074, Aachen, Germany
| | - Mira Jakovcevski
- Institute of Zoology (Biology 2), Division of Neuroepigenetics, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Daniel Pensold
- Institute of Zoology (Biology 2), Division of Neuroepigenetics, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany
| | - Olav Zimmermann
- Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Giulia Rossetti
- Jülich Supercomputing Centre, Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Department of Neurology, University Hospital Aachen, RWTH Aachen University, Aachen, Germany
- Institute of Neuroscience and Medicine (INM-9)/Institute of Advanced Simulations (IAS-5), Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Ivan G Costa
- Institute for Computational Genomics, RWTH Aachen University, Medical Faculty, 52074, Aachen, Germany
| | - Geraldine Zimmer-Bensch
- Institute of Zoology (Biology 2), Division of Neuroepigenetics, RWTH Aachen University, Worringerweg 3, 52074, Aachen, Germany.
- Research Training Group 2416 Multi Senses - Multi Scales, RWTH Aachen University, 52074, Aachen, Germany.
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Rilievo G, Cecconello A, Fouladi Ghareshiran N, Magro M, Simmel FC, Vianello F. Integration of DNA-RNA-triplex-based regulation of transcription into molecular logic gates. FEBS Lett 2023; 597:2461-2472. [PMID: 37591635 DOI: 10.1002/1873-3468.14721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/07/2023] [Accepted: 08/08/2023] [Indexed: 08/19/2023]
Abstract
In recent years, increasing numbers of noncoding RNA molecules were identified as possible components of endogenous DNA-RNA hybrid triplexes involved in gene regulation. Triplexes are potentially involved in complex molecular signaling networks that, if understood, would allow the engineering of biological computing components. Here, by making use of the enhancing and inhibiting effects of such triplexes, we demonstrate in vitro the construction of triplex-based molecular gates: 'exclusive OR' (XOR), 'exclusive NOT-OR' (XNOR), and a threshold gate, via transcription of a fluorogenic RNA aptamer. Precise modulation was displayed by the biomolecular-integrated systems over a wide interval of transcriptional outputs, ranging from drastic inhibition to significant enhancement. The present contribution represents a first example of molecular gates developed using DNA-RNA triplex nanostructures.
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Affiliation(s)
- Graziano Rilievo
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | - Alessandro Cecconello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | | | - Massimiliano Magro
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
| | - Friedrich C Simmel
- Physik Department, Technische Universitat München, Garching bei München, Germany
| | - Fabio Vianello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Italy
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10
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Ferreira RS, Assis RIF, Racca F, Bontempi AC, da Silva RA, Wiench M, Andia DC. Analyzes In Silico Indicate the lncRNAs MIR31HG and LINC00939 as Possible Epigenetic Inhibitors of the Osteogenic Differentiation in PDLCs. Genes (Basel) 2023; 14:1649. [PMID: 37628700 PMCID: PMC10454380 DOI: 10.3390/genes14081649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/10/2023] [Accepted: 08/14/2023] [Indexed: 08/27/2023] Open
Abstract
Chromatin conformation, DNA methylation pattern, transcriptional profile, and non-coding RNAs (ncRNAs) interactions constitute an epigenetic pattern that influences the cellular phenotypic commitment and impacts the clinical outcomes in regenerative therapies. Here, we investigated the epigenetic landscape of the SP7 transcriptor factor (SP7) and Distal-Less Homeobox 4 (DLX4) osteoblastic transcription factors (TFs), in human periodontal ligament mesenchymal cells (PDLCs) with low (l-PDLCs) and high (h-PDLCs) osteogenic potential. Chromatin accessibility (ATAC-seq), genome DNA methylation (Methylome), and RNA sequencing (RNA-seq) assays were performed in l- and h-PDLCs, cultured at 10 days in non-induced (DMEM) and osteogenic (OM) medium in vitro. Data were processed in HOMER, Genome Studio, and edgeR programs, and metadata was analyzed by online bioinformatics tools and in R and Python environments. ATAC-seq analyses showed the TFs genomic regions are more accessible in l-PDLCs than in h-PDLCs. In Methylome analyses, the TFs presented similar average methylation intensities (AMIs), without differently methylated probes (DMPs) between l- and h-PDLCs; in addition, there were no differences in the expression profiles of TFs signaling pathways. Interestingly, we identified the long non-coding RNAs (lncRNAs), MIR31HG and LINC00939, as upregulated in l-PDLCs, in both DMEM and OM. In the following analysis, the web-based prediction tool LncRRIsearch predicted RNA:RNA base-pairing interactions between SP7, DLX4, MIR31HG, and LINC00939 transcripts. The machine learning program TriplexFPP predicted DNA:RNA triplex-forming potential for the SP7 DNA site and for one of the LINC00939 transcripts (ENST00000502479). PCR data confirmed the upregulation of MIR31HG and LINC00939 transcripts in l-PDLCs (× h-PDLCs) in both DMEM and OM (p < 0.05); conversely, SP7 and DLX4 were downregulated, confirming those results observed in the RNA-Seq analysis. Together, these results indicate the lncRNAs MIR31HG and LINC00939 as possible epigenetic inhibitors of the osteogenic differentiation in PDLCs by (post)transcriptional and translational repression of the SP7 and DLX4 TFs.
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Affiliation(s)
- Rogério S. Ferreira
- School of Dentistry, Health Science Institute, Paulista University, São Paulo 04026-002, SP, Brazil; (R.S.F.); (A.C.B.)
| | - Rahyza I. F. Assis
- Department of Clinical Dentistry, Federal University of Espírito Santo, Vitória 29043-910, ES, Brazil
| | - Francesca Racca
- Periodontology Department, The Ohio State University College of Dentistry, Columbus, OH 43210-1267, USA;
| | - Ana Carolina Bontempi
- School of Dentistry, Health Science Institute, Paulista University, São Paulo 04026-002, SP, Brazil; (R.S.F.); (A.C.B.)
| | - Rodrigo A. da Silva
- Program in Environmental and Experimental Pathology, Paulista University, São Paulo 04026-002, SP, Brazil;
| | - Malgorzata Wiench
- School of Dentistry, Institute of Clinical Sciences, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B5 7EG, UK
| | - Denise C. Andia
- School of Dentistry, Health Science Institute, Paulista University, São Paulo 04026-002, SP, Brazil; (R.S.F.); (A.C.B.)
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11
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Cicconetti C, Lauria A, Proserpio V, Masera M, Tamburrini A, Maldotti M, Oliviero S, Molineris I. 3plex enables deep computational investigation of triplex forming lncRNAs. Comput Struct Biotechnol J 2023; 21:3091-3102. [PMID: 37273849 PMCID: PMC10236371 DOI: 10.1016/j.csbj.2023.05.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/15/2023] [Accepted: 05/15/2023] [Indexed: 06/06/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) regulate gene expression through different molecular mechanisms, including DNA binding via the formation of RNA:DNA:DNA triple helices (TPXs). Despite the increasing amount of experimental evidence, TPXs investigation remains challenging. Here we present 3plex, a software able to predict TPX interactions in silico. Given an RNA sequence and a set of DNA sequences, 3plex integrates 1) Hoogsteen pairing rules that describe the biochemical interactions between RNA and DNA nucleotides, 2) RNA secondary structure prediction and 3) determination of the TPX thermal stability derived from a collection of TPX experimental evidences. We systematically collected and uniformly re-analysed published experimental lncRNA binding sites on human and mouse genomes. We used these data to evaluate 3plex performance and showed that its specific features allow a reliable identification of TPX interactions. We compared 3plex with the other available software and obtained comparable or even better accuracy at a fraction of the computation time. Interestingly, by inspecting collected data with 3plex we found that TPXs tend to be shorter and more degenerated than previously expected and that the majority of analysed lncRNAs can directly bind to the genome by TPX formation. Those results suggest that an important fraction of lncRNAs can exert its biological function through this mechanism. The software is available at https://github.com/molinerisLab/3plex.
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Affiliation(s)
- Chiara Cicconetti
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, Candiolo 10060 (Torino), Italy
| | - Andrea Lauria
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, Candiolo 10060 (Torino), Italy
| | - Valentina Proserpio
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, Candiolo 10060 (Torino), Italy
| | - Marco Masera
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
| | - Annalaura Tamburrini
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, Candiolo 10060 (Torino), Italy
| | - Mara Maldotti
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, Candiolo 10060 (Torino), Italy
| | - Salvatore Oliviero
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, Candiolo 10060 (Torino), Italy
| | - Ivan Molineris
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
- Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, Candiolo 10060 (Torino), Italy
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12
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Kohestani H, Wereszczynski J. The effects of RNA.DNA-DNA triple helices on nucleosome structures and dynamics. Biophys J 2023; 122:1229-1239. [PMID: 36798026 PMCID: PMC10111275 DOI: 10.1016/j.bpj.2023.02.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 01/22/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
Noncoding RNAs (ncRNAs) are an emerging epigenetic factor and have been recognized as playing a key role in many gene expression pathways. Structurally, binding of ncRNAs to isolated DNA is strongly dependent on sequence complementary and results in the formation of an RNA.DNA-DNA (RDD) triple helix. However, in vivo DNA is not isolated but is rather packed in chromatin fibers, the fundamental unit of which is the nucleosome. Biochemical experiments have shown that ncRNA binding to nucleosomal DNA is elevated at DNA entry and exit sites and is dependent on the presence of the H3 N-terminal tails. However, the structural and dynamical bases for these mechanisms remain unknown. Here, we have examined the mechanisms and effects of RDD formation in the context of the nucleosome using a series of all-atom molecular dynamics simulations. Results highlight the importance of DNA sequence on complex stability, elucidate the effects of the H3 tails on RDD structures, show how RDD formation impacts the structure and dynamics of the H3 tails, and show how RNA alters the local and global DNA double-helical structure. Together, our results suggest ncRNAs can modify nucleosome, and potentially higher-order chromatin, structures and dynamics as a means of exerting epigenetic control.
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Affiliation(s)
- Havva Kohestani
- Department of Biology, Illinois Institute of Technology, Chicago, Illinois
| | - Jeff Wereszczynski
- Departments of Physics & Biology, Illinois Institute of Technology, Chicago, Illinois.
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13
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Warwick T, Brandes RP, Leisegang MS. Computational Methods to Study DNA:DNA:RNA Triplex Formation by lncRNAs. Noncoding RNA 2023; 9:ncrna9010010. [PMID: 36827543 PMCID: PMC9965544 DOI: 10.3390/ncrna9010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) impact cell function via numerous mechanisms. In the nucleus, interactions between lncRNAs and DNA and the consequent formation of non-canonical nucleic acid structures seems to be particularly relevant. Along with interactions between single-stranded RNA (ssRNA) and single-stranded DNA (ssDNA), such as R-loops, ssRNA can also interact with double-stranded DNA (dsDNA) to form DNA:DNA:RNA triplexes. A major challenge in the study of DNA:DNA:RNA triplexes is the identification of the precise RNA component interacting with specific regions of the dsDNA. As this is a crucial step towards understanding lncRNA function, there exist several computational methods designed to predict these sequences. This review summarises the recent progress in the prediction of triplex formation and highlights important DNA:DNA:RNA triplexes. In particular, different prediction tools (Triplexator, LongTarget, TRIPLEXES, Triplex Domain Finder, TriplexFFP, TriplexAligner and Fasim-LongTarget) will be discussed and their use exemplified by selected lncRNAs, whose DNA:DNA:RNA triplex forming potential was validated experimentally. Collectively, these tools revealed that DNA:DNA:RNA triplexes are likely to be numerous and make important contributions to gene expression regulation.
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Affiliation(s)
- Timothy Warwick
- Institute for Cardiovascular Physiology, Goethe University, 60590 Frankfurt, Germany
- German Centre of Cardiovascular Research (DZHK), Partner Site RheinMain, 60590 Frankfurt, Germany
| | - Ralf P. Brandes
- Institute for Cardiovascular Physiology, Goethe University, 60590 Frankfurt, Germany
- German Centre of Cardiovascular Research (DZHK), Partner Site RheinMain, 60590 Frankfurt, Germany
| | - Matthias S. Leisegang
- Institute for Cardiovascular Physiology, Goethe University, 60590 Frankfurt, Germany
- German Centre of Cardiovascular Research (DZHK), Partner Site RheinMain, 60590 Frankfurt, Germany
- Correspondence: ; Tel.: +49-69-6301-6996; Fax: +49-69-6301-7668
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14
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Zhang X, Jiang Q, Li J, Zhang S, Cao Y, Xia X, Cai D, Tan J, Chen J, Han JDJ. KCNQ1OT1 promotes genome-wide transposon repression by guiding RNA-DNA triplexes and HP1 binding. Nat Cell Biol 2022; 24:1617-1629. [PMID: 36266489 DOI: 10.1038/s41556-022-01008-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 09/07/2022] [Indexed: 01/18/2023]
Abstract
Transposon (de)repression and heterochromatin reorganization are dynamically regulated during cell fate determination and are hallmarks of cellular senescence. However, whether they are sequence specifically regulated remains unknown. Here we uncover that the KCNQ1OT1 lncRNA, by sequence-specific Hoogsteen base pairing with double-stranded genomic DNA via its repeat-rich region and binding to the heterochromatin protein HP1α, guides, induces and maintains epigenetic silencing at specific repetitive DNA elements. Repressing KCNQ1OT1 or deleting its repeat-rich region reduces DNA methylation and H3K9me3 on KCNQ1OT1-targeted transposons. Engineering a fusion KCNQ1OT1 with an ectopically targeting guiding triplex sequence induces de novo DNA methylation at the target site. Phenotypically, repressing KCNQ1OT1 induces senescence-associated heterochromatin foci, transposon activation and retrotransposition as well as cellular senescence, demonstrating an essential role of KCNQ1OT1 to safeguard against genome instability and senescence.
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Affiliation(s)
- Xiaoli Zhang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Quanlong Jiang
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiyang Li
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Shiqiang Zhang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yaqiang Cao
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xian Xia
- Department of Pharmacology, Nanjing University of Chinese Medicine, Nanjing, China
| | - Donghong Cai
- CAS Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiaqi Tan
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China
| | - Jiekai Chen
- CAS Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
| | - Jing-Dong J Han
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Center for Quantitative Biology (CQB), Peking University, Beijing, China.
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15
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Warwick T, Seredinski S, Krause NM, Bains JK, Althaus L, Oo JA, Bonetti A, Dueck A, Engelhardt S, Schwalbe H, Leisegang MS, Schulz MH, Brandes RP. A universal model of RNA.DNA:DNA triplex formation accurately predicts genome-wide RNA-DNA interactions. Brief Bioinform 2022; 23:6760135. [PMID: 36239395 PMCID: PMC9677506 DOI: 10.1093/bib/bbac445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/16/2022] [Accepted: 09/17/2022] [Indexed: 12/14/2022] Open
Abstract
RNA.DNA:DNA triple helix (triplex) formation is a form of RNA-DNA interaction which regulates gene expression but is difficult to study experimentally in vivo. This makes accurate computational prediction of such interactions highly important in the field of RNA research. Current predictive methods use canonical Hoogsteen base pairing rules, which whilst biophysically valid, may not reflect the plastic nature of cell biology. Here, we present the first optimization approach to learn a probabilistic model describing RNA-DNA interactions directly from motifs derived from triplex sequencing data. We find that there are several stable interaction codes, including Hoogsteen base pairing and novel RNA-DNA base pairings, which agree with in vitro measurements. We implemented these findings in TriplexAligner, a program that uses the determined interaction codes to predict triplex binding. TriplexAligner predicts RNA-DNA interactions identified in all-to-all sequencing data more accurately than all previously published tools in human and mouse and also predicts previously studied triplex interactions with known regulatory functions. We further validated a novel triplex interaction using biophysical experiments. Our work is an important step towards better understanding of triplex formation and allows genome-wide analyses of RNA-DNA interactions.
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Affiliation(s)
- Timothy Warwick
- Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern-Kai 7, D-60590, Frankfurt am Main, Germany,DZHK (German Center for Cardiovascular Research), Partner site Rhein-Main, Frankfurt am Main, Germany
| | - Sandra Seredinski
- Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern-Kai 7, D-60590, Frankfurt am Main, Germany,DZHK (German Center for Cardiovascular Research), Partner site Rhein-Main, Frankfurt am Main, Germany
| | - Nina M Krause
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Max-von-Laue-Str. 7, D-60438, Frankfurt am Main, Germany
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Max-von-Laue-Str. 7, D-60438, Frankfurt am Main, Germany
| | - Lara Althaus
- Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern-Kai 7, D-60590, Frankfurt am Main, Germany,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - James A Oo
- Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern-Kai 7, D-60590, Frankfurt am Main, Germany,DZHK (German Center for Cardiovascular Research), Partner site Rhein-Main, Frankfurt am Main, Germany
| | - Alessandro Bonetti
- Translational Genomics, Discovery Sciences, Bio Pharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 431 50 Mölndal, Sweden
| | - Anne Dueck
- Institute of Pharmacology and Toxicology, Technical University of Munich, Biedersteiner Str. 29, D-80802, Munich, Germany,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Stefan Engelhardt
- Institute of Pharmacology and Toxicology, Technical University of Munich, Biedersteiner Str. 29, D-80802, Munich, Germany,DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Goethe University, Max-von-Laue-Str. 7, D-60438, Frankfurt am Main, Germany
| | - Matthias S Leisegang
- Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern-Kai 7, D-60590, Frankfurt am Main, Germany,DZHK (German Center for Cardiovascular Research), Partner site Rhein-Main, Frankfurt am Main, Germany
| | - Marcel H Schulz
- Corresponding authors. Ralf P. Brandes, Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern-Kai 7, D-60590, Frankfurt am Main, Germany. E-mail: ; Marcel H. Schulz, Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern-Kai 7, D-60590, Frankfurt am Main, Germany. E-mail:
| | - Ralf P Brandes
- Corresponding authors. Ralf P. Brandes, Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern-Kai 7, D-60590, Frankfurt am Main, Germany. E-mail: ; Marcel H. Schulz, Institute for Cardiovascular Physiology, Goethe University, Theodor-Stern-Kai 7, D-60590, Frankfurt am Main, Germany. E-mail:
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16
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Kunkler CN, Schiefelbein GE, O'Leary NJ, McCown PJ, Brown JA. A single natural RNA modification can destabilize a U•A-T-rich RNA•DNA-DNA triple helix. RNA (NEW YORK, N.Y.) 2022; 28:1172-1184. [PMID: 35820700 PMCID: PMC9380742 DOI: 10.1261/rna.079244.122] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Recent studies suggest noncoding RNAs interact with genomic DNA, forming RNA•DNA-DNA triple helices, as a mechanism to regulate transcription. One way cells could regulate the formation of these triple helices is through RNA modifications. With over 140 naturally occurring RNA modifications, we hypothesize that some modifications stabilize RNA•DNA-DNA triple helices while others destabilize them. Here, we focus on a pyrimidine-motif triple helix composed of canonical U•A-T and C•G-C base triples. We employed electrophoretic mobility shift assays and microscale thermophoresis to examine how 11 different RNA modifications at a single position in an RNA•DNA-DNA triple helix affect stability: 5-methylcytidine (m5C), 5-methyluridine (m5U or rT), 3-methyluridine (m3U), pseudouridine (Ψ), 4-thiouridine (s4U), N 6-methyladenosine (m6A), inosine (I), and each nucleobase with 2'-O-methylation (Nm). Compared to the unmodified U•A-T base triple, some modifications have no significant change in stability (Um•A-T), some have ∼2.5-fold decreases in stability (m5U•A-T, Ψ•A-T, and s4U•A-T), and some completely disrupt triple helix formation (m3U•A-T). To identify potential biological examples of RNA•DNA-DNA triple helices controlled by an RNA modification, we searched RMVar, a database for RNA modifications mapped at single-nucleotide resolution, for lncRNAs containing an RNA modification within a pyrimidine-rich sequence. Using electrophoretic mobility shift assays, the binding of DNA-DNA to a 22-mer segment of human lncRNA Al157886.1 was destabilized by ∼1.7-fold with the substitution of m5C at known m5C sites. Therefore, the formation and stability of cellular RNA•DNA-DNA triple helices could be influenced by RNA modifications.
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Affiliation(s)
- Charlotte N Kunkler
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Grace E Schiefelbein
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Nathan J O'Leary
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Phillip J McCown
- Michigan Medicine, Department of Internal Medicine, Division of Nephrology, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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17
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Wu R, Liu T, Wu S, Li H, Song R, Song B. Synthesis, Antibacterial Activity, and Action Mechanism of Novel Sulfonamides Containing Oxyacetal and Pyrimidine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:9305-9318. [PMID: 35858046 DOI: 10.1021/acs.jafc.2c02099] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bacterial leaf blight (BLB) and bacterial leaf streak (BLS) are two serious bacterial diseases caused by Xanthomonas oryzae pv. oryzae (Xoo) and Xanthomonas oryzae pv. oryzicola (Xoc), respectively. However, the control of these diseases by conventional pesticides remains challenging due to development of resistances. We aimed to address this pending problem and developed a series of novel pyrimidine sulfonamide derivatives. Structurally, title compounds bear a unique oxyacetal group, which has a proven immune-activating effect. Compound E35 designed based on the 3D-QSAR model was demonstrated as the optimal in vitro activity against Xoo and Xoc, with EC50 values of 26.7 and 30.8 mg/L, respectively, which were higher than the positive controls bismerthiazol (29.9 and 32.7 mg/L) and thiodiazole copper (30.5 and 36.4 mg/L). On the prevention level, the biological activity test showed compound E35 had superior protective activity (43.7%) on BLS to thiodiazole copper (32.1%). The defense enzymes and proteomics results suggested that compound E35 could be a versatile candidate as it improved plant's resistance to disease.
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Affiliation(s)
- Rong Wu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
| | - Ting Liu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
| | - Sikai Wu
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
| | - Hongde Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
| | - Runjiang Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
| | - Baoan Song
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang 550025, P. R. China
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18
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Kretschmer M, Gapp K. Deciphering the RNA universe in sperm in its role as a vertical information carrier. ENVIRONMENTAL EPIGENETICS 2022; 8:dvac011. [PMID: 35633894 PMCID: PMC9134061 DOI: 10.1093/eep/dvac011] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/11/2022] [Accepted: 04/13/2022] [Indexed: 05/21/2023]
Abstract
The inheritance of neurophysiologic and neuropsychologic complex diseases can only partly be explained by the Mendelian concept of genetic inheritance. Previous research showed that both psychological disorders like post-traumatic stress disorder and metabolic diseases are more prevalent in the progeny of affected parents. This could suggest an epigenetic mode of transmission. Human studies give first insight into the scope of intergenerational influence of stressors but are limited in exploring the underlying mechanisms. Animal models have elucidated the mechanistic underpinnings of epigenetic transmission. In this review, we summarize progress on the mechanisms of paternal intergenerational transmission by means of sperm RNA in mouse models. We discuss relevant details for the modelling of RNA-mediated transmission, point towards currently unanswered questions and propose experimental considerations for tackling these questions.
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Affiliation(s)
- Miriam Kretschmer
- Department of Health Sciences and Technology, ETH Zurich, Laboratory of Molecular and Behavioral Neuroscience, Institute for Neuroscience, Winterthurerstrasse 190, Zurich 8057, Switzerland
- Neuroscience Centre Zurich, ETH Zurich and University of Zurich, Winterthurerstrasse 190, Zurich 8057, Switzerland
| | - Katharina Gapp
- *Correspondence address. Department of Health Sciences and Technology, Laboratory of Molecular and Behavioral Neuroscience, Y36 M 12, Winterthurerstrasse 190, Zurich 8057, Switzerland. Tel: +0041 44 633 85 89; E-mail:
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19
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Khan S, Singh A, Nain N, Gulati S, Kukreti S. Sequence-specific recognition of a coding segment of human DACH1 gene via short pyrimidine/purine oligonucleotides. RSC Adv 2021; 11:40011-40021. [PMID: 35494143 PMCID: PMC9044637 DOI: 10.1039/d1ra06604h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 12/03/2021] [Indexed: 12/18/2022] Open
Abstract
With growing in vivo evidence of the roles of triplexes in biological processes, oligonucleotide-directed targeting of double-helical DNA for selective modulation of gene functions has become imperative in their therapeutic aspects. This study comprises a comparative investigation of 17-mer Py- and Pu-TFO for the formation of an intermolecular triplex with a 27-bp genomic homopurine–homopyrimidine track present in the transcriptional element of the human DACH1 gene. The biochemical and biophysical studies have revealed that triplex formation takes place only with Py-TFO and not with its Pu-counterpart. Non-denaturating gel electrophoresis indicated the formation of an intermolecular triplex in Py-motif with an increasing amount of Py-TFO, whereas no such interaction was observed for the Pu-counterpart. UV-thermal melting (Tm), circular dichroism (CD) and thermal difference spectra (TDS) studies confirmed the pyrimidine motif triplex formation, which was observed to be significantly pH-dependent and stable at acidic pH (5.2) in the presence of 100 mM Na+ ions. Contrarily, Pu-TFO was not found to bind to the target predominantly, owing to its self-association properties. Further studies have revealed that the GA-rich Pu-TFO adopts a homoduplex structure leading to a limit in its availability for triplex formation. These results may add to our understanding of sequence-specific gene targeting and give insight into designing more specific TFOs depending on genomic targets. Schematic representation of the proposed model of intermolecular triplex and homoduplex of used DNA sequences.![]()
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Affiliation(s)
- Shoaib Khan
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi Delhi-110007 India
| | - Anju Singh
- Department of Chemistry, Ramjas College, University of Delhi Delhi-110007 India
| | - Nishu Nain
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi Delhi-110007 India
| | - Srishty Gulati
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi Delhi-110007 India
| | - Shrikant Kukreti
- Nucleic Acid Research Laboratory, Department of Chemistry, University of Delhi Delhi-110007 India
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20
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Three-dimensional genome organization via triplex-forming RNAs. Nat Struct Mol Biol 2021; 28:945-954. [PMID: 34759378 DOI: 10.1038/s41594-021-00678-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 09/30/2021] [Indexed: 11/08/2022]
Abstract
An increasing number of long noncoding RNAs (lncRNAs) have been proposed to act as nuclear organization factors during interphase. Direct RNA-DNA interactions can be achieved by the formation of triplex helix structures where a single-stranded RNA molecule hybridizes by complementarity into the major groove of double-stranded DNA. However, whether and how these direct RNA-DNA associations influence genome structure in interphase chromosomes remain poorly understood. Here we theorize that RNA organizes the genome in space via a triplex-forming mechanism. To test this theory, we apply a computational modeling approach of chromosomes that combines restraint-based modeling with polymer physics. Our models suggest that colocalization of triplex hotspots targeted by lncRNAs could contribute to large-scale chromosome compartmentalization cooperating, rather than competing, with architectural transcription factors such as CTCF.
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21
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Miao S, Bhunia D, Devari S, Liang Y, Munyaradzi O, Rundell S, Bong D. Bifacial PNAs Destabilize MALAT1 by 3' A-Tail Displacement from the U-Rich Internal Loop. ACS Chem Biol 2021; 16:1600-1609. [PMID: 34382766 DOI: 10.1021/acschembio.1c00575] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We report herein a new class of synthetic reagents for targeting the element for nuclear expression (ENE) in MALAT1, a long noncoding RNA upregulated in many cancers. The cis-acting ENE contains a U-rich internal loop (URIL) that forms an 11 base UAU-rich triplex stem with the truncated 3' oligo-A tail of MALAT1, protecting the terminus from exonuclease digestion and greatly extending transcript lifetime. Bifacial peptide nucleic acids (bPNAs) similarly bind URILs via base triple formation between two uracil bases and a synthetic base, melamine. We synthesized a set of low molecular weight bPNAs composed of α-linked peptide, isodipeptide, and diketopiperazine backbones and evaluated their ENE binding efficacy in vitro via oligo-A strand displacement and consequent exonuclease sensitivity. Degradation was greatly enhanced by bPNA treatment in the presence of exonucleases, with ENE half-life plunging to 6 min from >24 h. RNA digestion kinetics could clearly distinguish between bPNAs with similar URIL affinities, highlighting the utility of functional assays for evaluating synthetic RNA binders. In vitro activity was mirrored by a 50% knockdown of MALAT1 expression in pancreatic cancer (PANC-1) cells upon treatment with bPNAs, consistent with intracellular digestion triggered by a similar ENE A-tail displacement mechanism. Pulldown from PANC-1 total RNA with biotinylated bPNA enriched MALAT1 > 4000× , supportive of bPNA-URIL selectivity. Together, these experiments establish the feasibility of native transcript targeting by bPNA in both in vitro and intracellular contexts. Reagents such as bPNAs may be useful tools for the investigation of transcripts stabilized by cis-acting poly(A) binding RNA elements.
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Affiliation(s)
- Shiqin Miao
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Debmalya Bhunia
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Shekaraiah Devari
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Yufeng Liang
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Oliver Munyaradzi
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
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22
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Kaufmann B, Willinger O, Kikuchi N, Navon N, Kermas L, Goldberg S, Amit R. An Oligo-Library-Based Approach for Mapping DNA-DNA Triplex Interactions In Vitro. ACS Synth Biol 2021; 10:1808-1820. [PMID: 34374529 DOI: 10.1021/acssynbio.1c00122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
We present Triplex-seq, a deep-sequencing method that systematically maps the interaction space between an oligo library of ssDNA triplex-forming oligos (TFOs) and a particular dsDNA triplex target site (TTS). We demonstrate the method using a randomized oligo library comprising 67 million variants, with five TTSs that differ in guanine (G) content, at two different buffer conditions, denoted pH 5 and pH 7. Our results show that G-rich triplexes form at both pH 5 and pH 7, with the pH 5 set being more stable, indicating that there is a subset of TFOs that form triplexes only at pH 5. In addition, using information analysis, we identify triplex-forming motifs (TFMs), which correspond to minimal functional TFO sequences. We demonstrate, in single-variant verification experiments, that TFOs with these TFMs indeed form a triplex with G-rich TTSs, and that a single mutation in the TFM motif can alleviate binding. Our results show that deep-sequencing platforms can substantially expand our understanding of triplex binding rules and aid in refining the DNA triplex code.
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Affiliation(s)
- Beate Kaufmann
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Or Willinger
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Nanami Kikuchi
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Noa Navon
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Lisa Kermas
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Sarah Goldberg
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
| | - Roee Amit
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 32000, Israel
- Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa 32000, Israel
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23
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Alfeghaly C, Sanchez A, Rouget R, Thuillier Q, Igel-Bourguignon V, Marchand V, Branlant C, Motorin Y, Behm-Ansmant I, Maenner S. Implication of repeat insertion domains in the trans-activity of the long non-coding RNA ANRIL. Nucleic Acids Res 2021; 49:4954-4970. [PMID: 33872355 PMCID: PMC8136789 DOI: 10.1093/nar/gkab245] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 03/20/2021] [Accepted: 03/26/2021] [Indexed: 11/14/2022] Open
Abstract
Long non-coding RNAs have emerged as critical regulators of cell homeostasis by modulating gene expression at chromatin level for instance. Here, we report that the lncRNA ANRIL, associated with several pathologies, binds to thousands of loci dispersed throughout the mammalian genome sharing a 21-bp motif enriched in G/A residues. By combining ANRIL genomic occupancy with transcriptomic analysis, we established a list of 65 and 123 genes potentially directly activated and silenced by ANRIL in trans, respectively. We also found that Exon8 of ANRIL, mainly made of transposable elements, contributes to ANRIL genomic association and consequently to its trans-activity. Furthermore, we showed that Exon8 favors ANRIL's association with the FIRRE, TPD52L1 and IGFBP3 loci to modulate their expression through H3K27me3 deposition. We also investigated the mechanisms engaged by Exon8 to favor ANRIL's association with the genome. Our data refine ANRIL's trans-activity and highlight the functional importance of TEs on ANRIL's activity.
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Affiliation(s)
| | | | - Raphael Rouget
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | | | - Valérie Igel-Bourguignon
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
- Université de Lorraine, CNRS, INSERM, UMS2008 IBSLor, Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, F-54000 Nancy, France
| | - Virginie Marchand
- Université de Lorraine, CNRS, INSERM, UMS2008 IBSLor, Epitranscriptomics and RNA Sequencing (EpiRNA-Seq) Core Facility, F-54000 Nancy, France
| | | | - Yuri Motorin
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
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24
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Guerrini L, Alvarez-Puebla RA. Structural Recognition of Triple-Stranded DNA by Surface-Enhanced Raman Spectroscopy. NANOMATERIALS 2021; 11:nano11020326. [PMID: 33513847 PMCID: PMC7912272 DOI: 10.3390/nano11020326] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 11/24/2022]
Abstract
Direct, label-free analysis of nucleic acids via surface-enhanced Raman spectroscopy (SERS) has been continuously expanding its range of applications as an intriguing and powerful analytical tool for the structural characterization of diverse DNA structures. Still, interrogation of nucleic acid tertiary structures beyond the canonical double helix often remains challenging. In this work, we report for the first time the structural identification of DNA triplex structures. This class of nucleic acids has been attracting great interest because of their intriguing biological functions and pharmacological potential in gene therapy, and the ability for precisely engineering DNA-based functional nanomaterials. Herein, structural discrimination of the triplex structure against its duplex and tertiary strand counterparts is univocally revealed by recognizing key markers bands in the intrinsic SERS fingerprint. These vibrational features are informative of the base stacking, Hoogsteen hydrogen bonding and sugar–phosphate backbone reorganization associated with the triple helix formation. This work expands the applicability of direct SERS to nucleic acids analysis, with potential impact on fields such as sensing, biology and drug design.
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Affiliation(s)
- Luca Guerrini
- Department of Physical and Inorganic Chemistry—EMaS, Universitat Rovira I Virgili, Carrer de Marcel∙lí Domingo s/n, 43007 Tarragona, Spain
- Correspondence: (L.G.); (R.A.A.-P.)
| | - Ramon A. Alvarez-Puebla
- Department of Physical and Inorganic Chemistry—EMaS, Universitat Rovira I Virgili, Carrer de Marcel∙lí Domingo s/n, 43007 Tarragona, Spain
- ICREA, Passeig Lluís Companys 23, 08010 Barcelona, Spain
- Correspondence: (L.G.); (R.A.A.-P.)
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25
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Herbert A. Simple Repeats as Building Blocks for Genetic Computers. Trends Genet 2020; 36:739-750. [PMID: 32690316 DOI: 10.1016/j.tig.2020.06.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 06/17/2020] [Accepted: 06/22/2020] [Indexed: 11/15/2022]
Abstract
Processing of RNA involves heterogeneous nuclear ribonucleoproteins. The simple sequence repeats (SSRs) they bind can also adopt alternative DNA structures, like Z DNA, triplexes, G quadruplexes, and I motifs. Those SSRs capable of switching conformation under physiological conditions (called flipons) are genetic elements that can encode alternative RNA processing by their effects on RNA processivity, most likely as DNA:RNA hybrids. Flipons are elements of a binary, instructive genetic code directing how genomic sequences are compiled into transcripts. The combinatorial nature of this code provides a rich set of options for creating genetic computers able to reproduce themselves and use a heritable and evolvable code to optimize survival. The underlying computational logic potentiates a diverse set of genetic programs that modify cis-mediated heritability and disease risk.
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Affiliation(s)
- Alan Herbert
- Discovery, InsideOutBio, 42 8th Street, Charlestown, MA 02129, USA.
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26
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Brown JA. Unraveling the structure and biological functions of RNA triple helices. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1598. [PMID: 32441456 PMCID: PMC7583470 DOI: 10.1002/wrna.1598] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 04/06/2020] [Accepted: 04/15/2020] [Indexed: 02/06/2023]
Abstract
It has been nearly 63 years since the first characterization of an RNA triple helix in vitro by Gary Felsenfeld, David Davies, and Alexander Rich. An RNA triple helix consists of three strands: A Watson–Crick RNA double helix whose major‐groove establishes hydrogen bonds with the so‐called “third strand”. In the past 15 years, it has been recognized that these major‐groove RNA triple helices, like single‐stranded and double‐stranded RNA, also mediate prominent biological roles inside cells. Thus far, these triple helices are known to mediate catalysis during telomere synthesis and RNA splicing, bind to ligands and ions so that metabolite‐sensing riboswitches can regulate gene expression, and provide a clever strategy to protect the 3′ end of RNA from degradation. Because RNA triple helices play important roles in biology, there is a renewed interest in better understanding the fundamental properties of RNA triple helices and developing methods for their high‐throughput discovery. This review provides an overview of the fundamental biochemical and structural properties of major‐groove RNA triple helices, summarizes the structure and function of naturally occurring RNA triple helices, and describes prospective strategies to isolate RNA triple helices as a means to establish the “triplexome”. This article is categorized under:RNA Structure and Dynamics > RNA Structure and Dynamics RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems
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Affiliation(s)
- Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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27
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Yang H, Zhang Y, Xu X, Wang H, Huang Z, Luo Z, Deng X, Xue Q, Qing Z, Zou Z, Yang R. Visualization of Long Noncoding RNA MEG3 in Living Cells by a Triple-Helix-Powered 3D Catcher. ACS APPLIED BIO MATERIALS 2020; 3:2588-2596. [DOI: 10.1021/acsabm.9b01179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Hua Yang
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Food Engineering, Changsha University of Science and Technology, Changsha 410114, P. R. China
| | - Yufei Zhang
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Food Engineering, Changsha University of Science and Technology, Changsha 410114, P. R. China
| | - Xuan Xu
- Children’s Medical Center, People’s Hospital of Hunan Province, Changsha, Hunan 410002, P. R. China
| | - Huanxiang Wang
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Food Engineering, Changsha University of Science and Technology, Changsha 410114, P. R. China
| | - Ziyun Huang
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Food Engineering, Changsha University of Science and Technology, Changsha 410114, P. R. China
| | - Ziling Luo
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Food Engineering, Changsha University of Science and Technology, Changsha 410114, P. R. China
| | - Xiangxi Deng
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Food Engineering, Changsha University of Science and Technology, Changsha 410114, P. R. China
| | - Qian Xue
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Food Engineering, Changsha University of Science and Technology, Changsha 410114, P. R. China
| | - Zhihe Qing
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Food Engineering, Changsha University of Science and Technology, Changsha 410114, P. R. China
| | - Zhen Zou
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Food Engineering, Changsha University of Science and Technology, Changsha 410114, P. R. China
| | - Ronghua Yang
- Hunan Provincial Key Laboratory of Cytochemistry, School of Chemistry and Food Engineering, Changsha University of Science and Technology, Changsha 410114, P. R. China
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28
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Matveishina E, Antonov I, Medvedeva YA. Practical Guidance in Genome-Wide RNA:DNA Triple Helix Prediction. Int J Mol Sci 2020; 21:E830. [PMID: 32012884 PMCID: PMC7037363 DOI: 10.3390/ijms21030830] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/21/2020] [Accepted: 01/25/2020] [Indexed: 12/15/2022] Open
Abstract
Long noncoding RNAs (lncRNAs) play a key role in many cellular processes including chromatin regulation. To modify chromatin, lncRNAs often interact with DNA in a sequence-specific manner forming RNA:DNA triple helices. Computational tools for triple helix search do not always provide genome-wide predictions of sufficient quality. Here, we used four human lncRNAs (MEG3, DACOR1, TERC and HOTAIR) and their experimentally determined binding regions for evaluating triplex parameters that provide the highest prediction accuracy. Additionally, we combined triplex prediction with the lncRNA secondary structure and demonstrated that considering only single-stranded fragments of lncRNA can further improve DNA-RNA triplexes prediction.
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Affiliation(s)
- Elena Matveishina
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Science, 117312 Moscow, Russia
| | - Ivan Antonov
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Science, 117312 Moscow, Russia
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Yulia A Medvedeva
- Institute of Bioengineering, Research Center of Biotechnology, Russian Academy of Science, 117312 Moscow, Russia
- Department of Biological and Medical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
- Department of Computational Biology, Vavilov Institute of General Genetics, Russian Academy of Science, 117971 Moscow, Russia
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