Research Instructor

Megumi Shigematsu

Research Instructor

Short Bio

Megumi joined Dr. Kirino’s lab in early 2014 as a research assistant, then joined the Computational Medicine Center in early 2015. She received her Ph.D. from the University of Tokyo, where she studied tRNA biology in the yeast cell and tRNA biochemistry. During her postdoc career, she has been studying functions of non-coding RNAs including tRNA, by the combined strength of biochemistry, kinetics and cell biology. Her research goal is to develop a comprehensive understanding of protein–RNA and RNA–RNA interactions that regulate many of the indispensable cellular activity.

Publications

2024

  • Gumas, J, Kawamura, T, Shigematsu, M, Kirino, Y. Immunostimulatory short non-coding RNAs in the circulation of patients with tuberculosis infection. Mol Ther Nucleic Acids. 2024;35 (1):102156. doi: 10.1016/j.omtn.2024.102156. PubMed PMID:38481936 PubMed Central PMC10933579.

2022

  • Clemente, P, Calvo-Garrido, J, Pearce, SF, Schober, FA, Shigematsu, M, Siira, SJ, Laine, I, Spåhr, H, Steinmetzger, C, Petzold, K, Kirino, Y, Wibom, R, Rackham, O, Filipovska, A, Rorbach, J, Freyer, C, Wredenberg, A. ANGEL2 phosphatase activity is required for non-canonical mitochondrial RNA processing. Nat Commun. 2022;13 (1):5750. doi: 10.1038/s41467-022-33368-9. PubMed PMID:36180430 PubMed Central PMC9525292.
  • Shigematsu, M, Kirino, Y. Making Invisible RNA Visible: Discriminative Sequencing Methods for RNA Molecules with Specific Terminal Formations. Biomolecules. 2022;12 (5):. doi: 10.3390/biom12050611. PubMed PMID:35625540 PubMed Central PMC9138997.

2021

  • Shigematsu M, Kawamura T, Morichika K, Izumi N, Kiuchi T, Honda S, Pliatsika V, Matsubara R, Rigoutsos I, Katsuma S, Tomari Y, Kirino Y. RNase κ promotes robust piRNA production by generating 2',3'-cyclic phosphate-containing precursors. Nat Commun. 2021 Jul 23;12(1):4498. doi: 10.1038/s41467-021-24681-w. PubMed PMID:34301931.
  • Kawamura T, Shigematsu M, Kirino Y. In vitro production and multiplex quantification of 2',3'-cyclic phosphate-containing 5'-tRNA half molecules. Methods. 2021 May 4:S1046-2023(21)00124-9. doi: 10.1016/j.ymeth.2021.04.024. Epub ahead of print. PubMed PMID:33962012.

2020

2019

  • Shigematsu, M, Morichika, K, Kawamura, T, Honda, S, Kirino, Y. Genome-wide identification of short 2',3'-cyclic phosphate-containing RNAs and their regulation in aging. PLoS Genet. 2019 Nov 13;15(11):e1008469. doi: 10.1371/journal.pgen.1008469. PubMed PMID:31721758.
  • Pawar, K, Shigematsu, M, Loher, P, Honda, S, Rigoutsos, I, Kirino, Y. Exploration of CCA-added RNAs revealed the expression of mitochondrial non-coding RNAs regulated by CCA-adding enzyme. RNA Biol. 2019 Sep 12:1-9. doi: 10.1080/15476286.2019.1664885. PubMed PMID:31512554.

2018

  • Shigematsu, M, Kawamura, T, Kirino, Y. Generation of 2',3'-Cyclic Phosphate-Containing RNAs as a Hidden Layer of the Transcriptome. Front Genet. 2018;9 :562. doi: 10.3389/fgene.2018.00562. PubMed PMID:30538719 PubMed Central PMC6277466.
  • Pliatsika, V, Loher, P, Magee, R, Telonis, AG, Londin, E, Shigematsu, M, Kirino, Y, Rigoutsos, I. MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects. Nucleic Acids Res. 2018;46 (D1):D152-D159. doi: 10.1093/nar/gkx1075. PubMed PMID:29186503 PubMed Central PMC5753276.
  • Shigematsu, M, Honda, S, Kirino, Y. Dumbbell-PCR for Discriminative Quantification of a Small RNA Variant. Methods Mol. Biol. 2018;1680 :65-73. doi: 10.1007/978-1-4939-7339-2_4. PubMed PMID:29030841 .

2017

  • Honda, S, Loher, P, Morichika, K, Shigematsu, M, Kawamura, T, Kirino, Y, Rigoutsos, I, Kirino, Y. Increasing cell density globally enhances the biogenesis of Piwi-interacting RNAs in Bombyx mori germ cells. Sci Rep. 2017;7 (1):4110. doi: 10.1038/s41598-017-04429-7. PubMed PMID:28646211 PubMed Central PMC5482885.
  • Shigematsu, M, Honda, S, Loher, P, Telonis, AG, Rigoutsos, I, Kirino, Y. YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs. Nucleic Acids Res. 2017;45 (9):e70. doi: 10.1093/nar/gkx005. PubMed PMID:28108659 PubMed Central PMC5605243.
  • Shigematsu, M, Kirino, Y. 5"-Terminal nucleotide variations in human cytoplasmic tRNAHisGUG and its 5"-halves. RNA. 2017;23 (2):161-168. doi: 10.1261/rna.058024.116. PubMed PMID:27879434 PubMed Central PMC5238791.

2015

  • Shigematsu, M, Kirino, Y. tRNA-Derived Short Non-coding RNA as Interacting Partners of Argonaute Proteins. Gene Regul Syst Bio. 2015;9 :27-33. doi: 10.4137/GRSB.S29411. PubMed PMID:26401098 PubMed Central PMC4567038.
  • Honda, S, Loher, P, Shigematsu, M, Palazzo, JP, Suzuki, R, Imoto, I, Rigoutsos, I, Kirino, Y. Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers. Proc. Natl. Acad. Sci. U.S.A. 2015;112 (29):E3816-25. doi: 10.1073/pnas.1510077112. PubMed PMID:26124144 PubMed Central PMC4517238.
  • Kouno, T, Luengas, EM, Shigematsu, M, Shandilya, SM, Zhang, J, Chen, L, Hara, M, Schiffer, CA, Harris, RS, Matsuo, H. Structure of the Vif-binding domain of the antiviral enzyme APOBEC3G. Nat. Struct. Mol. Biol. 2015;22 (6):485-91. doi: 10.1038/nsmb.3033. PubMed PMID:25984970 PubMed Central PMC4456288.
  • Honda, S, Shigematsu, M, Morichika, K, Telonis, AG, Kirino, Y. Four-leaf clover qRT-PCR: A convenient method for selective quantification of mature tRNA. RNA Biol. 2015;12 (5):501-8. doi: 10.1080/15476286.2015.1031951. PubMed PMID:25833336 PubMed Central PMC4615770.
  • Simons, C, Griffin, LB, Helman, G, Golas, G, Pizzino, A, Bloom, M, Murphy, JL, Crawford, J, Evans, SH, Topper, S, Whitehead, MT, Schreiber, JM, Chapman, KA, Tifft, C, Lu, KB, Gamper, H, Shigematsu, M, Taft, RJ, Antonellis, A, Hou, YM, Vanderver, A. Loss-of-function alanyl-tRNA synthetase mutations cause an autosomal-recessive early-onset epileptic encephalopathy with persistent myelination defect. Am. J. Hum. Genet. 2015;96 (4):675-81. doi: 10.1016/j.ajhg.2015.02.012. PubMed PMID:25817015 PubMed Central PMC4385183.

2013

  • Shigematsu, M, Ogawa, T, Tanaka, W, Takahashi, K, Kitamoto, HK, Hidaka, M, Masaki, H. Evidence for DNA cleavage caused directly by a transfer RNA-targeting toxin. PLoS ONE. 2013;8 (9):e75512. doi: 10.1371/journal.pone.0075512. PubMed PMID:24069426 PubMed Central PMC3775755.

2012

  • Shigematsu, M, Ogawa, T, Kitamoto, HK, Hidaka, M, Masaki, H. Specific phase arrest of cell cycle restores cell viability against tRNA cleavage by killer toxin. Biochem. Biophys. Res. Commun. 2012;420 (4):750-4. doi: 10.1016/j.bbrc.2012.03.061. PubMed PMID:22450321 .

2009

  • Shigematsu, M, Ogawa, T, Kido, A, Kitamoto, HK, Hidaka, M, Masaki, H. Cellular and transcriptional responses of yeast to the cleavage of cytosolic tRNAs induced by colicin D. Yeast. 2009;26 (12):663-73. doi: 10.1002/yea.1725. PubMed PMID:19877125.

Contact Info

Email: Megumi.Shigematsu@jefferson.edu