Hou Research

• Christian, T, Maharjan, S, Yin, S, Yamaki, Y, Masuda, I, Li, F, Muraresku, C, Clever, S, Ganetzky*, RD, Hou*, YM. (2024) A kinetic model for compound heterozygous variants in tyrosyl-tRNA synthetase gene YARS2-associated neonatal phenotype. J. Biol. Chem. PMID: 39675712; DOI: 10.1016/j.jbc.2024.108092

• Maharjan, S, Gamper, H, Yamaki, Y, Christian, T, Henley, RY, Li, NS, Suzuki, T, Suzuki, T, Piccirilli, JA, Wanunu, M, Seifert, E, Wallace, DC, Hou, YM. (2024) Post-transcriptional methylation of mitochondrial-tRNA differentially contributes to mitochondrial pathology. Nature Commun 15(1):9008, doi: 10.1038/s41467-024-53318-x; PMID: 39424798; PMCID:PMC11489592

• Makhamreh, A, Tavakoli, S, Fallahi, A, Kang, X, Gamper, H, Nabizadehmashhadtoroghi, M, Jain, M, Hou, YM, Rouhanifard, SH, Wanunu, M. (2024) Nanopore signal deviations from pseudouridine modifications in RNA are sequence-specific; quantification requires dedicated synthetic controls. Sci Rep. 14(1): 22457. DOI: 10.1038/s41598-024-72994-9; PMID: 39341872; PMCID:PMC11438862.

• Namani, S, Kavetsky, K, Lin, CY, Maharjan, S, Gamper, H, Li, NS, Piccirilli, J, Hou, YM, Drndic, M. (2024) Unraveling RNA conformation dynamics in MELAS syndrome with solid-state nanopores. ACS Nano, PMID: 38906834, DOI:10.1021/acsnano.4c04625

• Masuda, I, Hou, YM. (2024) A tRNA modification pattern that facilitates interpretation of the genetic code. Submitted to Frontier in Microbiology, PMID: 38933027; PMCID: PMC11199890.

• Avila, YI, Rebolledo, LP, Skelly, E, de Freitas Saito, R, Wei, H, Lilley, D, Stanley RE, Hou, YM, Yang, H, Sztuba-Solinska, J, Chen, SJ, Dokholyan, NV, Tan, C, Li, K, He, X, Zhang, X, Miles, W, Franco, E, Binzel, DW, Guo, P, Afonin, KA (2024) Cracking the code: Enhancing molecular tools for progress in nanotechnology. ACS Applied Bio Materials, PMID: 38833534; PMCID: PMC11190997.

• Tubiana, L, Alexander, G, Barbensi, A, Buck, D, Cartwright, JHE, Chwastyk, M, Cieplak, M, Coluzza, I, Copar, S, Craik, DJ, Di Stefano, M, Everaers, R, Faisca, P, Ferrari, F, Giacometti, A, Goundaroulis, D, Haglund, E, Hou, YM, Ilieva, N, Jackson, S, Japaridze, A, Kaplan, N, Klotz, AR, Li, H. Likos, CN, Locatelli, E, Lopez-Leon, T, Machon, T, Micheletti, C, Michieletto, D, Niemi, A, Niemyska, W, Niewieczerzal, S, Nitti, F, Orlandini, E, Pasquali, S, Perlinska, AP, Podgornik, R, Potestio, R, Pugno, N, Ravnik, M, Ricca, R, Rohwer, CM, Rosa, A, Smrek, J, Souslov, A, Stasiak, A, Steer, D, Sulkowska, J, Sulkowski, P, Sumners, DL, Svaneborg, C, Szymczak, P, Tarenzi, T, Travasso, R, Virnau, P, Vlassopoulos, D, Ziherl, P, Zumer, S. (2024) Topology in soft and biological matter. Eutopia review. Physics Reports, https://doi.org/10.1016/j.physrep.2024.04.002. In press.

• Hou, YM, Nakano, Y. (2024) Breaking the deadlock in genetic code expansion. Invited for an article in News & Views, commenting on the paper in Nature “Adding a,a-disubstituted and b-linked monomers to the genetic code of an organism. Nature Chem Biology, PMID: 38467845.

• Gamper, H, McCormick, C, Makhamreh, A, Wanunu, M, Rouhanifard, SH, Hou, YM. (2023) Enzymatic synthesis of RNA standards for mapping and quantifying RNA modifications in sequencing analysis. Methods in Enzymology, Academic Press, https://doi.org/10.1016/bs.mie.2023.04.024. PMID: 37925177

• Jedrzejewski, M, Belza, B, Lewandowska, I, Sadlej, M, Perlinska, AP, Augustyniak, R, Christian, T, Hou, YM, Kalek, M, Sulkowska JI. (2023) Nucleolar essential protein 1 (Nep1): Elucidation of enzymatic catalysis mechanism by combined molecular dynamics simulation and quantum chemical calculations. Comput Struct Biotechnology J, 21: 3999-4008. PMID: 37649713; PMCID:PMC10462857

• Li, Y, Majumdar, S, Treen, R., Manjari, S, Corro, J, Gamper, HB, Banavali, N, Sharma, M, Rhee, K, Stallings, C, Hou, YM, Agrawal, RK, Ojha, AK. (2023) Starvation sensing by mycobacterial RelA/SpoT homologue through constitutive surveillance of translation. Proc Natl Acad Sci, May 30; 120(22): e2302006120. PMID: 37216503; PMCID: PMC10235957

• Avcilar-Kucukgoze, I, Gamper, H, Hou, YM, Kashina, A. (2023) Preparation of an enriched tRNAArg fraction for arginylation by expression in E. coli, Chapter 4 in “Protein Arginylation: Methods and Protocols”, 2nd edition, edited by Anna Kashina, Springer Nature series of “Methods in Molecular Biology” 2620:101-106. PMID: 37010754

• Yamaki, Y, Gamper, H, Hou, YM. (2023) Synthesis of stably charged Arg-tRNAArg for structural analysis, Chapter 28 in “Protein Arginylation: Methods and Protocols”, 2nd edition, edited by Anna Kashina, Springer Nature series of “Methods in Molecular Biology” 2620: 263-271. PMID: 37010769

• Masuda, I, Hou, YM. (2023) tRNA methylation resolves codon usage bias at the limit of cell viability. Yodosha company, Ltd, Jikken Igaku 41 (6): 955-956 (2023). https://www.yodosha.co.jp/jikkenigaku/articles/index.html?ci=40700. DOI: 10.18958/7223-00003-0000407-00

• Masuda, I, Hou, YM. (2023) Protocol to identify the core gene supported by an essential gene in E. coli bacteria using a genome-wide suppressor screen. Star Protocols DOI: 10.1016/j.xpro.2023.102196

• Tavakoli, S, Nabizadeh, M, Makhamreh, A, Gamper, H, Rezapour, NK, Hou, YM, Wanunu, M, Rouhanifard, SH. (2023) Semi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct, long-read sequencing. Nat Commun 14(1):334. PMCID:PMC9852470

• Masuda, I, Yamaki, Y, Detroja, R, Tagore, S, Moore, H, Maharjan, S, Nakano, Y, Christian, T, Matsubara, R, Lowe, T, Frenkel-Morgenstern, M, Hou, YM. (2022) tRNA methylation resolves codon usage bias at the limit of cell viability. Cell Reports 41(4):111539. PMID: 36288695

• Cui, Z, Li, X, Gamper, H, Hou, YM, Sacchettini, JC, Zhang, J. (2022) Interplay between an ATP-binding cassette F protein and the ribosome from Mycobacterium tuberculosis. Nat Communications, PMID: 35064151.

• Gamper, H, Masuda, I, Hou, YM. (2022) Genome expansion by tRNA +1 frameshifting at quadruplet codons. J. Mol Biol, in press. PMID: 34995554

• Carbone, C, Loveland, AB, Gamper, HB, Hou, YM, Demo, G, Korostelev, AA. (2021) Time-resolved cryo-EM visualizes ribosomal translocation with EF-G and GTP. Nat Communications, PMID: 34903725; PMCID:PMC8668904

• Gamper, H, Mao, Y, Masuda, I, McGuigan, H, Blaha, G, Wang, Y, Xu, S, Hou, YM. (2021) Twice exploration of tRNA +1 frameshifting in an elongation cycle of protein synthesis. Nucleic Acids Res, in press. PMID:34417618; PMCID:PMC8464047

• Masuda, I, Hwang, JY, Christian, T, Maharjan, S, Mohammad, F, Gamper, H, Buskirk, AR, Hou, YM. (2021) Loss of N1-methylation of G37 in tRNA induces ribosome stalling and reprograms gene expression. eLife, 10:e70619. PMID: 34382933; PMCID: PMCID: PMC8384417

• Demo, G, Gamper, H, Loveland, AB, Masuda, I, Svidritskiy, E, Hou*, YM, Korostelev*, AA. (2021) Structural basis for +1 ribosomal frameshifting during EF-G-catalyzed translocation. Nat Communications, 12(1):4644. PMID:34330903. (*: co-corresponding author) PMCID: PMC8324841

• Cai, J, Kropf, E, Hou, YM, Iacovitti, L. (2021) A stress-free strategy to correct point mutations in patient iPS cells. Stem Cell Res, https://doi.org/10.1016/j.scr.2021.102332, PMID: 33857832; PMCID:PMC8283763

• Gamper, H, Li, H, Masuda, I, Robkis, DM, Christian, T, Conn, AB, Blaha, G, Petersson, EJ, Gonzalez, R, Hou, YM. (2021) Insights into genome recoding from the mechanism of a classic +1-frameshifting tRNA. Nat Communications, 12(1):328. PMID:33436566; PMCID:PMC7803779

• Avcilar-Kucukgoze, I, Gamper, H, Hou, YM, Kashina, A. (2020) Purification and use of tRNA for enzymatic addition of amino acids to proteins. Star Protocols (Cell press), https://doi.org/10.1016/j.xpro.2020.100207. PMID: 33377101; PMCID:PMC7757669

• Gamper H, Hou YM. A Label-Free Assay for Aminoacylation of tRNA. Genes (Basel). 2020 Oct 7;11(10):E1173. doi: 10.3390/genes11101173. PMID: 33036365

• Perlinska, AP, Kalek*, M, Christian T, Hou*, YM, Sulkowska*, JI. (2020) Mg2+-dependent methyl transfer by a knotted protein: a molecular dynamics simulation and quantum mechanics study (* denotes co-corresponding authors). ACS Catalysis. In press. Selected as the featured cover of vol. 10, issue 15, 2020. PMID: 32904895

• Fay AJ, Garcia Y, Margeta M, Maharjan S, Jürgensen C, Briceño J, Garcia M, Yin S, Bassaganyas L, McMahon T, Hou YM, Fu YH, Ptáček LJ.Ann. A Mitochondrial tRNA Mutation Causes Axonal CMT in a Large Venezuelan Family. Neurol. 2020 Jul 26. doi: 10.1002/ana.25854. Online ahead of print. PMID: 32715519

• Luo, J, Liu, L, Chen, S, Yu, M, Ge, C, Ren, M, Liu, B, Yang, X, Christian, T, Hou, YM, Zou, J, Zhu, W. (2020) Deacetylation of HSD17B10 by SIRT3 regulates cell growth and cell resistance under stress. Cell Death and Disease 11, 563. PMID: 32703935

• Avcilar-Kucukgoze I, Gamper H, Polte C, Ignatova Z, Kraetzner R, Shtutman M, Hou YM, Dong DW, Kashina A. tRNAArg-Derived Fragments Can Serve as Arginine Donors for Protein Arginylation. Cell Chem Biol. 2020 Jun 11:S2451-9456(20)30190-2. doi: 10.1016/j.chembiol.2020.05.013. Online ahead of print. PMID: 32553119

• Hou YM, Masuda I, Foster LJ. tRNA methylation: An unexpected link to bacterial resistance and persistence to antibiotics and beyond. Wiley Interdiscip Rev RNA. 2020 Jun 13:e1608. doi: 10.1002/wrna.1609. Online ahead of print. PMID: 32533808 Review.

2019

1. Morelli, KH, Griffin, LB, Pyne, NK, Wallace, LM, Fowler, AM, Oprescu, SN, Takase, R, Wei, N, Meyer-Schuman, R, Mellacheruvau, D, Kitzman, JO, Kocen, SG, Lupski, JR, Nesvizhskii, A, Mancias, P, Butler, I, Yang, XL, Hou, YM, Antonellis, A, Harper, SQ, Burgress, RW. (2019) Allele-specific RNA interference: Precision gene therapy for dominant inherited neuropathy. J. Clinical Investigation 129: 5568-5583. PMID: 31557132; PMCID:PMC6877339. 
2. Yin S, Dhital B, Hou YM. How to Untie a Protein Knot. Structure, 2019.
3. Kuo ME, Theil AF, Kievit A, Malicdan MC, Introne WJ, Christian T, Verheijen FW, Smith DEC, Mendes MI, Hussaarts-Odijk L, van der Meijden E, van Slegtenhorst M, Wilke M, Vermeulen W, Raams A, Groden C, Shimada S, Meyer-Schuman R, Hou YM, Gahl WA, Antonellis A, Salomons GS, Mancini GMS. Cysteinyl-tRNA Synthetase Mutations Cause a Multi-System, Recessive Disease That Includes Microcephaly, Developmental Delay, and Brittle Hair and Nails. Am J Hum Genet. 7 March 2019.
4. Masuda I, Matsubara R, Christian T, Rojas ER, Yadavalli SS, Zhang L, Goulian M, Foster L, Huang KC, Hou YM. tRNA Methylation Is a Global Determinant of Bacterial Multi-drug Resistance. Cell Systems 10 April 2019.
5. Sun C, Song J, Jiang Y, Zhao C, Lu J, Li Y, Wang Y, Gao M, Xi J, Luo S, Li M, Donaldson K, Oprescu SN, Slavin TP, Lee S, Magoulas PL, Lewis AM, Emrick L, Lalani SR, Niu Z, Landsverk ML, Walkiewicz M, Person RE, Mei H, Rosenfeld JA, Yang Y, Antonellis A, Hou YM, Lin J, Zhang VW. Loss-of-function mutations in Lysyl-tRNA synthetase cause various leukoencephalopathy phenotypes. Neurology Genetics. April 2019.
6. Hou YM, Masuda I, Gamper H. (2019) Codon-Specific Translation by m1G37 Methylation of tRNA. Front. Genet. 10 January 2019

2018

1. Masuda, I, Takase, R, Matsubara, R, Paulines, MJ, Gamper, H, Limbach, PA, Hou, YM. (2018) Selective terminal methylation of a tRNA wobble base. Nucleic Acids Res, 46 (7):e37.

2. Weterman, MAJ, Kuo, M, Kenter, SB, Gordillo, S, Karjosukarso, D, Takase, R, Bronk, M, Oprescu, S, de Wissel, M, van Ruissen, F, Breuning, M, Hou, YM, de Visser, M, Antonellis, A, Baas, F. (2018) Hypermorphic and hypomorphic AARS alleles in patients with CMT2N expands clinical and molecular heterogeneities. Human Molecular Genetics, in press.

3. Gamper, H, Hou, YM. (2018) tRNA 3'-amino-tailing for stable amino acid attachment. RNA.

4. Kwon NH, Lee JY, Ryu YL, Kim C, Kong J, Oh S, Kim SH, Ahn SG, Jeong J, Kim HK, Kim JH, Han DY, Park MC, Takase R, Masuda I, Hou YM, Jang SI, Chang YS, Lee DK, Guo M, Kang BS, Wang MW, Basappa B, Lee JH, Kim S.  (2018) Stabilization of cyclin dependent kinase 4 by methionyl-tRNA synthetase in p16INK4a-negative cancer. ACS Pharmacology & Translational Science, 1, 21-31.

2017

1. Fan H, Conn AB, Williams PB, Diggs S, Hahm J, Gamper HB Jr, Hou YM, O'Leary SE, Wang Y, Blaha GM. Transcription-translation coupling: direct interactions of RNA polymerase with ribosomes and ribosomal subunits. Nucleic Acids Res. 2017 Nov.

2. Oprescu SN, Chepa-Lotrea X, Takase R, Golas G, Markello TC, Adams DR, Toro C, Gropman AL, Hou YM, Malicdan MCV, Gahl WA, Tifft CJ, Antonellis A. Compound heterozygosity for loss-of-function GARS variants results in a multisystem developmental syndrome that includes severe growth retardation. Hum Mutat. 2017 Oct.

3. Hou YM, Matsubara R, Takase R, Masuda I, Sulkowska JI. TrmD: A Methyl Transferase for tRNA Methylation With m1G37. Enzymes. 41:89-115. 2017.

4. Po P, Delaney E, Gamper H, Szantai-Kis DM, Speight L, Tu L, Kosolapov A, Petersson EJ, Hou YM, Deutsch C. Effect of Nascent Peptide Steric Bulk on Elongation Kinetics in the Ribosome Exit Tunnel. J Bol Miol. 429(12):1873-1888. Jun16 2017.

5. Masuda I, Igarashi T, Sakaguchi R, Nitharwal RG, Takase R, Han KY, Leslie BJ, Liu C, Gamper H, Ha T, Sanyal S, Hou YM. A genetically encoded fluorescent tRNA is active in live-cell protein synthesis. Nucleic Acids Res. Apr 20, 2017

2016

1. Gall AR, Datsenko KA, Figueroa-Bossi N, Bossi L, Masuda I, Hou YM, Csonka LN. Mg2+ regulates transcription of mgtA in Salmonella Typhimurium via translation of proline codons during synthesis of the MgtL peptide. Proc Natl Acad Sci USA. Dec 27 2016.
2. Ardell DH, Hou YM. Initiator tRNA genes template the 3' CCA end at high frequencies in bacteria. BMC Genomics. 8 Dec 2016
3. Sakaguchi R, Hou YM. (2016) タンパク質の結び目構造からのシグナルによるtRNAのメチル化修飾. DOI:10.7875/first.author.2016.097.. First Author's
4. Christian T, Sakaguchi R, Perlinska AP, Lahoud G, Ito T, Taylor EA, Yokoyama S, Sulkowska JI, Hou YM. Methyl transfer by substrate signaling from a knotted protein fold.. Nat Struct Mol Biol. Aug 29, 2016
5. Liu C, Stonestrom AJ, Christian T, Yong J, Takase R, Hou YM, Yang X. Molecular Basis and Consequences of the Cytochrome c-tRNA Interaction.. J Biol Chem, 291, 10426-36. May 6, 2016
6. Falk MJ, Gai X, Shigematsu M, Vilardo E, Takase R, McCormick E, Christian T, Place E, Pierce EA, Consugar M, Gamper HB, Rossmanith W, Hou YM. A novel HSD17B10 mutation impairing the activities of the mitochondrial RNase P complex causes X-linked intractable epilepsy and neurodevelopmental regression.. RNA Biol, 13, 477-85 . May 3, 2016

2015

1. Ito, T, Masuda, I, Yoshida, K, Goto-Ito, S, Suh, SW, Hou, YM, Yokoyama, S. Structural mechanism of site-specific RNA modification by the bacterial tRNA(m1G37)-methyltransferase TrmD. Proc Natl Acad Sci, 112, E4197-204. Aug 4 2015

2. Gamper, H, Masuda, I, Frenkel-Morgenstern, M, Hou, YM. The UGG isoacceptor of tRNAPro is naturally prone to frameshifts. Int J. Mol Sci. 16, 14866-14883. Jul 1, 2015

3. Hou, YM, Gamper, H, Yang, W. (2015) Post-transcriptional modifications of tRNA – A response to the genetic code degeneracy. RNA 21, 642-644. Apr 2015

4. Hou, YM, Masuda, I. (2015) Kinetic analysis of tRNA methyltransferases. Methods in Enzymology. Edited by Chuan He, 560, 91-116.

5. Gamper HB, Masuda I, Frenkel-Morgenstern M, Hou YM, Maintenance of protein synthesis reading frame by EF-P and m1G37-tRNAAm J Human Benetics96(4):675-81. doi: 10.1016, April2, 2015

6. Ya-Ming Hou et al., Loss-of-Function Alanyl-tRNA Synthetase Mutations Cause an Autosomal-Recessive Early-Onset Epileptic Encephalopathy with Persistent Myelination DefectAm J Human Genetics96(4):675-81. doi: 10.1016, April2, 2015