論文 - 遠藤 玉樹
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Nearest-neighbor parameters for the prediction of RNA duplex stability in diverse in vitro and cellular-like crowding conditions. 査読あり 国際誌
Saptarshi Ghosh, Shuntaro Takahashi, Dipanwita Banerjee, Tatsuya Ohyama, Tamaki Endoh, Hisae Tateishi-Karimata, Naoki Sugimoto
Nucleic acids research 51 ( 9 ) 4101 - 4111 2023年5月
RNA performs various spatiotemporal functions in living cells. As the solution environments significantly affect the stability of RNA duplexes, a stability prediction of the RNA duplexes in diverse crowded conditions is required to understand and modulate gene expression in heterogeneously crowded intracellular conditions. Herein, we determined the nearest-neighbor (NN) parameters for RNA duplex formation when subjected to crowding conditions with an ionic concentration relevant to that found in cells. Determination of the individual contributions of excluded volume effect and water activity to each of the NN parameters in crowded environments enabled prediction of the thermodynamic parameters and their melting temperatures for plenty of tested RNA duplex formation in vitro and in cell with significant accuracy. The parameters reported herein will help predicting RNA duplex stability in different crowded environments, which will lead to an improved understanding of the stability-function relationship for RNAs in various cellular organelles with different molecular environments.
DOI： 10.1093/nar/gkad020
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Endogenous G-quadruplex-forming RNAs inhibit the activity of SARS-CoV-2 RNA polymerase. 招待あり 査読あり 国際誌
Tamaki Endoh, Shuntaro Takahashi, Naoki Sugimoto
Chemical communications (Cambridge, England) 59 ( 7 ) 872 - 875 2023年1月
担当区分：筆頭著者
Replication of RNA viruses is catalysed by virus-specific polymerases, which can be targets of therapeutic strategies. In this study, we used a selection strategy to identify endogenous RNAs from a transcriptome library derived from lung cells that interact with the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2. Some of the selected RNAs weakened the activity of RdRp by forming G-quadruplexes. These results suggest that certain endogenous RNAs, which potentially form G-quadruplexes, can reduce the replication of viral RNAs.
DOI： 10.1039/d2cc05858h
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Cladogenetic Orthogonal Light-Up Aptamers for Simultaneous Detection of Multiple Small Molecules in Cells. 査読あり 国際共著 国際誌
Tamaki Endoh, Jia-Heng Tan, Shuo-Bin Chen, Naoki Sugimoto
Analytical chemistry 95 ( 2 ) 976 - 985 2023年1月
担当区分：筆頭著者, 責任著者
Recent successes in construction of light-up RNA aptamers allowed fluorescence-based live-cell imaging of RNAs. In addition, light-up aptamers have been converted into signaling aptamers that enable fluorometric detection of small chemicals. To date, only a single target chemical has been detected at a time in cells. In this study, we selected cladogenetic orthogonal light-up aptamers that output three different colors from the RNA library having the same ligand binding core. Two of the three functioned in mammalian cells. These two aptamers, which fluoresce blue and green upon binding of cognate fluorogen, were converted into signaling aptamers. Using these signaling aptamers in combination with a previously described light-up aptamer with red fluorescence, we demonstrated simultaneous detection of multiple chemicals in living cells. The cladogenetic orthogonal light-up aptamers developed in this study and the simple strategy for rational designing of the signaling aptamers will provide innovative advances in the field of RNA-based bioimaging.
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High-temperature adaptation of an OsNRT2.3 allele is thermoregulated by small RNAs. 査読あり 国際共著 国際誌
Yong Zhang, Hisae Tateishi-Karimata, Tamaki Endoh, Qiongli Jin, Kexin Li, Xiaoru Fan, Yingjun Ma, Limin Gao, Haiyan Lu, Zhiye Wang, Art E Cho, Xuefeng Yao, Chunming Liu, Naoki Sugimoto, Shiwei Guo, Xiangdong Fu, Qirong Shen, Guohua Xu, Luis Rafael Herrera-Estrella, Xiaorong Fan
Science advances 8 ( 47 ) eadc9785 2022年11月
Climate change negatively affects crop yield, which hinders efforts to reach agricultural sustainability and food security. Here, we show that a previously unidentified allele of the nitrate transporter gene OsNRT2.3 is required to maintain high yield and high nitrogen use efficiency under high temperatures. We demonstrate that this tolerance to high temperatures in rice accessions harboring the HTNE-2 (high temperature resistant and nitrogen efficient-2) alleles from enhanced translation of the OsNRT2.3b mRNA isoform and the decreased abundance of a unique small RNA (sNRT2.3-1) derived from the 5' untranslated region of OsNRT2.3. sNRT2.3-1 binds to the OsNRT2.3a mRNA in a temperature-dependent manner. Our findings reveal that allelic variation in the 5' untranslated region of OsNRT2.3 leads to an increase in OsNRT2.3b protein levels and higher yield during high-temperature stress. Our results also provide a breeding strategy to produce rice varieties with higher grain yield and lower N fertilizer input suitable for a sustainable agriculture that is resilient against climate change.
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Applicability of the nearest-neighbour model for pseudoknot RNAs. 査読あり 国際誌
Sagar Satpathi, Tamaki Endoh, Naoki Sugimoto
Chemical Communications 58 ( 40 ) 5952 - 5955 2022年5月
The validity of the nearest-neighbour (NN) model was verified in an RNA pseudoknot (PK) structure. The thermodynamic parameters of the second hairpin stem (S2) region, which separates the PK from a hairpin structure, were monitored using CD and UV melting. Different PKs with identical NN base pairs in the S2 region exhibited similar thermodynamic parameters, highlighting the validity of the NN model in this RNA tertiary structure motif.
DOI： 10.1039/d1cc07094k
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Correction to 'Improved nearest-neighbor parameters for the stability of RNA/DNA hybrids under a physiological condition'. 国際誌
Dipanwita Banerjee, Hisae Tateishi-Karimata, Tatsuya Ohyama, Saptarshi Ghosh, Tamaki Endoh, Shuntaro Takahashi, Naoki Sugimoto
Nucleic acids research 49 ( 18 ) 10796 - 10799 2021年10月
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Transcriptome screening followed by integrated physicochemical and structural analyses for investigating RNA-mediated berberine activity. 査読あり 国際共著 国際誌
Sagar Satpathi, Tamaki Endoh, Peter Podbevšek, Janez Plavec, Naoki Sugimoto
Nucleic acids research 49 ( 15 ) 8449 - 8461 2021年9月
担当区分：筆頭著者
Non-coding RNAs are regarded as promising targets for the discovery of innovative drugs due to their abundance in the genome and their involvement in many biological processes. Phytochemicals (PCs) are the primary source of ligand-based drugs due to their broad spectrum of biological activities. Since many PCs are heterocyclic and have chemical groups potentially involved in the interaction with nucleic acids, detailed interaction analysis between PCs and RNA is crucial to explore the effect of PCs on RNA functions. In this study, an integrated approach for investigating interactions between PCs and RNAs were demonstrated to verify the RNA-mediated PCs functions by using berberine (BRB) as a model PC. RNA screening of a transcriptome library followed by sequence refinement found minimal RNA motif consisting of a cytosine bulge with U-A and G-U neighbouring base pairs for interaction with BRB. NMR-based structure determination and physicochemical analyses using chemical analogues of BRB demonstrated the importance of electrostatic and stacking interactions for sequence selective interaction and RNA stabilization. The selective interaction with a relatively small RNA motif based on a chemical structure of a planer heterocyclic highlights the biological activities of various PCs mediated by the interactions with particular functional RNAs. In addition, the systematic and quantitative investigations demonstrated in this study could be useful for the development of therapeutic chemicals targeting functional RNAs, based on the PCs, in the future.
DOI： 10.1093/nar/gkab189
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Triple-Helical Binding of Peptide Nucleic Acid Inhibits Maturation of Endogenous MicroRNA-197. 査読あり 国際共著 国際誌
Tamaki Endoh, Nikita Brodyagin, Dziyana Hnedzko, Naoki Sugimoto, Eriks Rozners
ACS chemical biology 16 ( 7 ) 1147 - 1151 2021年7月
担当区分：筆頭著者
Sequence specific recognition and functional inhibition of biomedically relevant double-helical RNAs is highly desirable but remains a formidable problem. The present study demonstrates that electroporation of a triplex-forming peptide nucleic acid (PNA), modified with 2-aminopyridine (M) nucleobases, inhibited maturation of endogenous microRNA-197 in SH-SY5Y cells, while having little effect on maturation of microRNA-155 or -27a. In vitro RNA binding and Dicer inhibition assays suggested that the observed biological activity was most likely due to a sequence-specific PNA-RNA triplex formation that inhibited the activity of endonucleases responsible for microRNA maturation. The present study is the first example of modulation of activity of endogenous noncoding RNA using M-modified triplex-forming PNA.
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Naoki Sugimoto, Tamaki Endoh, Shuntaro Takahashi, Hisae Tateishi-Karimata
Bulletin of the Chemical Society of Japan 94 ( 7 ) 1970 - 1998 2021年7月
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Effects of Modifying Thioflavin T at the N3-Position on Its G4 Binding and Fluorescence Emission. 査読あり 国際誌
Yuka Kataoka, Hiroto Fujita, Tamaki Endoh, Naoki Sugimoto, Masayasu Kuwahara
Molecules (Basel, Switzerland) 25 ( 21 ) 2020年10月
We previously synthesized thioflavin T (ThT) with a hydroxyethyl group introduced at the N3-position (ThT-HE), which binds predominantly to the parallel G-quadruplex (G4) structure found in c-Myc and emits strong fluorescence. In this study, to investigate the effects of introduced substituents on G4 binding and fluorescence emission, a ThT derivative in which the hydroxyl group of ThT-HE was replaced with an amino group (ThT-AE) was synthesized for the first time. Furthermore, three other N3-modified ThT derivatives (ThT-OE2, ThT-SP, and ThT-OE11) having different substituent structures were synthesized by the N-acylation of the terminal amino group of ThT-AE, and their G4-binding and emission properties were investigated. The results showed that, although ThT-AE shows binding selectivity depending on the type of G4, its emission intensity is significantly decreased as compared to that of ThT-HE. However, ThT-OE11, which features an 11-unit oxyethylene chain attached to the terminal amino group of ThT-AE, regained about one-half of the emission intensity of ThT-HE while retaining selectivity for G4s. Accordingly, ThT-OE11 may be used as a key intermediate for synthesizing the conjugates of G4 binders and probes.
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Improved nearest-neighbor parameters for the stability of RNA/DNA hybrids under a physiological condition. 査読あり 国際誌
Dipanwita Banerjee, Hisae Tateishi-Karimata, Tatsuya Ohyama, Saptarshi Ghosh, Tamaki Endoh, Shuntaro Takahashi, Naoki Sugimoto
Nucleic acids research 48 ( 21 ) 12042 - 12054 2020年7月
共著
The stability of Watson-Crick paired RNA/DNA hybrids is important for designing optimal oligonucleotides for ASO (Antisense Oligonucleotide) and CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-Cas9 techniques. Previous nearest-neighbour (NN) parameters for predicting hybrid stability in a 1 M NaCl solution, however, may not be applicable for predicting stability at salt concentrations closer to physiological condition (e.g. ∼100 mM Na+ or K+ in the presence or absence of Mg2+). Herein, we report measured thermodynamic parameters of 38 RNA/DNA hybrids at 100 mM NaCl and derive new NN parameters to predict duplex stability. Predicted ΔG°37 and Tm values based on the established NN parameters agreed well with the measured values with 2.9% and 1.1°C deviations, respectively. The new results can also be used to make precise predictions for duplexes formed in 100 mM KCl or 100 mM NaCl in the presence of 1 mM Mg2+, which can mimic an intracellular and extracellular salt condition, respectively. Comparisons of the predicted thermodynamic parameters with published data using ASO and CRISPR-Cas9 may allow designing shorter oligonucleotides for these techniques that will diminish the probability of non-specific binding and also improve the efficiency of target gene regulation.
DOI： 10.1093/nar/gkaa572
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Nearest-neighbor parameters for predicting DNA duplex stability in diverse molecular crowding conditions. 査読あり 国際誌
Saptarshi Ghosh, Shuntaro Takahashi, Tatsuya Ohyama, Tamaki Endoh, Hisae Tateishi-Karimata, Naoki Sugimoto
Proceedings of the National Academy of Sciences of the United States of America 117 ( 25 ) 14194 - 14201 2020年6月
共著
The intracellular environment is crowded and heterogeneous. Although the thermodynamic stability of nucleic acid duplexes is predictable in dilute solutions, methods of predicting such stability under specific intracellular conditions are not yet available. We recently showed that the nearest-neighbor model for self-complementary DNA is valid under molecular crowding condition of 40% polyethylene glycol with an average molecular weight of 200 (PEG 200) in 100 mM NaCl. Here, we determined nearest-neighbor parameters for DNA duplex formation under the same crowding condition to predict the thermodynamics of DNA duplexes in the intracellular environment. Preferential hydration of the nucleotides was found to be the key factor for nearest-neighbor parameters in the crowding condition. The determined parameters were shown to predict the thermodynamic parameters (∆H°, ∆S°, and ∆G°37) and melting temperatures (Tm) of the DNA duplexes in the crowding condition with significant accuracy. Moreover, we proposed a general method for predicting the stability of short DNA duplexes in different cosolutes based on the relationship between duplex stability and the water activity of the cosolute solution. The method described herein would be valuable for investigating biological processes that occur under specific intracellular crowded conditions and for the application of DNA-based biotechnologies in crowded environments.
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Signaling Aptamer Optimization through Selection Using RNA-Capturing Microsphere Particles. 査読あり 国際誌
Tamaki Endoh, Naoki Sugimoto
Analytical chemistry 92 ( 11 ) 7955 - 7963 2020年6月
共著
担当区分：筆頭著者, 責任著者
An RNA signaling aptamer is composed of two units: a sensing aptamer that binds the input target molecule and a working aptamer that binds the output target molecule to result in a detectable signal. A conformational change of the signaling aptamer that induces an allosteric interaction with the output target molecule in response to the input target molecule depends on a junction region, which connects the two aptamer units. Efficient and effective optimization of the junction region remains a technical challenge. In this study, we demonstrate a simple strategy for optimizing the junction region through functional RNA selection using RNA-capturing microsphere particles. From approximately 0.2 million sequence variants, a signaling aptamer that enabled intracellular detection of S-adenosyl methionine with a high signal-to-noise ratio, which is approximately 2-fold higher relative fluorescence increment compared to the previously reported signaling aptamer, was obtained after single round of selection. The technology demonstrated here can be used to select RNA sequences that carry out specific functions in response to particular stimuli.
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RNA-capturing microsphere particles (R-CAMPs) for optimization of functional aptamers 招待あり 査読あり
Endoh T., Ohyama T., and Sugimoto N.
Small 15 ( 26 ) e1808062 2019年6月
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Conformational dynamics of the RNA G-quadruplex and its effect on translation efficiency 招待あり 査読あり
Endoh T. and Sugimoto N.
Molecules 24 ( 8 ) E1613 2019年4月
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Validation of the nearest-neighbor model for Watson-Crick self-complementary DNA duplexes in molecular crowding condition 査読あり
Ghosh S., Takahashi S., Endoh T., Tateishi-Karimata H., Hazra S., and Sugimoto N.
Ncleic Acids Res. 47 ( 7 ) 3284 - 3294 2019年4月
共著
DOI： 10.1093/nar/gkz071
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Co-transcriptional molecular assembly results in a kinetically controlled irreversible RNA conformational switch 査読あり
Endoh T. and Sugimoto N.
Anal. Chem. 90 ( 19 ) 11193 - 11197 2018年10月
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Pursuing origins of (poly)ethylene glycol-induced G-quadruplex structural modulations 査読あり 国際共著
M. Trajkovski,* T, Endoh,* H. Tateishi-Karimata, T. Ohyama, S. Tanaka, J. Plavec and N. Sugimoto [* Equal contribution]
Nucleic Acids Res. 46 4301 - 4315 2018年5月
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Cotranslational protein assembly imposes evolutionary constraints on homomeric proteins 査読あり 国際共著
E. Natan, T. Endoh, L. Haim-Vilmovsky, T. Flock, G. Chalancon, J. T. S. Hopper, B. Kintses, P. Horvath, L. Daruka, G. Fekete, C. Pál, B. Papp, E. Oszi, Z. Magyar, J. A. Marsh, A. H. Elcock, M. N. Babu, C. V. Robinson, N. Sugimoto, and S. A. Teichmann
Nat. Struct. Mol. Biol. 25 279 - 288 2018年3月
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Synthetic Chlorophyll-A Derivatives Stabilize DNA G-Quadruplex Structures
Nagano Yasunobu, Endoh Tamaki, Ogasawara Shin, Sugimoto Naoki, Tamiaki Hitoshi
BIOPHYSICAL JOURNAL 114 ( 3 ) 599A 2018年2月
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