Volume 4, Issue 2, June 2018, Pages: 18-23
Received: Jul. 9, 2018;
Accepted: Jul. 26, 2018;
Published: Aug. 16, 2018
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Riki Kurokawa, Division of Gene Structure and Function, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Japan
Reina Komiya, Science and Technology Group, Okinawa Institute Science and Technology Graduate University, Tancha, Japan; Japan Science and Technology Agency, PRESTO, Kawaguchi, Japan
Takanori Oyoshi, Department of Chemistry, Graduate School of Science, Shizuoka University, Suruga, Japan
Yoko Matsuno, Division of Clinical Preventive Medicine, Niigata University, Niigata, Japan
Hidenori Tani, Environmental Management Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
Masato Katahira, Institute of Advanced Energy, Kyoto University, Kyoto, Japan; Graduate School of Energy Science, Kyoto University, Kyoto, Japan
Keisuke Hitachi, Division for Therapies against Intractable Diseases, Fujita Health University, Toyoake, Japan
Yuji Iwashita, Department of Tumor Pathology, Hamamatsu University School of Medicine, Hamamatsu, Japan
Takefumi Yamashita, Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, the University of Tokyo, Tokyo, Japan
Keiko Kondo, Institute of Advanced Energy, Kyoto University, Kyoto, Japan
Ryoma Yoneda, Division of Gene Structure and Function, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Japan
Yudai Yamaoki, Institute of Advanced Energy, Kyoto University, Kyoto, Japan
Naomi Ueda, Division of Gene Structure and Function, Research Center for Genomic Medicine, Saitama Medical University, Hidaka, Japan
Tsukasa Mashima, Institute of Advanced Energy, Kyoto University, Kyoto, Japan; Graduate School of Energy Science, Kyoto University, Kyoto, Japan
Naohiro Kobayashi, Institute for Protein Research, Osaka University, Suita, Japan
Takashi Nagata, Institute of Advanced Energy, Kyoto University, Kyoto, Japan; Graduate School of Energy Science, Kyoto University, Kyoto, Japan
Ayaka Kiyoishi, Graduate School of Energy Science, Kyoto University, Kyoto, Japan
Masayuki Miyake, Graduate School of Energy Science, Kyoto University, Kyoto, Japan
Fumi Kano, Cell Biology Center, Institute of Innovative Research, Tokyo Institute of Technology, Tokyo, Japan
Masayuki Murata, Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, Japan
Nesreen Hamad, Institute of Advanced Energy, Kyoto University, Kyoto, Japan; Graduate School of Energy Science, Kyoto University, Kyoto, Japan
Kohei Sasaki, Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, the University of Tokyo, Tokyo, Japan
Naoyuki Shoji, Laboratory for Systems Biology and Medicine, Research Center for Advanced Science and Technology, the University of Tokyo, Tokyo, Japan
This review article aims at demonstration of complexity or multiplicity of long noncoding RNA. The presentations of the meeting cover variety of biomedical sciences to indicate significance of long noncoding RNA in each field. The achievements of the meeting are to confirm a point of view of long noncoding RNAs in living cells. It should be in complexity. We will be able to analyze complicated phenomena of lncRNA biological actions and might have resolved the vailed rules in divergent biological programs. In the plant system, its long noncoding RNAs possesses unique property compared to mammalian systems, but tells us an unveiled fundamental principle behind all creatures in the globe. Then, experimental data from structural biology mainly by NMR analysis show that interaction of nucleic acids to RNA binding proteins focusing on TLS/FUS. Analyses of TLS are also performed by biochemistry and molecular biology to indicate precise figures of RNA binding specificity and also methylation effect on TLS. Biological meaning of the DNA local conformation like G-quadruplex is presented. XIST, one of the best known long noncoding RNA, related to X chromosome inactivation, has been linked to novel finding in epigenetic functional redundancy such as long noncoding RNA -chromatin associations. In the iPS cells, their long noncoding RNA s have been identified as a potential marker for chemical stress responses. Cellular differentiation is also regulated by specific long noncoding RNA. Computational analysis is another approach to make progress. Transcriptome mining indicates an association between aging and sets of long noncoding RNAs with previously unidentified function. Molecular dynamics simulation of RNA presents unprecedented pathway to future of the field. The data in the manuscript are based upon the 2nd Annual Meeting of the long noncoding RNA study group. On Thursday, May 24 in 2018, 2nd Annual Meeting of the long noncoding RNA study group was held at Research Center for Advanced Science and Technology (RCAST), the University of Tokyo, Tokyo in Japan. The purpose of the meeting is to present recent data and have discussion regarding long noncoding RNA and related topics. We had thirteen sessions and exciting and fruitful debates there. The meeting has been successfully prorogued. We utilize the data to boost the activity of the field of long noncoding RNA.
Multiplicity in Long Noncoding RNA in Living Cells, Biomedical Sciences.
Vol. 4, No. 2,
2018, pp. 18-23.
Komiya R, Ohyanagi H, Niihama M, Watanabe T, Nakano M, Kurata N & Nonomura K (2014) Rice germline-specific Argonaute MEL1 protein binds to phasiRNAs generated from more than 700 lincRNAs. Plant J 78, 385-397, doi: 10.1111/tpj.12483.
Komiya R (2017) Biogenesis of diverse plant phasiRNAs involves an miRNA-trigger and Dicer-processing. J Plant Res 130, 17-23, doi: 10.1007/s10265-016-0878-0.
Takahama K, Takada A, Tada S, Shimizu M, Sayama K, Kurokawa R & Oyoshi T (2013) Regulation of telomere length by G-quadruplex telomere DNA- and TERRA-binding protein TLS/FUS. Chemistry & biology 20, 341-350, doi: 10.1016/j.chembiol.2013.02.013.
Takahama K & Oyoshi T (2013) Specific binding of modified RGG domain in TLS/FUS to G-quadruplex RNA: tyrosines in RGG domain recognize 2'-OH of the riboses of loops in G-quadruplex. J Am Chem Soc 135, 18016-18019, doi: 10.1021/ja4086929.
Kondo K, Mashima T, Oyoshi T. Yagi R, Kurokawa R, Kobayashi N, Nagata T & Katahira M (2018) Plastic roles of phenylalanine and tyrosine residues of an RGG motif of TLS/FUS in binary and ternary complex formation with the G-quadruplex structures of telomeric DNA and TERRA, Sci Rep 8, 2864, doi: 10.1038/s41598-018-21142-1.
Yoneda R, Suzuki S, Mashima T, Kondo K, Nagata T, Katahira M & Kurokawa R (2016) The binding specificity of Translocated in LipoSarcoma/FUsed in Sarcoma with lncRNA transcribed from the promoter region of cyclin D1. Cell & bioscience 6, 4, doi: 10.1186/s13578-016-0068-8.
Hansel R, Luh LM, Corbeski I, Trantirek L & Dotsch V (2014) In-cell NMR and EPR spectroscopy of biomacromolecules. Angew Chem Int Ed Engl 53, 10300-10314, doi: 10.1002/anie.201311320.
Giassa IC, Rynes J, Fessl T, Foldynova-Trantirkova S & Trantirek L (2018) Advances in the cellular structural biology of nucleic acids. FEBS letters, doi: 10.1002/1873-3468.13054.
Yamaoki Y, Kiyoishi A, Miyake M, Kano F, Murata M, Nagata T & Katahira M (2018) The first successful observation of in-cell NMR signals of DNA and RNA in living human cells. Phys Chem Chem Phys 20, 3109-3117, doi: 10.1039/c7cp05188c.
Cui W, Yoneda R, Ueda N & Kurokawa R (2018) Arginine methylation of translocated in liposarcoma (TLS) inhibits its binding to long noncoding RNA, abrogating TLS-mediated repression of CBP/p300 activity. The Journal of biological chemistry, doi: 10.1074/jbc.RA117.000598
Thandapani P, O'Connor TR, Bailey TL & Richard S (2013) Defining the RGG/RG motif. Molecular Cell 50, 613-623, doi: 10.1016/j.molcel.2013.05.021.
Sun X, Haider Ali MSS & Moran M (2017) The role of interactions of long non-coding RNAs and heterogeneous nuclear ribonucleoproteins in regulating cellular functions. The Biochemical journal 474, 2925-2935, doi: 10.1042/BCJ20170280.
Wang X, Arai S, Song X, Reichart D, Du K, Pascual G, Tempst P, Rosenfeld MG, Glass CK & Kurokawa R (2008) Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 454, 126-130, doi: nature06992 [pii]10.1038/nature06992.
Wang X, Schwartz JC & Cech TR (2015) Nucleic acid-binding specificity of human FUS protein. Nucleic Acids Research 43, 7535-7543, doi: 10.1093/nar/gkv679.
Tani H, Okuda S, Nakamura K, Aoki M & Umemura T (2017) Short-lived long non-coding RNAs as surrogate indicators for chemical exposure and LINC00152 and MALAT1 modulate their neighboring genes. PLoS One 12, e0181628, doi: 10.1371/journal.pone.0181628.
Yamashita T (2018) Toward rational antibody design: recent advancements in molecular dynamics simulations. Int Immunol 30, 133-140, doi: 10.1093/intimm/dxx077.
Yamashita T (2016) Towards Physical Understanding of Molecular Recognition in the Cell: Recent Evolution of Molecular Dynamics Techniques and Free Energy Theories. Biomedical Sciences 2, 34-47 doi: 10.11648/j.bs.20160205.11.
Yamashita T, Ueda A, Mitsui T, Tomonaga A, Matsumoto S, Kodama T & Fujitani H (2015) The Feasibility of an Efficient Drug Design Method with High-Performance Computers. Chemical and Pharmaceutical Bulletin 63, 147-155, doi: 10.1248/cpb.c14-00596.
Yamashita T (2015) Improvement in Empirical Potential Functions for Increasing the Utility of Molecular Dynamics Simulations, JPS Conf Proc, 5, 010003. doi:10.7566/JPSCP.5.010003
Tan D, Piana S, Dirks RM & Shaw DE (2018) RNA force field with accuracy comparable to state-of-the-art protein force fields. Proceedings of the National Academy of Sciences of the United States of America 115, E1346-E1355, doi: 10.1073/pnas.1713027115.