Kirino Research


Name: Yohei Kirino, PhD
Position: Associate Professor, Computational Medicine Center, Department of Biochemistry and Molecular Biology

Jefferson Alumni Hall
1020 Locust Street, Suite 222
Philadelphia, PA 19107

Contact Number(s):

Recent Publications


RNase κ promotes robust piRNA production by generating 2',3'-cyclic phosphate-containing precursors
Shigematsu, M#, Kawamura, T#, Morichika, K, Izumi, N, Kiuchi, T, Honda, S, Pliatsika, V, Matsubara, R, Rigoutsos, I, Katsuma, S, Tomari, Y, Kirino, Y*. 
Nat Commun 12(1):4498, 2021. [Pubmed]
# Equal contribution.

In vitro production and multiplex quantification of 2',3'-cyclic phosphate-containing 5'-tRNA half molecules
Kawamura, T#, Shigematsu, M#, Kirino, Y*.  Methods, 2021. [Pubmed]
# Equal contribution.


Infection-induced 5'-half molecules of tRNAHisGUG activate Toll-like receptor 7
Pawar, K, Shigematsu, M, Sharbati, S, Kirino, Y*. 
PLoS Biol 18(12):e3000982, 2020. [Pubmed]

Complete chemical structures of human mitochondrial tRNAs
Suzuki, T, Yashiro, Y, Kikuchi, I, Ishigami, Y, Saito, H, Matsuzawa, I, Okada, S, Mito, M, Iwasaki, S, Ma, D, Zhao, X, Asano, K, Lin, H, Kirino, Y, Sakaguchi, Y, Suzuki, T.
Nat Commun 11(1):4269, 2020. [Pubmed]

Oxidative stress enhances the expression of 2',3'-cyclic phosphate-containing RNAs
Shigematsu, M, Kirino, Y*. 
RNA Biol 17(8):1060-1069, 2020. [Pubmed]

Modulation of Aub-TDRD interactions elucidates piRNA amplification and germplasm formation
Vrettos, N, Maragkakis, M, Alexiou, P, Sgourdou, P, Ibrahim, F, Palmieri, D, Kirino, Y, Mourelatos, Z. Life Sci Alliance 4(3): e202000912, 2020. [Pubmed]


Genome-wide identification of short 2',3'-cyclic phosphate-containing RNAs and their regulation in aging
Shigematsu, M, Morichika, K, Kawamura, T, Honda, S, Kirino, Y*. 
PLoS Genet 15(11):e1008469, 2019. [Pubmed]

Exploration of CCA-added RNAs revealed the expression of mitochondrial non-coding RNAs regulated by CCA-adding enzyme
Pawar, K, Shigematsu, M, Loher, P, Honda, S, Rigoutsos, I, Kirino, Y*. 
RNA Biol 16(12):1817-1825, 2019. [Pubmed]

Short RNA regulators: the past, the present, the future, and implications for precision medicine and health disparities
Rigoutsos, I*, Londin, E*, Kirino, Y*. 
Curr Opin Biotechnol 58:202-210, 2019. [Pubmed]

tRNA Fragments Show Intertwining with mRNAs of Specific Repeat Content and Have Links to Disparities
Telonis, AG, Loher, P, Magee, R, Pliatsika, V, Londin, E, Kirino, Y, Rigoutsos, I. 
Cancer Res 79(12):3034-3049, 2019. [Pubmed]


Generation of 2',3'-Cyclic Phosphate-Containing RNAs as a Hidden Layer of the Transcriptome
Shigematsu, M, Kawamura, T, Kirino, Y*. 
Front Genet 9:562, 2018. [Pubmed]

MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects
Pliatsika, V, Loher, P, Magee, R, Telonis, AG, Londin, E, Shigematsu, M, Kirino, Y, Rigoutsos, I.
Nucleic Acids Res 46(D1):D152-D159, 2018. [Pubmed]

Dumbbell-PCR for Discriminative Quantification of a Small RNA Variant
Shigematsu, M, Honda, S, Kirino, Y*. 
Methods Mol Biol 1680:65-73, 2018. [Pubmed]


5'-Terminal nucleotide variations in human cytoplasmic tRNAHisGUG and its 5'-halves
Shigematsu, Kirino, Y*. 
RNA 23(2):161-168, 2017. [Pubmed]

The biogenesis pathway of tRNA-derived piRNAs in Bombyx germ cells
Honda, S, Kawamura, T, Loher, P, Morichika, K, Rigoutsos, I, Kirino, Y*.
Nucleic Acids Res 45(15):9108-9120, 2017. [Pubmed]

Increasing cell density globally enhances the biogenesis of Piwi-interacting RNAs in Bombyx mori germ cells
Honda, S, Loher, P, Morichika, K, Shigematsu, M, Kawamura, T, Kirino, Y, Rigoutsos, I, Kirino, Y*. 
Sci Rep 7(1):4110, 2017. [Pubmed]

YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs
Shigematsu, M#, Honda, S#, Loher, P, Telonis, AG, Rigoutsos, I, Kirino, Y*.
Nucleic Acids Res 45(9):e70, 2017. [Pubmed]


Selective amplification and sequencing of cyclic phosphate-containing RNAs by the cP-RNA-seq method
Honda, S, Morichika, K, Kirino, Y*.
Nat Protoc 11(3):476-89, 2016. [Pubmed]

Identification and Functional Analysis of the Pre-piRNA 3' Trimmer in Silkworms
Izumi, N, Shoji, K, Sakaguchi, Y, Honda, S, Kirino, Y, Suzuki, T, Katsuma, S, Tomari, Y.
Cell 164(5):962-73, 2016. [Pubmed]

Consequential considerations when mapping tRNA fragments. BMC Bioinformatics
Telonis, AG, Loher, P, Kirino, Y, Rigoutsos, I.
BMC Bioinformatics 17:123, 2016. [Pubmed]

Morphological and histomorphological structures of testes and ovaries in early developmental stages of the silkworm, Bombyx mori
Sakai, H, Kirino, Y, Kastuma, S, Aoki, F, Suzuki, MG.
J Insect Biotechnol Sericology 85(1):15-20, 2016. [Pubmed]


SHOT-RNAs: a novel class of tRNA-derived functional RNAs expressed in hormone-dependent cancers
Honda, S, Kirino, Y*.
Mol Cell Oncol 3(2):e1079672, 2015. [Pubmed]

tRNA-Derived Short Non-coding RNA as Interacting Partners of Argonaute Proteins
Shigematsu, M, Kirino, Y*.
Gene Regul Syst Bio
 9:27-33, 2015. [Pubmed]

Sex hormone-dependent tRNA halves enhance cell proliferation in breast and prostate cancers
Honda, S, Loher, P, Shigematsu, M, Palazzo, JP, Suzuki, R, Imoto, I, Rigoutsos, I, Kirino, Y*. 
Proc Natl Acad Sci USA 112(29):E3816-25, 2015. [Pubmed]

tRNA-derived fragment complexities using personalized transcriptomes reveals novel fragment classes and unexpected dependencies
Telonis, AG, Loher, P, Honda, S, Jing, Y, Palazzo, J, Kirino, Y, Rigoutsos, I.
Oncotarget 6(28):24797-822, 2015. [Pubmed]

Mitochondrial tRNA-lookalikes in nuclear chromosomes: could they be functional?
Telonis, AG, Kirino, Y, Rigoutsos, I.
RNA Biol 12(4):375-80, 2015. [Pubmed]

Four-leaf clover qRT-PCR: A convenient method for selective quantification of mature tRNA
Honda, S, Shigematsu, M, Morichika, K, Telonis, AG, Kirino, Y*.
RNA Biol 12(5):501-8, 2015. [Pubmed]

Dumbbell-PCR: a method to quantify specific small RNA variants with a single nucleotide resolution at terminal sequences
Honda, S, Kirino, Y*.
Nucleic Acids Res 43(12):e77, 2015. [Pubmed]

Analysis of 13 cell types reveals evidence for the expression of numerous novel primate- and tissue-specific microRNAs
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.
Proc Natl Acad Sci USA 112(10):E1106-15, 2015. [Pubmed]


Analysis of sDMA modifications of PIWI proteins
Honda, S, Kirino, Y, Kirino, Y*. 
Methods Mol Biol 1093:137-48, 2014. [Pubmed]

Nuclear and mitochondrial tRNA-lookalikes in the human genome
Telonis, AG, Loher, P, Kirino, Y, Rigoutsos, I.
Front Genet 5:344, 2014. [Pubmed]

Transfer RNA as a Source of Small Functional RNA
Shigematsu, M, Honda, S, Kirino, Y*. 
J Mol Biol Mol Imaging 1(2), 2014. [Pubmed]


Mitochondrial protein BmPAPI modulates the length of mature piRNAs
Honda, S, Kirino, Y, Maragkakis, M, Alexiou, P, Ohtaki, A, Murali, R, Mourelatos, Z, Kirino, Y*. 
RNA 19(10):1405-18, 2013. [Pubmed]

PIWIL1 (piwi-like RNA-mediated gene silencing 1)
Honda, S, Kirino, Y*. 
Atlas Genet Cytogenet Oncol Haematol 17(12):833-836, 2013. [Genes/PIWIL1ID46561ch12q24]


PIWI Expression and Function in Cancer
Suzuki, R, Honda, S, Kirino, Y*. 
Front Genet 3:204, 2012. [Pubmed]

Mili and Miwi target RNA repertoire reveals piRNA biogenesis and function of Miwi in spermiogenesis
Vourekas, A, Zheng, Q, Alexiou, P, Maragkakis, M, Kirino, Y, Gregory, BD, Mourelatos, Z.
Nat Struct Mol Biol 19(8):773-81, 2012. [Pubmed]


Role of arginine methylation in the Piwi-interacting RNA pathway
Kirino, Y*.
Seikagaku 83(4):312-6, 2011. [Pubmed]

Immunoprecipitation of piRNPs and directional, next generation sequencing of piRNAs
Kirino, Y, Vourekas, A, Khandros, E, Mourelatos, Z.
Methods Mol Biol 725:281-93, 2011. [Pubmed]


Reversible infantile respiratory chain deficiency: a clinical and molecular study
Mimaki, M, Hatakeyama, H, Komaki, H, Yokoyama, M, Arai, H, Kirino, Y, Suzuki, T, Nishino, I, Nonaka, I, Goto, Y.
Ann Neurol 68(6):845-54, 2010. [Pubmed]

Elective affinities: a Tudor-Aubergine tale of germline partnership
Vourekas, A, Kirino, Y, Mourelatos, Z.
Genes Dev 124(18):1963-6, 2010. [Pubmed]

Arginine methylation of vasa protein is conserved across phyla
Kirino, Y,
Vourekas, A, Kim, N, de Lima Alves, F, Rappsilber, J, Klein, PS, Jongens, TA, Mourelatos, Z.
J Biol Chem 285(11):8148-54, 2010. [Pubmed]

Arginine methylation of Aubergine mediates Tudor binding and germ plasm localization
Kirino, Y,
Vourekas, A, Sayed, N, de Lima Alves, F, Thomson, T, Lasko, P, Rappsilber, J, Jongens, TA, Mourelatos, Z.
RNA 16(1):70-8, 2010. [Pubmed]


Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stability
Kirino, Y, Kim, N, de Planell-Saguer, M, Khandros, E, Chiorean, S, Klein, PS, Rigoutsos, I, Jongens, TA, Mourelatos, Z. 
Nat Cell Biol 11(5):652-8, 2009. [Pubmed]


Site-specific crosslinking of human microRNPs to RNA targets
Kirino, Y, Mourelatos, Z. 
RNA 14(10):2254-9, 2008. [Pubmed]

Modified uridines with C5-methylene substituents at the first position of the tRNA anticodon stabilize U.G wobble pairing during decoding
Kurata, S, Weixlbaumer, A, Ohtsuki, T, Shimazaki, T, Wada, T, Kirino, Y, Takai, K, Watanabe, K, Ramakrishnan, V, Suzuki, T. 
J Biol Chem 1283(27):18801-11, 2008. [Pubmed]


2'-O-methyl modification in mouse piRNAs and its methylase
Kirino, Y, Mourelatos, Z. 
Nucleic Acids Symp Ser (51):417-8, 2007. [Pubmed]

The mouse homolog of HEN1 is a potential methylase for Piwi-interacting RNAs
Kirino, Y, Mourelatos, Z. 
RNA 13(9):1397-401, 2007. [Pubmed]

Mouse Piwi-interacting RNAs are 2'-O-methylated at their 3' termini
Kirino, Y, Mourelatos, Z. 
Nat Struct Mol Biol 14(4):347-8, 2007. [Pubmed]


Biosynthesis of wybutosine, a hyper-modified nucleoside in eukaryotic phenylalanine tRNA
Noma, A, Kirino, Y, Ikeuchi, Y, Suzuki, T. 
EMBO J 25(10):2142-54, 2006. [Pubmed]

Acquisition of the wobble modification in mitochondrial tRNALeu(CUN) bearing the G12300A mutation suppresses the MELAS molecular defect
Kirino, Y,
Yasukawa, T, Marjavaara, SK, Jacobs, HT, Holt, IJ, Watanabe, K, Suzuki, T.
Hum Mol Genet 15(6):897-904, 2006. [Pubmed]


Human mitochondrial diseases associated with tRNA wobble modification deficiency
Kirino, Y, Suzuki, T.  
RNA Biol 2(2):41-4, 2005. [Pubmed]

Wobble modification deficiency in mutant tRNAs in patients with mitochondrial diseases
Yasukawa, T#, Kirino, Y#, Ishii, N, Holt, IJ, Jacobs, HT, Makifuchi, T, Fukuhara, N, Ohta, S, Suzuki, T, Watanabe, K
FEBS Lett 579(13):2948-52, 2005. [Pubmed]

Specific correlation between the wobble modification deficiency in mutant tRNAs and the clinical features of a human mitochondrial disease
Kirino, Y, Goto, Y, Campos, Y, Arenas, J, Suzuki, T.  
Proc Natl Acad Sci USA 102(20):7127-32, 2005. [Pubmed]

MELAS A3243G mutation and tRNA modification disorder
Kirino, Y, Suzuki, T.  
Rinshoukensa 49:89-95, 2005. 


Codon-specific translational defect caused by a wobble modification deficiency in mutant tRNA from a human mitochondrial disease
Kirino, Y, Yasukawa, T, Ohta, S, Akira, S, Ishihara, K, Watanabe, K, Suzuki, T.
Proc Natl Acad Sci USA 101(42):15070-5, 2004. [Pubmed]

Variable penetrance of a familial progressive necrotising encephalopathy due to a novel tRNA(Ile) homoplasmic mutation in the mitochondrial genome
Limongelli, A, Schaefer, J, Jackson, S, Invernizzi, F, Kirino, Y, Suzuki, T, Reichmann, H, Zeviani, M.
J Med Genet 41(5):342-9, 2004. [Pubmed]


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