Assistant Professor in Department of Biochemistry and Molecular Biology, and Computational Medicine Center at TJU Yohei Kirino

Assistant Professor in Department of Biochemistry and Molecular Biology, and Computational Medicine Center at TJU

Short Bio

Dr. Kirino is Assistant Professor (Principal Investigator) in Computational Medicine Center and Department of Biochemistry and Molecular Biology at Thomas Jefferson University (TJU) where he joined in mid-2013. The overall research goal of his lab is to understand biogenesis and molecular function of small regulatory RNAs, and use the knowledge for the development of novel biomarkers and therapeutic applications in diseases. Small regulatory RNAs have emerged recently as one of the most novel and exciting areas of gene expression regulation. By taking advantage of RNA biochemistry and molecular/cellular biology, the Kirino lab is particularly focused on PIWI-interacting RNAs (piRNAs), the most recently discovered small regulatory RNAs expressed in the germline. The Kirino lab has also been tackling tRNA researches to develop novel biomarkers and therapeutic applications for cancers and mitochondrial diseases. Prior to joining TJU, Dr. Kirino was Assistant Professor in Department of Biomedical Sciences at Cedars Sinai Medical Center (2010-2013) where he started his independent academic career. Together with his Postdoc period in Dr. Zissimos Mourelatos’ lab at the University of Pennsylvania School of Medicine (2006-2010), his studies in the piRNA pathway discovered both RNA and protein modifications that play important roles in piRNA biogenesis and function. Dr. Kirino received his BSc (2001), MSc (2003) and PhD (2006) from The University of Tokyo, Japan. In Dr. Tsutomu Suzuki’s lab, he investigated molecular pathogenesis of mitochondrial diseases caused by tRNA modification disorder.

Publications

Papers

 

2017

  • 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.
  • 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.
  • Honda, S, Kawamura, T, Loher, P, Morichika, K, Rigoutsos, I, Kirino, Y. The biogenesis pathway of tRNA-derived piRNAs in Bombyx germ cells. Nucleic Acids Res. 2017;45 (15):9108-9120. doi: 10.1093/nar/gkx537. PubMed PMID:28645172 PubMed Central PMC5587776.
  • 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.

2016

  • Telonis, AG, Loher, P, Kirino, Y, Rigoutsos, I. Consequential considerations when mapping tRNA fragments. BMC Bioinformatics. 2016;17 :123. doi: 10.1186/s12859-016-0921-0. PubMed PMID:26961774 PubMed Central PMC4785646.
  • Izumi, N, Shoji, K, Sakaguchi, Y, Honda, S, Kirino, Y, Suzuki, T, Katsuma, S, Tomari, Y. Identification and Functional Analysis of the Pre-piRNA 3' Trimmer in Silkworms. Cell. 2016;164 (5):962-73. doi: 10.1016/j.cell.2016.01.008. PubMed PMID:26919431 PubMed Central PMC4856147.
  • Honda, S, Morichika, K, Kirino, Y. Selective amplification and sequencing of cyclic phosphate-containing RNAs by the cP-RNA-seq method. Nat Protoc. 2016;11 (3):476-89. doi: 10.1038/nprot.2016.025. PubMed PMID:26866791 PubMed Central PMC4852555.
  • Sakai, H, Kirino, Y, Kastuma, S, Aoki, F, Suzuki, MG. Morphological and histomorphological structures of testes and ovaries in early developmental stages of the silkworm, Bombyx mori. Journal of Insect Biotechnology and Sericology 2016; 85: 15-20

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.
  • Telonis, AG, Loher, P, Honda, S, Jing, Y, Palazzo, J, Kirino, Y, Rigoutsos, I. Dissecting tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies. Oncotarget. 2015;6 (28):24797-822. doi: 10.18632/oncotarget.4695. PubMed PMID:26325506 PubMed Central PMC4694795.
  • 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.
  • Telonis, AG, Kirino, Y, Rigoutsos, I. Mitochondrial tRNA-lookalikes in nuclear chromosomes: could they be functional?. RNA Biol. 2015;12 (4):375-80. doi: 10.1080/15476286.2015.1017239. PubMed PMID:25849196 PubMed Central PMC4615777.
  • 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.
  • Honda, S, Kirino, Y. Dumbbell-PCR: a method to quantify specific small RNA variants with a single nucleotide resolution at terminal sequences. Nucleic Acids Res. 2015;43 (12):e77. doi: 10.1093/nar/gkv218. PubMed PMID:25779041 PubMed Central PMC4499115.
  • Londin, E, Loher, P, Telonis, AG, Quann, K, Clark, P, Jing, Y, Hatzimichael, E, Kirino, Y, Honda, S, Lally, M, Ramratnam, B, Comstock, CE, Knudsen, KE, Gomella, L, Spaeth, GL, Hark, L, Katz, LJ, Witkiewicz, A, Rostami, A, Jimenez, SA, Hollingsworth, MA, Yeh, JJ, Shaw, CA, McKenzie, SE, Bray, P, Nelson, PT, Zupo, S, Van Roosbroeck, K, Keating, MJ, Calin, GA, Yeo, C, Jimbo, M, Cozzitorto, J, Brody, JR, Delgrosso, K, Mattick, JS, Fortina, P, Rigoutsos, I. Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs. Proc. Natl. Acad. Sci. U.S.A. 2015;112 (10):E1106-15. doi: 10.1073/pnas.1420955112. PubMed PMID:25713380 PubMed Central PMC4364231.
  • Honda, S, Kirino, Y. SHOT-RNAs: a novel class of tRNA-derived functional RNAs expressed in hormone-dependent cancers. Molecular & Cellular Oncology. 2015;3:2. doi: 10.1080/23723556.2015.1079672.

2014

  • Telonis, AG, Loher, P, Kirino, Y, Rigoutsos, I. Nuclear and mitochondrial tRNA-lookalikes in the human genome. Front Genet. 2014;5 :344. doi: 10.3389/fgene.2014.00344. PubMed PMID:25339973 PubMed Central PMC4189335.
  • Honda, S, Kirino, Y, Kirino, Y. Analysis of sDMA modifications of PIWI proteins. Methods Mol. Biol. 2014;1093 :137-48. doi: 10.1007/978-1-62703-694-8_11. PubMed PMID:24178562 PubMed Central PMC4376280.
  • Shigematsu, M, Honda, S, Kirino, Y (2014) "Transfer RNA as a Source of Small Functional RNA"J Mol Biol & Mol Imaging 1(2): 8 doi: Download

2013

  • Honda, S, Kirino, Y, Maragkakis, M, Alexiou, P, Ohtaki, A, Murali, R, Mourelatos, Z, Kirino, Y. Mitochondrial protein BmPAPI modulates the length of mature piRNAs. RNA. 2013;19 (10):1405-18. doi: 10.1261/rna.040428.113. PubMed PMID:23970546 PubMed Central PMC3854531.
  • Honda, S and Kirino, Y (2013) “PIWIL1 (piwi-like RNA-mediated gene silencing 1)” Atlas Genet Cytogenet Oncol Haematol. 17(12):833-836. doi: Genes/PIWIL1ID46561ch12q24

2012

  • Suzuki, R, Honda, S, Kirino, Y. PIWI Expression and Function in Cancer. Front Genet. 2012;3 :204. doi: 10.3389/fgene.2012.00204. PubMed PMID:23087701 PubMed Central PMC3472457.
  • Vourekas, A, Zheng, Q, Alexiou, P, Maragkakis, M, Kirino, Y, Gregory, BD, Mourelatos, Z. Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis. Nat. Struct. Mol. Biol. 2012;19 (8):773-81. doi: 10.1038/nsmb.2347. PubMed PMID:22842725 PubMed Central PMC3414646.

2011

  • Kirino, Y. [Role of arginine methylation in the Piwi-interacting RNA pathway]. Seikagaku. 2011;83 (4):312-6. . PubMed PMID:21626884 .
  • Kirino, Y, Vourekas, A, Khandros, E, Mourelatos, Z. Immunoprecipitation of piRNPs and directional, next generation sequencing of piRNAs. Methods Mol. Biol. 2011;725 :281-93. doi: 10.1007/978-1-61779-046-1_18. PubMed PMID:21528460 .

2010

  • Mimaki, M, Hatakeyama, H, Komaki, H, Yokoyama, M, Arai, H, Kirino, Y, Suzuki, T, Nishino, I, Nonaka, I, Goto, Y. Reversible infantile respiratory chain deficiency: a clinical and molecular study. Ann. Neurol. 2010;68 (6):845-54. doi: 10.1002/ana.22111. PubMed PMID:21194154 .
  • Vourekas, A, Kirino, Y, Mourelatos, Z. Elective affinities: a Tudor-Aubergine tale of germline partnership. Genes Dev. 2010;24 (18):1963-6. doi: 10.1101/gad.1977010. PubMed PMID:20844011 PubMed Central PMC2939360.
  • Kirino, Y, Vourekas, A, Kim, N, de Lima Alves, F, Rappsilber, J, Klein, PS, Jongens, TA, Mourelatos, Z. Arginine methylation of vasa protein is conserved across phyla. J. Biol. Chem. 2010;285 (11):8148-54. doi: 10.1074/jbc.M109.089821. PubMed PMID:20080973 PubMed Central PMC2832966.
  • Kirino, Y, Vourekas, A, Sayed, N, de Lima Alves, F, Thomson, T, Lasko, P, Rappsilber, J, Jongens, TA, Mourelatos, Z. Arginine methylation of Aubergine mediates Tudor binding and germ plasm localization. RNA. 2010;16 (1):70-8. doi: 10.1261/rna.1869710. PubMed PMID:19926723 PubMed Central PMC2802038.

2009

  • Kirino, Y, Kim, N, de Planell-Saguer, M, Khandros, E, Chiorean, S, Klein, PS, Rigoutsos, I, Jongens, TA, Mourelatos, Z. Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stability. Nat. Cell Biol. 2009;11 (5):652-8. doi: 10.1038/ncb1872. PubMed PMID:19377467 PubMed Central PMC2746449.

2008

  • Kirino, Y, Mourelatos, Z. Site-specific crosslinking of human microRNPs to RNA targets. RNA. 2008;14 (10):2254-9. doi: 10.1261/rna.1133808. PubMed PMID:18719246 PubMed Central PMC2553735.
  • Kurata, S, Weixlbaumer, A, Ohtsuki, T, Shimazaki, T, Wada, T, Kirino, Y, Takai, K, Watanabe, K, Ramakrishnan, V, Suzuki, T. Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U.G wobble pairing during decoding. J. Biol. Chem. 2008;283 (27):18801-11. doi: 10.1074/jbc.M800233200. PubMed PMID:18456657 .

2007

  • Kirino, Y, Mourelatos, Z. 2'-O-methyl modification in mouse piRNAs and its methylase. Nucleic Acids Symp Ser (Oxf). 2007; (51):417-8. doi: 10.1093/nass/nrm209. PubMed PMID:18029764 .
  • Kirino, Y, Mourelatos, Z. The mouse homolog of HEN1 is a potential methylase for Piwi-interacting RNAs. RNA. 2007;13 (9):1397-401. doi: 10.1261/rna.659307. PubMed PMID:17652135 PubMed Central PMC1950760.
  • Kirino, Y, Mourelatos, Z. Mouse Piwi-interacting RNAs are 2'-O-methylated at their 3' termini. Nat. Struct. Mol. Biol. 2007;14 (4):347-8. doi: 10.1038/nsmb1218. PubMed PMID:17384647 .

2006

  • Noma, A, Kirino, Y, Ikeuchi, Y, Suzuki, T. Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA. EMBO J. 2006;25 (10):2142-54. doi: 10.1038/sj.emboj.7601105. PubMed PMID:16642040 PubMed Central PMC1462984.
  • Kirino, Y, Yasukawa, T, Marjavaara, SK, Jacobs, HT, Holt, IJ, Watanabe, K, Suzuki, T. Acquisition of the wobble modification in mitochondrial tRNALeu(CUN) bearing the G12300A mutation suppresses the MELAS molecular defect. Hum. Mol. Genet. 2006;15 (6):897-904. doi: 10.1093/hmg/ddl007. PubMed PMID:16446307 .

2005

  • Kirino, Y, Suzuki, T. Human mitochondrial diseases associated with tRNA wobble modification deficiency. RNA Biol. 2005;2 (2):41-4. . PubMed PMID:17132941 .
  • Yasukawa, T, Kirino, Y, Ishii, N, Holt, IJ, Jacobs, HT, Makifuchi, T, Fukuhara, N, Ohta, S, Suzuki, T, Watanabe, K. Wobble modification deficiency in mutant tRNAs in patients with mitochondrial diseases. FEBS Lett. 2005;579 (13):2948-52. doi: 10.1016/j.febslet.2005.04.038. PubMed PMID:15893315 .
  • Kirino, Y, Goto, Y, Campos, Y, Arenas, J, Suzuki, T. Specific correlation between the wobble modification deficiency in mutant tRNAs and the clinical features of a human mitochondrial disease. Proc. Natl. Acad. Sci. U.S.A. 2005;102 (20):7127-32. doi: 10.1073/pnas.0500563102. PubMed PMID:15870203 PubMed Central PMC1129107.
  • Kirino, Y. and Suzuki, T (2005) "MELAS A3243G mutation and tRNA modification disorder" Rinsyoukensa 49: 89-95

2004

  • Kirino, Y, Yasukawa, T, Ohta, S, Akira, S, Ishihara, K, Watanabe, K, Suzuki, T. Codon-specific translational defect caused by a wobble modification deficiency in mutant tRNA from a human mitochondrial disease. Proc. Natl. Acad. Sci. U.S.A. 2004;101 (42):15070-5. doi: 10.1073/pnas.0405173101. PubMed PMID:15477592 PubMed Central PMC524061.
  • Limongelli, A, Schaefer, J, Jackson, S, Invernizzi, F, Kirino, Y, Suzuki, T, Reichmann, H, Zeviani, M. Variable penetrance of a familial progressive necrotising encephalopathy due to a novel tRNA(Ile) homoplasmic mutation in the mitochondrial genome. J. Med. Genet. 2004;41 (5):342-9. . PubMed PMID:15121771 PubMed Central PMC1735786.

2003

  • Kurata, S, Ohtsuki, T, Wada, T, Kirino, Y, Takai, K, Saigo, K, Watanabe, K, Suzuki, T. Decoding property of C5 uridine modification at the wobble position of tRNA anticodon. Nucleic Acids Res. Suppl. 2003; (3):245-6. . PubMed PMID:14510472 .

To see the group's publications please click here or go to Research -> Publications

Contact Info